Probiotics, Prebiotics, Synbiotics, and Postbiotics: Human Microbiome and Human Health 9819914620, 9789819914623

Citation preview

Vijay Kothari · Prasun Kumar · Subhasree Ray   Editors

Probiotics, Prebiotics, Synbiotics, and Postbiotics Human Microbiome and Human Health

Probiotics, Prebiotics, Synbiotics, and Postbiotics

Vijay Kothari • Prasun Kumar • Subhasree Ray Editors

Probiotics, Prebiotics, Synbiotics, and Postbiotics Human Microbiome and Human Health

Editors Vijay Kothari Institute of Science Nirma University Ahmedabad, India

Prasun Kumar Chemical Engineering Yeungnam University, Korea Gyeongsan, Korea (Republic of)

Subhasree Ray Department of Life Sciences School of Basic Sciences & Research, Sharda University Greater Noida, Uttar Pradesh, India

ISBN 978-981-99-1462-3 ISBN 978-981-99-1463-0 https://doi.org/10.1007/978-981-99-1463-0

(eBook)

© The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd. 2023 This work is subject to copyright. All rights are solely and exclusively licensed by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. The publisher, the authors, and the editors are safe to assume that the advice and information in this book are believed to be true and accurate at the date of publication. Neither the publisher nor the authors or the editors give a warranty, expressed or implied, with respect to the material contained herein or for any errors or omissions that may have been made. The publisher remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. This Springer imprint is published by the registered company Springer Nature Singapore Pte Ltd. The registered company address is: 152 Beach Road, #21-01/04 Gateway East, Singapore 189721, Singapore

We dedicate this book to all those Teachers who taught us at any level right from kindergarten to doctorate.

Preface

With a lot of data being generated on the Human Microbiome, quite many correlations are being uncovered between the microbiome composition and human health/ diseases. Almost every aspect of human health and behavior, e.g., obesity, functioning of the immune system and nervous system, susceptibility to various infections, and mood fluctuations, seems to be correlated with the microbiome composition. Although the microbiomes of the skin, oral cavity, nasal cavity, and vagina have their own importance, much research has focused on the microbiome of the intestine since the gut harbors the greatest number of resident microorganisms within the human body. As we are developing more and more understanding of the human microbiome and its role in the regulation of the human system, more interest is being generated in finding ways of manipulating this microbiome toward the “healthier” direction. This manipulation of the human microbiome seems to be possible through the use of the following: • Probiotics: Live microbial strains which, upon ingestion, are expected to confer some health benefit. • Prebiotics: Selectively fermented ingredients causing specific changes in the composition and/or activity of the gut microbiota, thereby offering beneficial health effects to the host. • Synbiotics: A mix of probiotics and prebiotics that can confer some beneficial effect on the host by improving the survival and activity of beneficial microorganisms in the intestine. • Postbiotics: Metabolic products of the fermentation by probiotics in the intestine. There is a hope that if we can gain sufficient knowledge of the human microbiome composition and of the ways of manipulating it, this can enable us to manage many of the complex metabolic disorders by careful designing of the diet, i.e., simple dietary adjustments can be a major part of disease/health management strategy. In the above-mentioned context, this contributory volume features manuscripts from researchers working on a different aspect of the Human Microbiome and its manipulation for better health. In this collection, we have tried to showcase the vii

viii

Preface

current status of research in the field and also to point toward future directions, not only from an academic but also from an industrial and regulatory perspective. The editors thank all the contributing authors and acknowledge support from the publisher. Wish you all a happy reading! May we all enjoy a healthy microbiome throughout life! Ahmedabad, Gujarat, India Gyeongsan, Republic of Korea Greater Noida, Uttar Pradesh, India January 2023

Vijay Kothari Prasun Kumar Subhasree Ray

Contents

Part I

Current State of Knowledge Regarding the Human Microbiome Structure, Function, and Diversity

Impact of Dietary Habits, Ethnicity, and Geographical Provenance in Shaping Human Gut Microbiome Diversity . . . . . . . . . . . . . . . . . . . . Payal G. Patel, Ajay C. Patel, Prasenjit Chakraborty, and Haren B. Gosai

3

Methods Used for Studying Human Microbiome . . . . . . . . . . . . . . . . . . Chinmayi Joshi and Vijay Kothari

29

Factors Affecting the Composition of the Human Microbiome . . . . . . . . Madangchanok Imchen, Simi Asma Salim, Ranjith Kumavath, and Siddhardha Busi

49

Part II

Correlation of the Human Microbiome to Specific Health/Disease Conditions

Mapping the Microbial Metabolites in Metabolic Disorder with Special Reference to Type-2 Diabetes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sunny Kumar, Zeel Bhatia, and Sriram Seshadri Human Microbiome in Malnutrition . . . . . . . . . . . . . . . . . . . . . . . . . . . Mehul Chauhan, Priya Mori, and Vijay Kumar

67 81

Association of Probiotics and Prebiotics with Human Microbiome and the Functioning of Immune System . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101 Pia Dey, Samir Kumar Mukherjee, and Debaprasad Parai Human Microbiome and the Susceptibility to Infections . . . . . . . . . . . . . 117 V. T. Anju, Siddhardha Busi, Mahima S. Mohan, and Madhu Dyavaiah Human Microbiome and the Neurological Disorders . . . . . . . . . . . . . . . 139 Rajesh Pamanji and Joseph Selvin

ix

x

Contents

Exploring the Unexplored Arena: Butyrate as a Dual Communicator in Gut–Brain Axis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153 Zeel Bhatia, Sunny Kumar, and Sriram Seshadri Human Microbiome and Lifestyle Disorders . . . . . . . . . . . . . . . . . . . . . 165 Ankit Gupta and Abhilasha Jha Correlation of Human Microbiome and Immune Functioning with COVID-19 Infections: An Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . 195 Purnima Khatri, Asha Rani, Ramendra Pati Pandey, and Saif Hameed Exploring the Pathoprofiles of SARS-COV-2 Infected Human Gut–Lungs Microbiome Crosstalks . . . . . . . . . . . . . . . . . . . . . . . . . . . . 217 Sisir Nandi, Sarfaraz Ahmed, Aaruni Saxena, and Anil Kumar Saxena Role of Human Microbiome in Cardiovascular Disease: Therapeutic Potential and Challenges . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 237 Sathiya Maran, Wendy Wai Yeng Yeo, Kok Song Lai, and Swee Hua Erin Lim The Human Microbiome and Respiratory Diseases . . . . . . . . . . . . . . . . 255 Oksana Zolnikova and Vladimir Ivashkin Part III

Manipulation of the Human Microbiome for Better Health

Probiotics: An Emerging Strategy for Oral Health Care . . . . . . . . . . . . 275 Subramani Parasuraman, Venkata Kanthi Vaishnavi Vedam, and Gokul Shankar Sabesan Dietary Modulation of the Nervous and Immune System: Role of Probiotics/Prebiotics/Synbiotics/Postbiotics . . . . . . . . . . . . . . . . . . . . . 307 Priya Mori, Mehul Chauhan, Ishita Modasiya, and Vijay Kumar Probiotics for Skin Health . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 329 Chinmayi Joshi, Ritul Suthar, Aryushi Patel, Feni Patel, and Drashti Makwana Human Microbiome and Autism-Spectrum Disorders . . . . . . . . . . . . . . 347 Rishi Gupta and Shailendra Raghuvanshi Psychobiotics as an Emerging Category of Probiotic Products . . . . . . . . 361 Sahdev Choudhary, Kumari Shanu, and Sarita Devi Probiotics for Vaginal Health . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 393 Emi Grace Mary Gowshika Rajendran Interactions Between Microbial Therapeutics and the Endogenous Microbiome . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 421 Haley Anne Hallowell, Anne Lulu Gao, Kristen E. Kelly, and Jotham Suez

Contents

Part IV

xi

Applied and Translational Aspects

Bacillus Endospore Probiotics Are a Promising Intervention for Mitigation of Metabolic Endotoxemia . . . . . . . . . . . . . . . . . . . . . . . . . . . 453 Kiran Krishnan, Sujit Nair, and Dilip Mehta Characterization and Authentication of Probiotic Preparations . . . . . . . 479 Vijay Kothari, Anselm de Souza, and Dilip Mehta A Survey of Commercially Available Probiotics . . . . . . . . . . . . . . . . . . . 489 Swati Misra and Shailendra Raghuwanshi Regulatory Aspects Relevant to Probiotic Products . . . . . . . . . . . . . . . . 513 Parul Chugh, Swati Misra, Mahesh S. Dhar, and Shailendra Raghuwanshi Probiotic Identity from Spore: Focus on Bacillus Probiotics . . . . . . . . . . 535 Bhanuramanand K., Veena P. V. S., Haritha Rani B., Dilip Mehta, Anselm Desouza, and Madhusudhana Rao Nalam

About the Editors

Vijay Kothari Ph.D. is a microbiologist. His current research is in the areas of AMR (antimicrobial resistance), traditional medicine, prebiotic and immunomodulatory properties of natural products, microbial response to sonic stimulation, etc. His group is actively involved in investigating antimicrobial/anti-virulence potential of natural products as well as synthetic compounds. In recent past, his lab has extensively investigated the anti-pathogenic/prophylactic activity of various traditional medicine formulations, e.g., Panchvalkal, Panchgavya, and Triphala, against different antibiotic-resistant bacterial strains. His lab was awarded SRISTI-DBT-BIRAC Appreciation Award (2017) for validation of anti-infective potential of a polyherbal formulation inspired from folk medicine— Herboheal. He has also been awarded two AIMS (Artificial Intelligence Molecular Screen) award (2020– 2022) projects by Atomwise Inc., USA, for identifying novel anti-infective leads. Dr. Kothari has also contributed substantially to the field as an active editor and reviewer, and has been conferred the Sentinel of Science award (2016) by Publons recognizing his contribution as a peer reviewer. He has 88 research/review/book chapter publications to his credit. His publications have enjoyed a wide readership as evident from more than 253,000 reads from ResearchGate alone. Vijay derives great satisfaction from the hitherto output of the M.Sc. dissertations guided by him. During the period 2007–2019, he guided 84 M.Sc. students for their dissertation projects, of which 71 (i.e., 84.52%) xiii

xiv

About the Editors

could publish research/review papers in different peerreviewed, indexed journals (or a citable preprint), based on their master’s dissertation.

Prasun Kumar Ph.D. holds a Ph.D. in Biotechnology from CSIR-Institute of Genomics and Integrative Biology, Delhi, India. He is presently working as a Scientific Officer at DBT-IOC Center for Advanced Bioenergy Research, Faridabad. Earlier, he was working as an Assistant Professor at the Department of Chemical Engineering, Yeungnam University, Republic of Korea. He has over 7 years of experience in applied microbiological research including about 2 years of experience in industrial R&D. His main areas of research are biopolymers, microbial biodiversity, bioenergy, microbial biofilms, quorum sensing, quorum quenching, and genomics. His present research is oriented toward valorizing lignocellulosic biowastes into value-added products such as biopolymer, 2G ethanol, bioenergy, and antibiofilm compounds. To his credit, there are over 34 articles in SCI journals, 5 books, and 11 chapters with international publishers. He has been serving the scientific society by reviewing articles for several SCI journals and delivering guest lectures. Publons awarded him the peer review award in the year 2018. He also serves as the editorial board member of a few international journals.

Subhasree Ray Ph.D. is currently working as an Assistant professor at Sharda University, Greater Noida, Uttar Pradesh, India. She earned her Ph.D. degree from CSIR-IGIB, Delhi, in 2018. She received the prestigious CSIR-SRF fellowship. Her main research was focused on producing biopolymers from waste biomass. After Ph.D., she joined as a postdoctoral researcher at Ewha University and the University of Seoul, South Korea. Here, her main focus was the anaerobic digestion of food wastes for methane production. She also studied methanogenesis at a 4000 L pilotscale plant. After the successful completion of 1 year, she joined another project at Yeungnam University, South Korea. During that period, she worked on several fungal toxins and their inhibition from fermented food.

About the Editors

xv

She also worked on biofilm inhibition of pathogenic organisms by natural bioactive compounds. To her credit, she has 13 research papers published in peerreviewed journals and 8 book chapters. In addition, she is a life member of various scientific societies and also a member of various committees at Sharda University for Graduate and Undergraduate programs.

Part I

Current State of Knowledge Regarding the Human Microbiome Structure, Function, and Diversity

Impact of Dietary Habits, Ethnicity, and Geographical Provenance in Shaping Human Gut Microbiome Diversity Payal G. Patel, Ajay C. Patel, Prasenjit Chakraborty, and Haren B. Gosai

Abstract Human gut microbiome is comprised of billions of microorganisms that reside within gastrointestinal tract and form a symbiotic bond with humans. This unique relationship between microbes and human is possible through gut–brain axis which enables bidirectional communication between central and enteric nervous system. The diversity of the gut microbiome, i.e., the composition of the microbes living in the human gut is influenced by various external and internal factors. The dietary habits of an individual not only play a major role in determining which kinds of microbes exist in the gut but also effect the interaction among the different species of microbes. Dietary habits in turn are shaped by the culture, lifestyle, ethnicity, and geographical location of a population. People belonging to same ethnicity have similar dietary habitats; however, their lifestyle and geographical variation may lead to different microbiome composition. Different ethnic groups within same geographical location have been observed to have diverse microbiome; meanwhile, migration has proven to westernize the gut microbiome. The evident data suggests that ethnicity, dietary habits, and geographical provenance are closely interlinked, and their interrelationship is a key player in determining gut microbiome diversity. In this chapter, the authors attempt to elucidate how and to what extent these three factors impact the microbiome composition and diversity. Keywords Gut microbiome · Dietary habits · Ethnicity · Geographical provenance

1 Introduction Microorganisms play a crucial role in the daily life and functioning of human beings. From microbial products that we use in our day-to-day life to the microorganisms that reside within our body, we depend on them for a variety of reasons. Microorganisms are ubiquitous and constitute a large part of nature’s living matter, and

P. G. Patel · A. C. Patel · P. Chakraborty · H. B. Gosai (✉) Department of Biosciences, School of Sciences, Indrashil University, Mehsana, Gujarat, India e-mail: [email protected] © The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd. 2023 V. Kothari et al. (eds.), Probiotics, Prebiotics, Synbiotics, and Postbiotics, https://doi.org/10.1007/978-981-99-1463-0_1

3

4

P. G. Patel et al.

humans are not an exception. Microorganisms have resided synergistically within our body, undergoing co-evolution with humans, and have continued to influence human health for centuries (Chauhan 2019; Rackaityte and Lynch 2020). Human gastrointestinal tract (GI) consists of millions of diverse bacteria, archaea, and eukaryotes that form a symbiotic relationship with the host (Thursby and Juge 2017). Microorganisms that inhabit the GI form the human ‘gut microbiome’, a collection of genomes from all the microorganisms living together in the GI (Zhu et al. 2010). While ‘microbiome’ signifies the entire habitat, ‘microbiota’ refers solely to the microbes that reside within that specific habitat or GI in this case (Valdes et al. 2018). Human gut microbiome has also been described by some researchers as the second genome or metagenome of the human body (Zhu et al. 2010; Grice and Segre 2012). It has been estimated that more than 3.3 million microbial genes are present within gut microbiome which is approximately 150 times the number of genes in the human genome (Ehrlich 2016). Gut microbiota also makes up approximately 1.5–2 kg of the total body weight in humans (Mazidi et al. 2016). Gut microbiome (GM) in addition to prominent bacterial species also comprises archaea (mostly Methanobrevibacter smithii), yeast, fungi, and viruses (mostly phages). Moreover, the mycobiome, archaea, and virus provide an extra dimension to the mutually beneficial interactions between host and microbiota (Lozupone et al. 2012; Cani 2018). Every individual has a ‘core microbiome’ that remains similar universally, but the overall gut microbiome is as distinguishable as a person’s fingerprint (Lozupone et al. 2012; Franzosa et al. 2015). Core GM consists of more than 1000 species of microorganisms, but three phyla Bacteroidetes, Firmicutes, and Actinobacteria are most prominent. While Proteobacteria and Verrucomicrobia make up only small percentage of the core microbiome (Eckburg et al. 2005; Tap et al. 2009; Kho and Lal 2018). Aside from GM, microorganisms are also concentrated at other different environments within human body including oral cavity, oesophagus, vagina, and skin. However, diversity and composition of these microbiomes differ from that of GM (Gilbert et al. 2018). Until last decade, the idea that GM could have significant influence on human health was considered fringe science. However, due to advancements and breakthroughs in the field of metagenomics, it is now possible to elucidate the relationship between microbiota and host organism (D’Argenio and Salvatore 2015). GM encodes several genes that enable production of hydrolytic enzymes. These enzymes breakdown the otherwise indigestible components present in the meal (Flint et al. 2012). Apart from digestion, GM has been proved to be responsible for vitamin synthesis (Magnúsdóttir et al. 2015), development of immune system (Kau et al. 2011), providing defence against pathogens (Sekirov et al. 2010), behaviour development (Cryan and O’Mahony 2011), and promotion of intestinal angiogenesis (Franks 2013). GM diversity, i.e., the composition of the microbes living in the human gut is affected by a wide range of external and internal factors. External factors include lifestyle choices, dietary habits, geographical location, antibiotic usage, etc., whereas internal factors refer to host genetics, owing to particular ethnicity, population or individual genome (van Best et al. 2015; Kho and Lal 2018). ‘We Are What We Eat’

Impact of Dietary Habits, Ethnicity, and Geographical Provenance. . .

5

is a phrase that is often used, but in case of GM this phrase is indeed true. Evidences have revealed that our diet choices, nutritional uptake, and even frequency of meals have a correlation with the GM (De Filippis and Ercolini 2018; Wang et al. 2019). Our daily meals not only provide nutrition to us, but they also supply essential metabolites to GM. In humans, gut microbiome is established by 2–3 years age, and the food consumed during these initial ‘first 1000 days’ affect the diversity of GM (Laursen et al. 2017). However, in adults, type of long-term dietary patterns, e.g., westernized or traditional, is also related with particular gut microbial profiles (Wang et al. 2019). The dietary patterns of an individual are often shaped by their ethnicity as different culture and civilization have their own food customs and distinctive cuisine (Low et al. 2021). Ethnic groups are formed over a long period of time as a result of isolation, adaptation, and migration. As a result, different ethnic groups have specific inherent genotype, which further influences their GM (Dehingia et al. 2019). Under similar external conditions (socioeconomic status, environment, age), ethnicity was reported to be the most influential factor in regulating alpha diversity of GM (Liu et al. 2020). Apart from that, one cannot dismiss the role of geographical provenance since they not only mould the lifestyle or diet choices but, in some instances, impact gut microbiome at physiological level (Senghor et al. 2018; Mazel 2019). Studies have suggested that individuals from high latitude have higher Firmicutes and lower Bacteroidetes proportion. These two phyla are associated with increase in body weight by regulating fat storage and energy extraction from diet (Suzuki and Worobey 2014). Effects of dietary habits, ethnicity, and geography on GM have been studied at individual level but limited numbers of reports have focused on the interrelationship between these three factors. As illustrated in Fig. 1, all three factors are interlinked and play a key role in shaping GM diversity and composition. In this

Fig. 1 Interaction between dietary habits, ethnicity, and geographical provenance and its correlation with gut microbiome

6

P. G. Patel et al.

chapter, the authors attempt to elucidate this intertwined relationship between geography, diet, and ethnicity. This chapter also shed light on their individual and combined impact on diversity and composition of human GM.

2 Significance of GM It is now a well-established fact that the composition of the GM is responsible for the overall health and well-being of a particular individual. With each passing year, the relationship between GM and human health is being increasingly recognized. The vast majority of these microbes are classified into five different phyla, namely Firmicutes, Actinobacteria, Bacteroidetes, Proteobacteria, and Fusobacteria (Andersson et al. 2008). Though in an infant, the GM lacks any obvious principle of organization, by the age of 3 years it starts resembling the adult microflora. Even in adult, temporal and spatial dissimilarities exist in microbial distribution across the digestive system. Due to their extensive importance, next-generation sequencing technologies are being employed to study these microorganisms. Gut microbiota directly interacts with its host to control the host metabolism, along with maintenance of structural integrity of the gut mucosal barrier, and immunomodulation. Several factors such as diet, antibiotics, age, drug metabolism, and diseases are at play in determining the make-up of normal gut microbiota. Among them, misuse of antibiotics is a major cause of concern affecting the normal healthy GM. Generation of multidrug resistance species and horizontal transfer of these resistance genes could affect the composition of normal GM. The microbiome present in the gut has been associated with a large number of diseases, such as inflammatory bowel diseases, irritable bowel syndrome, allergic disease, neurodevelopmental illnesses, obesity, and diabetes (Bisgaard et al. 2011; Ferreira et al. 2014; Karlsson et al. 2013; Kennedy et al. 2014). It has intrigued scientists for decades and is still a field of very active research. Various microbiome and metagenomics projects carried out by the USA and European consortiums have established the benefits of having a healthy gut flora to the genetic level (Gevers et al. 2012; Qin et al. 2010). If we consider the perspective of an immunologist, microorganisms are foreign pathogens that need to be eliminated by the immune system of the host. So, according to that logic, microflora inhabiting our guts should have been eradicated. However, the majority of the gut bacteria are non-pathogenic and have established a symbiotic relationship with the enterocytes. This is only possible because these microorganisms and the immune system have co-evolved to form a symbiotic relationship. Apart from aiding in various metabolic activities, these healthy microorganisms help to maintain intestinal barrier function and to prevent the colonization of pathogenic microorganisms. There are over 35,000 bacterial species residing in the human gut with approximately ten million non-redundant genes (Frank et al. 2007). It is not just the number and type of bacterial species, but the total gene count of those species that has huge implications for health and disease. The high gene count (HGC) of some microbial

Impact of Dietary Habits, Ethnicity, and Geographical Provenance. . .

7

species like Akkermansia sp., Anaerotruncus colihominis, Butyrivibrio crossotus, and Faecalibacterium sp. is effective in controlling obesity (Le Chatelier et al. 2013). Not only the overall count but also the ratio of certain microbial species is important. A high ratio of Akkermansia sp.:Ruminococcus gnavus is beneficial for digestive health. Some of the salient features to look out for in the HGC microbiome favouring digestive health are 1. 2. 3. 4.

The enhanced percentage of butyrate-producing organisms. Increased tendency to produce hydrogen. Establishment of methanogenic/acetogenic ecosystem. A reduction in the capability to produce hydrogen sulfide.

In contrast, individuals with a low gene count (LGC) of the above-mentioned bacterial species harbour a higher percentage of pro-inflammatory bacteria like Ruminococcus gnavus and Staphylococcus sp., causing inflammatory bowel disease. In addition to this, LGC individuals possess bacterial metabolites modules for degradation of aromatic amino acids and β-glucuronide that are deleterious health effects. Conversely, HGC individuals have robust gut microbiome functionality with a lower frequency of metabolic disorders. Now, let us look at the important functional aspects of the gut microbiota in more details.

2.1

Antimicrobial Protection

GM plays a major role in maintaining homeostasis within the gut mucosal immune system by being tolerant to advantageous commensals yet preventing harmful pathogens. Unlike the large intestine, antimicrobial proteins (AMP) are of great importance in the small intestine as the mucus layer in the small intestine is discontinuous and inadequate. Synthesis of AMP such as C-type lectins, cathelicidins, and defensins is induced by the gut microbiota, via its structural components and metabolites (Hooper 2009). Crosstalk between the pattern recognition receptor (PRR) and microbe associated molecular patterns (MAMP) results in the activation of signalling pathways essential for promoting the production of AMPs, mucin glycoproteins, mucosal barrier function, and immunoglobulin A (IgA). Due to its location in the base of the small intestinal crypts, the concentration of AMPs is maximum in Paneth cells. A healthy and composite microbiota may seem as a prerequisite for AMP production but Bacteroides thetaiotaomicron and Lactobacillus innocua are the key individual species that promote production of AMPs. Bacteroides thetaiotaomicron can also promote the cleavage of prodefensin to active defensin. Apart from benefitting in the process of digestion, lactic acid produced by Lactobacillus sp. can enhance the antimicrobial activity of the host lysozyme. It has been proven beyond doubt that AMP expression is a two-way interactive mechanism. Bacterial metabolites such as short-chain fatty acids (SCFA) and lithocholic acid stimulate the expression of short cationic peptides that are part

8

P. G. Patel et al.

of the innate immune system by mechanisms of epigenetic alterations and mitogenactivated protein kinase/extracellular signal-regulated kinases pathway.

2.2

Nutrients Metabolism

GM is involved in the metabolism of almost all the essential nutrients required by our body, be it carbohydrates, proteins, lipids, vitamins, and/or polyphenols. Carbohydrates are the main source of energy for the microorganisms residing in the gut. Bacteroides sp., Bifidobacterium sp., Enterobacteria sp., Faecalibacterium sp., and Roseburia sp. can ferment indigestible carbohydrates to SCFA and provide ample energy to the host (Samuel et al. 2008). SCFA such as butyrate can avert built-up of D-lactate, a toxic metabolic by-product. Some of these bacterial species like Bacteroides thetaiotaomicron encodes more hydrolases than the human genome. Oxalate is a common by-product obtained from the fermentation of carbohydrates. Accumulation of oxalate can lead to the formation of kidney stones. Oxalobacter formigenes along with Bifidobacterium and Lactobacillus species can counter oxalate, preventing the formation of kidney stones. Amino acids can enter the gut microbiota from the intestinal lumen via transporters present on the cell wall of bacteria. Several enzymes, such as histamine decarboxylase and glutamate decarboxylases present within the bacteria convert those amino acids into small signalling molecules and/or bacteriocins. Apart from carbohydrates and protein, gut microbiota also has a positive influence on lipid metabolism (Hooper et al. 2001). Bacteroides thetaiotaomicron can upregulate the expression of a colipase required for lipid digestion. Moreover, some microbes can counteract the inhibition of lipoprotein lipase activity in adipocytes. Among other major nutrient metabolism functions of gut microbiota are: (a) synthesis of vitamins, conjugated linoleic acid, secondary bile acids; (b) increasing the concentrations of pyruvic acid, citric acid, fumaric acid, and malic acid in serum; (c) breakdown of polyphenols consumed in the diet (Valdes et al. 2018).

2.3

Immunomodulation

GM can modulate innate as well as adaptive immune systems. Dendritic cells in the lamina propria, group 3 innate lymphoid cells, gut-associated lymphoid tissues (GALT), IgA producing plasma B cells, resident macrophages, and T cells are regulated by microbes inhabiting the human gut. For example, commensals and pathogens can stimulate the tissue-resident dendritic cells to secrete several factors required for the production and class switching of antibodies (Jandhyala et al. 2015). In the past decade, research has provided a comprehensive picture of the crosstalk between the gut microbiome and regulatory T cells (Zheng et al. 2020). These regulatory T cells in turn amplify cytotoxic CD8+ T cells, high-affinity antibody

Impact of Dietary Habits, Ethnicity, and Geographical Provenance. . .

9

responses, and memory B cells. An axis of Follicular helper T cells and microbiota may play significant roles in autoimmune diseases. Crosstalk between the immune system and gut microbes is a bidirectional communication process. Disturbance in the microbiome by environmental factors and genetic susceptibility can lead to immune dysregulation, which in turn can cause more microbiome disturbance. This can lead to serious diseases like inflammatory bowel disorders. Still, more mechanistic studies are required to explore the roles of the commensal microbiome in impacting immunity in health and disease.

2.4

Metabolism of Various Drugs and Xenobiotics

Growing scientific evidences have elucidated the role of the GM in xenobiotics and drugs metabolism (Valdes et al. 2018; Jandhyala et al. 2015; Zheng et al. 2020). GM could play a vital role in treatment of several diseases in future. Cardiac glycosides like digoxin are known to upregulate a cytochrome containing operon in organisms belonging to Actinobacteria phyla resulting in the inactivation of digoxin. Furthermore, p-Cresol, a metabolite derived from gut microbes, can decrease liver’s metabolism against acetaminophen by competitive inhibition of hepatic sulfotransferases. Microbes residing in our gut can also metabolize anticancer drugs; an interesting example is the deconjugation of the anticancer drug irinotecan catalysed by the enzyme ß-glucuronidase.

2.5

Faecal Microbiota Transplantation

Faecal microbiota transplantation (FMT) therapy is emerging as one of the most intriguing applications of GM studies. Here, faecal microbiota present in stool from a healthy individual is transplanted into a patient suffering from a gut microbiotarelated disease. The aim is to reconstitute or restore the gut microbiota balance in the patient to overcome GM dysbiosis (Cammarota et al. 2014). GM of patients who underwent antibiotic treatment before stem cell transplantation has been successfully reconstituted through the means of FMT therapy (Taur et al. 2018). Obesity and gut microbiome dysbiosis have been known to be interlinked but now with the help of FMT therapy, this connection is being thoroughly investigated. By transplanting faecal microbiota from a healthy person into an obese person or vice-a-versa, the immediate effect of gut microbiota can be studied (Kang and Cai 2017). Since gaining traction within last decade, FMT has been accepted for treatment of Clostridium difficile infection by FDA. Moreover, several stool banks including OpenBiome have been established for providing faecal microbiota (Smith et al. 2014).

10

P. G. Patel et al.

3 Dietary Habits and Their Influence on the Gut Microbiome In addition to heredity and anthropometry, environmental factors like diet and drugs also play a major role in determining the composition of GM in an individual (Goodrich et al. 2014; Rothschild et al. 2018). Among all these factors, the influence of diet is particularly important, because nourishing the GM with probiotics or dietary fibre can provide far-reaching health benefits. Almost all the food ingredients that we consume affect the microbes living in and around the stomach. Rampant use of pesticides for agriculture is harming the microbiota diversity. The medical community is considering microbiota as a key component of nutrition as it can be used to personalize diet plans. To maintain beneficial microbes in the gut, greater importance has to be given to our dietary habits. Many diabetic patients and even calorie conscious individuals switch to artificial and high-intensity sweeteners as alternatives to white sugar. Although food regulatory agencies consider them safe, studies on animal models have revealed that they can cause GM dysbiosis (Nettleton et al. 2016). Sugar substitutes induce metabolic disturbances and impart glucose intolerance that leads to change in GM population. Drastic alteration in GM population may cause gut dysbiosis and other health problems as evident by previously reported studies (Li et al. 2022; Ruiz-Ojeda et al. 2019). A widely used sugar substitute when fed to rats changed the proportion of total aerobic bacteria in their guts (Abou-Donia et al. 2008). It also caused a spike in the amount of cytochrome p-450 and p-glycoprotein in the intestine. Similar results have been obtained in experiments with mice also, where it was found to cause liver inflammation (Bian et al. 2017). Even the addition of emulsifiers to the diet can potentially decrease the diversity of microbial flora. Especially affected are species belonging to the phylum Verrucomicrobia and order Bacteroidales (Chassaing et al. 2015). Food additives also cause an increase in the population of pro-inflammatory gram-negative bacteria belonging to the phylum Pseudomonadota. This can lead to serious health disorders such as colitis and metabolic syndrome. Numerous people, especially millennials, are switching to restrictive diet plans trying to lose weight or for some other reasons. Some of these diet plans like the low FODMAP (fermentable oligosaccharides, disaccharides, monosaccharides, and polyols) diet increase the beneficial Actinobacteria richness and diversity and are used to treat irritable bowel syndrome (Chumpitazi 2020). If we take the example of people on strict vegan diets and compare it to normal omnivores, little difference was observed in composition and diversity composition of microflora, but significant differences in metabolomic profile (Wu et al. 2016). The gut microbiota helps to ferment many non-digestible substrates like dietary fibres and endogenous intestinal mucus, in turn providing the main energy source for human colonocytes (De Vadder et al. 2014). Moreover, the metabolites generated from this fermentation process can have beneficial effects through neural circuits. The incorporation of gluten-free bread helps people with coeliac disease and/or gluten sensitivity (Bevilacqua et al. 2016). The addition of cheese to the diet in

Impact of Dietary Habits, Ethnicity, and Geographical Provenance. . .

11

human observational and interventional studies has been shown to increase the beneficial Bifidobacteria and decrease Bacteroides and Clostridia associated with intestinal infections (Montel et al. 2014; Zheng et al. 2015). It also enhances the production of short-chain fatty acids (SCFA) and reduces the amount of trimethylamine N-oxide. Consumption of live microorganisms can influence the abundance of different types of bacteria in the gut. Mixtures of such live beneficial microbes (bacteria, yeast, etc.) are referred to as probiotics. It is now a well-established fact that probiotics have several health benefits. They are often taken as food supplements all around the globe. The most commonly used microbes as probiotics belong to the genus Lactobacillus, usually present in the yoghurt. Probiotics also help in the process of wound healing, improving immune system and decrease in obesity (Hori et al. 2020; Fijan et al. 2019). Table 1 describes the probiotic products commercially available worldwide for direct consumption. Prebiotics, however, is Table 1 Probiotic products available in global market Probiotic brand/market name Yakult

Manufacturing company Yakult

Type of probiotic Yoghurtbased drink

Coco biotic

Body ecology

GoodBelly probiotics Actimel

NextFoods

Tropicana essential probiotics Toyo Kombucha Vitafytea Bififlor

PepsiCo

Ferment coconut water drink Fermented fruit juice Yoghurtbased drink Fermented fruit juice

Danone

K95 foods Eko-bio

Organic gut shot

Farmhouse CULTURE

PERKii sparkling probiotic drink Lactovit

PERKii

Velbiom

Vitality

Müller dairy

Fermented black tea Freeze-dried formula Fermented vegetable drink Soda with added bacterial strain Freeze-dried formula Yoghurtbased drink

Country Japan (available worldwide) USA

Bacterial strain Lactobacillus casei Shirota

USA

Lactobacillus plantarum 299V Lactobacillus casei DN-114001 Bifidobacterium lactis

Worldwide USA

India Netherland

USA

Lactobacillus acidophilus, L. delbrueckii

Acetic acid bacteria and yeast consortium Lactobacillus rhamnosus, L. acidophilus, and Bifidobacterium bifidum Lactobacillus (from sauerkraut and vinegar brine)

Australia

Bifidobacterium

India

Bacillus coagulans, Lactobacillus Lactobacillus acidophillus, Bifidobacterium sp.

UK

12

P. G. Patel et al.

defined as substrates for beneficial host microorganisms. Prebiotics include all the fermentable carbohydrates and dietary fibre used by the GM. So, it is quite obvious that prebiotics can modulate the population of host microbiota. Observational studies and experimental models have provided evidence for the therapeutic benefits of prebiotics in fighting allergies. If we combine prebiotics with probiotics in a specific formulation, we will get a product termed a synbiotics. Synbiotics provide the advantages of both probiotics and prebiotics. Apart from adding beneficial organisms to food or feed, it will also stimulate the proliferation of native bacterial strains already present in the gastrointestinal tract. One of the most popular synbiotics in use employs a combination of Bifidobacterium or Lactobacillus genus bacteria with fructooligosaccharides (Markowiak and Ślizewska 2017). The field of probiotics, prebiotics, and synbiotics has witnessed exponential research growth in the past few decades. Apart from these, different ethnic groups across the globe have their own indigenous fermented foods and beverages whose consumption provides live microorganisms (Table 2). These food items have several health benefits and some of them such as Yakult, kimchi, kombucha, etc. have gained popularity in recent years. Consumption of tempeh, a traditional Indonesian food item made from fermented soybean has been reported to improve cognitive functions in older people. In a recent study by Handajani et al. (2020) 90 subjects aged above 60 years with mild cognitive disorder consumed tempeh for 6 months. At the end of experiment, cognitive improvement was demonstrated by the subjects. All these studies reinforce a greater impact of diet in influencing the long-term metabolome derived from the bacterial community than just the short-term bacterial community. An important point to consider is that the effect of dietary habits on the microbiome composition may not be a one-way process, as the microbes in the gut can also influence one’s food choices and appetite.

4 Role of Ethnicity in Shaping Gut Microbiome While ethnicity has been studied as one of the factors that shapes human gut microbiome, it has been often viewed under biological and genetical lenses. Several times ethnicity is used interchangeably with race when used in context of scientific studies. However, ethnicity is more than shared genetic factors within a population (Fortenberry 2013). Ethnic groups refer to the population or group that has similar culture orientation, history, biology, religious beliefs, and lifestyle patterns. Thus, study of microbiome profiles required combination of extensive and intensive differences among various ethnicities (Irvine et al. 2002; Findley et al. 2016). A large percentage of microbiome studies have been focused on GM of people living in Western countries. Therefore, inclusion of diverse ethnic groups in microbiome studies could help in elucidating role of GM in health disparity among various ethnicities (Findley et al. 2016). Studies on infant GM have revealed that ethnicity is a vital element in early GM development. One longitudinal study by Xu et al. has included infants from three different ethnic groups, Chinese, Malay, and

Impact of Dietary Habits, Ethnicity, and Geographical Provenance. . .

13

Table 2 Regional fermented foods and beverages with probiotic potential Fermented food/ beverage Kefir

Type of food/ beverage Fermented milk beverage

Tempeh

Fermented dehulled and boiled soybean

Indonesia

Sauerkraut

Fermented cabbage

Central and East Europe

Kimchi

Fermented vegetables

Korea

Natto

Fermented soybean

Japan

Miso

Fermented soybean paste

Japan

Aspergillus oryzae, Enterococcus, Staphylococcus, Tetragenococcus, and Leuconostoc

Dahi

Fermented milk yoghurt

South Asia

Lactococcus, Leuconostoc, and Lactobacillus

Kombucha

Fermented black/ green tea

China

Gluconacetobacter, Lactobacillus, Lactococcus, and Zygosaccharomyces

Tuaither

Fermented bamboo shoots

India

Boza

Fermented cerealbased beverage

Turkey, Balkans

Lactobacillus, Corynebacterium sp., Sphingobacterium sp., and Pseudomonas sp. Lactobacillus, Candida, and Pischia sp.

Place of origin Caucasus

Microflora Lactobacillus kefiranofaciens, Enterobacter, Acinetobacter, and Enterococcus sp. Rhizopus oligosporus, Lactobacillus, Enterococcus, Streptococcus, and Weissella Leuconostoc, Lactobacillus, Lactococcus, and Enterobacteriaceae Weissella, Pediococcus, and Leuconostoc Bacillus subtilis natto

Health benefit Antimicrobial activity, improves lactose digestion, helps with constipation Enhance immune system, improve cognitive functions

Anti-inflammatory, anti-oxidant, counteracts effects of carcinogens Anti-mutagenic activity, antioxidant, anticancer Anti-fibrinolytic, reduces hypertension, improves digestion Decreased gastrointestinal reflux, lower risk of mortality, antidiabetic, antiinflammatory Helps with intestinal disorders, improved digestion, anti-bacterial effect in gut Anti-diabetic, anticarcinogenic, improves gastric ulcers, immune response Anti-oxidant, cardioprotective, anti-ageing, and weight loss

Antimicrobial activity, enhance digestion

References Dertli and Çon (2017)

Yulandi et al. (2020)

Zabat et al. (2018)

Hong et al. (2016) Nagai (2015)

Allwood et al. (2021)

Joishy et al. (2019)

Marsh et al. (2014)

Deka et al. (2021)

Botes et al. (2007)

14

P. G. Patel et al.

Indian, within same geographical location. Ethnicity was an influential factor at 3 months, before introduction of solid foods and remained so up till 1 year in Chinese and Indian infants. Microbiota of Chinese infant had high percentage of Bacteroides and Akkermansia; however, Indian infants had predominantly Bifidobacterium and Lactobacillus composition (Xu et al. 2020). Another similar study has compared gut microbiome of South Asian and Caucasian infants born in Canada. Results suggest that from birth to 12 months of age, both ethnicity and breast-feeding habits are influential factors in initial establishment and composition of gut microbiome. South Asian infants had higher abundance of lactic acid bacteria, while Caucasian infants had higher Clostridiales genera. These differences in gut microbiome profile have been attributed to variation in maternal and infant diet among the two ethnic groups (Stearns et al. 2017). GM composition of several ethnic groups residing in USA were analysed by Brooks et al. in order to understand the correlation between GM variation and chronic illnesses that generally plagues ethnical minorities. After studying GM of 1267 individuals from four different ethnicities, 12 taxa were found to reproducibly vary among the four groups. Christensenellaceae was the most reproducibly heritable taxon along with majority of microbial taxa which indicates a possibility of genetic inheritance within specific ethnic groups (Brooks et al. 2018). In another study, geographical variation was ruled out by selecting 25,000 individuals living in Amsterdam, Netherlands. Ethnicity emerged as the major contributor to gut microbiome composition and individuals from same ethnic group had similar gut microbiome. Three main poles demarcated by operational taxonomic unit (OTU) were identified among different ethnic groups, Clostridiales (Dutch), Prevotella (Turks, Ghanaians, Moroccans), and Bacteroides (South Asian Surinamese, African Surinamese) (Deschasaux et al. 2018). Dwiyanto studied the GM profiles in a multiethnic middle-income Malaysian district, Segamat. Members of four different ethnicities Malay, Chinese, Indian and, Jakun were included in the study, and ethnicity displayed major influence over gut microbiome diversity. The differences in lifestyle patterns and dietary choices were considered as the cause of the dissimilarity within gut microbiome (Dwiyanto et al. 2021). GM composition of young children has also been examined in some studies to understand early microbiome development. One such study by Liu et al. focused on ethnic groups living in Qinghai-Tibet plateau. 141 school children (age 8–12 years) belonging to Tibetan, Han, and Hui population were tested for their gut microbiome similarities and dissimilarities. Through 16S sequencing it was proved that Firmicutes (47.61%) and Bacteroides (38.05%) were the predominant phyla among all three ethnicities. However, the Tibetan population had highest alpha diversity, with comparatively high percentage of Oscillibacter and Barnesiella. Since the environment and dietary habits were similar between the Tibetan, Han, and Hui population, ethnicity was responsible for alpha diversity (Liu et al. 2020). Khine et al. determined the significance of ethnicity on gut microbiome when geographical variation is included. Pre-adolescent children from two ethnic groups (Chinese and Malay) geographically separated across three different cities (Guangzhou, Penang, and Kelantan) took part in this study. Here,

Impact of Dietary Habits, Ethnicity, and Geographical Provenance. . .

15

differences in GM among the two ethnicities within the same city were due to variation in diet and food habits (Khine et al. 2019). Ethnic groups that are isolated from other populations with distinct cultural, food, and lifestyle patterns have been reported to have a unique GM. These ethnic groups are often geographically isolated or have limited interaction with other populations. Nomadic Fulani group living in Nigeria have a pastoral lifestyle that is a combination of Paleolithic and Neolithic style. On comparing the GM profile of Fulani group with their urban contemporaries, the Fulani had lower microbial diversity. Notably, their GM comprised several microbial phyla that are associated with hunter-gatherer or foraging communities such as Prevotellaceae, Bacteroides, and Spirochaetes. Fulani had higher percentage of pathogenic microbes within their GM as a result of their nomadic diet and lifestyle choices (Afolayan et al. 2019). Inuit population residing in Canada has traditional dietary habits that have been formed over centuries and responsible for a distinct and dynamic gut microbiome. These dietary choices have formed as a result of geography and seasonal availability. GM of Inuit population differs from those of urbanized European population with Western diet patterns (Dubois et al. 2017). Inuit group had higher abundance of Akkermansia phyla which is associated with diet as well as geography, observed within Arctic region (Girard et al. 2017). Assimilation and lifestyle change often lead to variation within GM of isolated ethnic groups. This pattern was observed when Nicobaresetribal community living in remote areas relocated to rural and urban areas. As dietary and lifestyle patterns were altered the GM composition changed as well. Group from remote location had higher GM diversity compared to their rural and urban groups. While the remote group had predominantly Prevotella genus owing to the carbohydrate-rich diet, the urban group is comprised mainly of Bifidobacterium (Anwesh et al. 2016). However, in a contradictory study, GM composition of previously nomadic Irish Traveller community was similar to that of non-industrialized rural gut microbiome. Since the diet of the community is similar to their urban contemporaries, non-dietary factors such as living conditions and horizontal microbiome transfer (Keohane et al. 2020) were assumed to be responsible for these variations. Occurrence of gastrointestinal diseases or other similar disorders has been linked to GM composition. Moreover, certain diseases are prevalent in certain ethnic groups and through means of GM profiling, this correlation can be elucidated. Furthermore, this could help in development of personalized treatment for some of the diseases. Prideaux et al. studied GM of individuals with gastrointestinal diseases and their results suggest that ethnicity plays a role in altering the GM composition. Chinese patients of ulcerative colitis had reduced microbiome diversity and inflammatory bowel disease (IBD) was more likely to occur in case of Chinese individuals. Chinese IBD patients tended to have Western style compared to more traditional Chinese diet of healthier individuals (Prideaux et al. 2013). Mar et al. revealed though their study on ulcerative colitis patients that distinct microbiome cohort is present in different ethnic groups that may be responsible for disease severity (Mar et al. 2016). Association between type-2 diabetes and GM composition has also been studied in various ethnic groups. Trans-ethnic study between type-2 diabetes patients

16

P. G. Patel et al.

from Sweden and India showed distinct GM composition in the two groups (Alvarez-Silva et al. 2021). Though, when ethnic groups from same geographical region were tested for alteration in GM no significant changes were observed. But when metformin treated patients were analysed, alpha diversity was lower in South Asian Surinamese subjects compared to African Surinamese and had unique gut microbiome biomarkers (Balvers et al. 2021). Chronic kidney disease (CKD), a renal impairment disease, is one of the ailments that has been associated with dysbiosis of the GM. Changes in GM composition are responsible for production of uremic toxins (indoles, creatinines, hippuric acid, etc.) that accumulates over time and induce CKD-related complications (Nallu et al. 2017). Although several attempts have been made to diagnose CKD using GM as biomarkers, a consensus has yet to be reached. Multiple studies have revealed that occurrence of CKD may differ based on ethnicity, with South Asians and Africans more likely to contract CKD than Caucasians (Dreyer et al. 2009; Mathur et al. 2018; Liyanage et al. 2022). As observed in other metabolic or cardiovascular diseases, GM composition of CKD patients may differ based on their ethnicity, which may further hinder identification of specific biomarkers. GM analysis of Han Chinese population with CKD suggested significant reduction in gut bacteria, with Bacteroides being the most dominant phyla. Additionally, creatinine and cystatin C were determined as uremic compounds that altered gut microbiota (Jiang et al. 2017). Role of probiotics in CKD progression has also been evaluated in a metaanalysis of published reports. Ten trials carried out in eight different countries revealed that while administration of probiotics reduced urea levels, it did not have significant impact on uremic acid, C-reactive proteins, and creatinine (Tao et al. 2019).

5 Does Geographical Variation Impact GM? Every geographical region has different agricultural products, food products, and various region-specific cultural goods that impact the overall GM development and diversity (Senghor et al. 2018). The composition of GM is dependent on the demographics, diets, and even the geographical location (Dwiyanto et al. 2021). In recent years, studies on GM have become global as shown in Fig. 2 and the international GM composition database is continuously expanding. The widely accepted Burgmann’s rule has proved to be applicable on humans as well. As per the law, in geographical area with high latitude, population has large body mass, whereas in lower latitude area low body mass is observed. Firmicutes and Bacteroides phyla are responsible for fat extraction and energy storage and thereby influence the body. In their study, Suzuki and Worobey found link between these two microbial phyla composition and geography (Suzuki and Worobey 2014), with increased proportion of these phyla at high latitude. Physiological factors such as high altitude can also alter the gut microflora. In high altitude regions, low thermal energy and reduced oxygen concentration lead to adaptation in blood circulation.

Impact of Dietary Habits, Ethnicity, and Geographical Provenance. . .

17

Stearns et al., 2018 Liu et al., 2016 Lan et al., 2017 Alvarez-Silva et al., 2021 Xu et al., 2020 Lin et al., 2013 Fontana et al., 2019 Yatsuneko et al., 2012 Afolayan et al., 2019 Deschasaux et al., 2018 Kabwe et al., 2020 Shin et al., 2019

Fig. 2 Internationalization of GM studies (edited from Ecklu-Mensah et al. 2022)

Mazel performed experiments to analysis how high altitude affect mouse GM. Their study demonstrated high prevalence of Prevotella phyla at high altitude environment. Prevotella are organisms that generate short-chain fatty acids (SCFA), through saccharolysis of carbohydrates from host diet. High concentration of SCFA increases nutrition uptake in high altitude region that could improve blood circulation (Mazel 2019). Another similar study exhibited that Bacteroides to Prevotella ratio increases after exposure to high altitude induced stress. Since the subjects were initially tested at lower altitude and the diet remained constant throughout the duration of the study, alterations in GM are due to physiological stress (Karl et al. 2018). Aside from altitude, exposure to cold has also been documented to cause alteration in GM. Studies on mice models or native model found in colder regions have indicated that GM plays a key factor in mediating homeostasis during prolonged cold exposure. Transplantation of acclimatized cold microbiota from a mice to regular, healthy mice resulted in acquisition of cold-tolerance and other features (Chevalier et al. 2015). Prolonged cold exposure also reduces potentially pathogenic as well as beneficial microflora in mice models (Wang et al. 2022). There are various such studies show that geographical variations also impact the GM. Lin et al. have conducted GM study on subjects from two geographically separated countries: USA and Bangladesh. On comparing young children from Bangladesh and USA, children from Bangladesh had higher GM diversity. The study indicates that these dissimilarities in GM are due to combination of factors including environment, dietary choices, lifestyle, genetic factor, and socioeconomic status (Lin et al. 2013). To understand the diversity within GM across different continents, Mobeen et al. have studied GM of individuals from 15 different countries. Firmicutes and Bacteroidetes turned out to be the major phyla in the GM globally. At the inter-continental level Bacteroides, Bifidobacterium and Prevotella were reported, while at intra-continental level higher variations were observed. In case of America—two phyla Bacteroides and Ruminococcaceae, for Europe—four

18

P. G. Patel et al.

phyla Prevotella, Faecalibacterium, Clostrdiales and Bacteroides, and finally for Asia—three phyla Bacteroides, Bifidobacterium, Prevotella were identified. These variations within the GM diversity are attributed to environment and climate and geographical variations (Mobeen et al. 2018). A short pilot study carried out by Afolayan et al. demonstrated that geographical relocation for a brief time duration can also alter gut microbiome. This study examined the gut microbiome of subject after 2 months stay in Italy followed by another 2 months stay in Nigeria. The diet choices were constant throughout the duration of 4 months. Within 2 months of stay in Italy, gut microbiome diversity and Firmicutes percentage reduced, which was quickly restored to the original Prevotella and Treponema composition on return to Nigeria (Afolayan et al. 2021). Therefore, geography variation has a significant influence on the gut microbiome even if the separation lasts for short period. In modern world immigration has become the new normal and people frequently relocate for various purposes like study, business, and medical treatment. Migration to another country leads to cultural assimilation that includes new foodstuffs, change in weather condition, and altered lifestyle. All of these adaptations induce significant changes in the overall composition of the GM. In USA many immigrants have been reported to become obese, have increased heart-conditions, chronic diseases, and gastrointestinal diseases. Rapid lifestyle changes for better cultural assimilation have been regarded as the major cause of these problems (Sonnenburg and Sonnenburg 2018). Thus, it is important to analyse the microbial diversity of gut as well as immediate and long-term effect of migration on GM. Most of the studies involving migration have been focused on USA as they have the largest number of immigrants. As of 2015, about 21% of their total population is comprised of immigrants (United Nations 2017). Vangay et al. performed several experiments to determine the effect of migration on GM of South-East Asian women. They analysed gut microbiomes of 514 healthy females of two different ethnicity originally from Thailand (Hmong Thai and Karen Thai). European American females were used as control to compare the changes within GM. Initially the immigrants and control population had different microflora in gut before migration. However, 6 months after migration, reanalysis of the GM showed drastic changes in the gut microflora. Originally, they contained high number of Prevotella phyla which have plant polysaccharide-degrading capacity but after moving to USA Prevotella were displaced by Bacteroides. Secondgeneration immigrants lacked Prevotella in their gut and were completely replaced by Bacteroides (Vangay et al. 2018). Recently, Copeland et al. carried out similar research on effect of migration on GM of South Asian immigrants in Canada. Here, first generation immigrant and children born to immigrant parents in Canada underwent gut microbiome profiling. The analysis demonstrated that South Asians who immigrated in early life had similar gut microflora as that of second-generation children born in Canada. However, the subjects that had migrated recently had different GM composition from that of second-generation South Asians and Canadians. South Asians GM is predominated by Prevotella copri, whereas secondgeneration children have gut microflora dominated by Bacteroides spp. or Clostridia spp. and Dialister invisus. But with the time Bacteroidia spp. replaced the original Prevotella copri as the effect of immigration becomes more prominent (Copeland

Impact of Dietary Habits, Ethnicity, and Geographical Provenance. . .

19

et al. 2021). Both of these studies prove that geographical relocation due to migration can completely reshape the fundamental GM composition. While several studies have revealed geographical provenance to be a major factor in determining gut microbial diversity, there have been certain contradictory studies that suggest otherwise. When GM within similar geographical area but with different ethnicities and socioeconomic status was examined, variation in the gut microbial profiles was reported. Amaruddin et al. and Chong et al. studied GM of individuals from Makassar, Indonesia and Perak, Malaysia, respectively. In both cases dissimilarities in GM composition were attributed to either ethnicity or socioeconomic differences among the subjects (Amaruddin et al. 2020; Chong et al. 2015). Similarly, Quin and Gibson suggest that in case of infants within same geographical region, human behaviour, i.e., maternal diet, mode of delivery, and infant feeding habits are responsible for differences in GM (Quin and Gibson 2020). From the studies mentioned, it is evident that rather than a single determinant, a combination of factors shapes the overall composition of the human GM. Therefore, for GM studies instead of concentrating on a single factor, it is more advantageous to focus on the interconnected relationship between various factors and their combined impact on gut microbiome. Table 3 here summarizes the most prominent GM phyla in different populations along with their ethnicity, dietary habits, and geographical location.

6 Conclusion The composition and diversity of GM is a complex matter that is interlinked with a variety of factors. One cannot predict the composition of a particular GM based on a single factor, rather one must look at how these factors are associated with each other. In case of dietary habits, ethnicity, and geographical provenance, change in one factor leads to change in other factors. Migration, i.e., geographical variation led to alterations in dietary patterns that ultimately transformed GM. Similarly, individuals belonging to different ethnic groups had dissimilarities in their GM profile despite being from same geographical location. Type of diet followed by individuals of same ethnicity within same location also plays a key role in the overall GM composition. Two people having drastically different dietary habits will have variation in their GM profile. Therefore, when studying GM these factors should not be segregated into distinct categories but instead viewed as an interwoven cycle. Any interaction within this cycle alters overall balance and how it influences the GM. Previously, majority of GM-based studies originated from Western countries. However, within last few years the GM research has become truly global. Nowadays many studies being published that includes diverse ethnic groups and population from unexplored regions. Technological advances made within recent years have helped with the continuous expansion of global GM database. In future it may be possible to diagnose a specific disease based on dysbiosis within GM. Future studies

1. Florence, Italy 2. Rural Burkina Faso Thailand 1. Central (Bangkok) 2. Northeast (Khon Khaen)

India 1. North-Central 2. South India Oklahoma, USA

Papua New Guinea Tanzania

Geographical location Seoul, South Korea

Processed carbohydrate and protein-based diet

NativeAmerican 1. Cheyenne 2. Arapaho 1. Italian 2. Mossi tribe Thai

1. Typical Western diet 2. Traditional plant-based rural diet 1. Mixed diet (traditional + processed foods) 2. Traditional Thai diet

Non-processed plant-based traditional diet Seasonal hunting/gathering based diet 1. Plant-based diet 2. Omnivorous diet

Dietary habits 1. Traditional Korean 2. Western-American

Pacific Islander Hazda tribe Indian

Ethnicity Korean

Table 3 GM composition of various populations across the globe

1. Firmicutes and Proteobacteria 2. Prevotella, Xylanibacter (Bacteroidetes), and Treponema (Spirochaetes) 1. Bifidobacterium spp., Enterobacteriaceae, and Methanogens 2. Lactobacilli, Clostridium coccoides, Eubacterium rectale, Clostridium leptum, Prevotella, and Bacteroides fragilis

Firmicutes, Actinobacteria, Bacteroidetes, and Proteobacteria

GM composition 1. Coprococcus, Blautia, and Weissella 2. Bifidobacterium, Faecalibacterium, Lactobacillus, and Lachnospira Prevotella (Coriobacteriaceae, Slackia, and Propionibacterium) Firmicutes (Streptococcus, Staphylococcus, Eubacterium) Prevotellaceae, Succinivibrionaceae, Paraprevotellaceae, and Spirochaetaceae 1. Prevotella 2. Bacteroides, Ruminococcus, and Faecalibacterium

La-ongkham et al. (2015)

de Filippo et al. (2017)

Sankaranarayanan et al. (2015)

Martínez et al. (2015) Fragiadakis et al. (2019) Dhakan et al. (2019)

References Shin et al. (2019)

20 P. G. Patel et al.

Impact of Dietary Habits, Ethnicity, and Geographical Provenance. . .

21

may also focus on developing biomarker for various metabolic or digestive disorders, personalized probiotic treatment, and optimizing diet for a well-balanced GM.

References Abou-Donia MB, El-Masry EM, Abdel-Rahman AA et al (2008) Splenda alters gut microflora and increases intestinal P-glycoprotein and cytochrome P-450 in male rats. J Toxicol Environ Heal Part A 71(21):1415–1429. https://doi.org/10.1080/15287390802328630 Afolayan AO, Ayeni FA, Moissl-Eichinger C et al (2019) Impact of a nomadic pastoral lifestyle on the gut microbiome in the Fulani living in Nigeria. Front Microbiol 10:1–11. https://doi.org/10. 3389/fmicb.2019.02138 Afolayan AO, Biagi E, Rampelli S et al (2021) The gut microbiota of an individual varies with intercontinental four-month stay between Italy and Nigeria: a pilot study. Front Cell Infect Microbiol 11:1–8. https://doi.org/10.3389/fcimb.2021.725769 Allwood JG, Wakeling LT, Bean DC (2021) Fermentation and the microbial community of Japanese koji and miso: a review. J Food Sci 86(6):2194–2207. https://doi.org/10.1111/ 1750-3841.15773 Alvarez-Silva C, Kashani A, Hansen TH et al (2021) Trans-ethnic gut microbiota signatures of type 2 diabetes in Denmark and India. Genome Med 13:1–13. https://doi.org/10.1186/s13073-02100856-4 Amaruddin AI, Hamid F, Koopman JPR et al (2020) The bacterial gut microbiota of schoolchildren from high and low socioeconomic status: a study in an urban area of Makassar, Indonesia. Microorganisms 8(6):1–12. https://doi.org/10.3390/microorganisms8060961 Andersson AF, Lindberg M, Jakobsson H et al (2008) Comparative analysis of human gut microbiota by barcoded pyrosequencing. PLoS One 3(7):e2836. https://doi.org/10.1371/ JOURNAL.PONE.0002836 Anwesh M, Kumar KV, Nagarajan M et al (2016) Elucidating the richness of bacterial groups in the gut of Nicobarese tribal community—perspective on their lifestyle transition. Anaerobe 39:68– 76. https://doi.org/10.1016/j.anaerobe.2016.03.002 Balvers M, Deschasaux M, van den Born BJ et al (2021) Analyzing type 2 diabetes associations with the gut microbiome in individuals from two ethnic backgrounds living in the same geographic area. Nutrients 13(9):1–23. https://doi.org/10.3390/nu13093289 Bevilacqua A, Costabile A, Bergillos-Meca T et al (2016) Impact of gluten-friendly bread on the metabolism and function of in vitro gut microbiota in healthy human and coeliac subjects. PLoS One 11(9):e0162770. https://doi.org/10.1371/JOURNAL.PONE.0162770 Bian X, Chi L, Gao B et al (2017) Gut microbiome response to sucralose and its potential role in inducing liver inflammation in mice. Front Physiol 8:487. https://doi.org/10.3389/FPHYS.2017. 00487/BIBTEX Bisgaard H, Li N, Bonnelykke K et al (2011) Reduced diversity of the intestinal microbiota during infancy is associated with increased risk of allergic disease at school age. J Allergy Clin Immunol 128(3):646–652.e5. https://doi.org/10.1016/J.JACI.2011.04.060 Botes A, Todorov SD, von Mollendorff JW et al (2007) Identification of lactic acid bacteria and yeast from boza. Process Biochem 42(2):267–270. https://doi.org/10.1016/j.procbio.2006. 07.015 Brooks AW, Priya S, Blekhman R, Bordenstein SR (2018) Gut microbiota diversity across ethnicities in the United States. PLoS Biol 16(12):1–24. https://doi.org/10.1101/342915 Cammarota G, Ianiro G, Bibbò S, Gasbarrini A (2014) Gut microbiota modulation: probiotics, antibiotics or fecal microbiota transplantation? Intern Emerg Med 9:365–373. https://doi.org/10. 1007/s11739-014-1069-4

22

P. G. Patel et al.

Cani PD (2018) Human gut microbiome: hopes, threats and promises. Gut 67(9):1716–1725. https://doi.org/10.1136/gutjnl-2018-316723 Chassaing B, Koren O, Goodrich JK et al (2015) Dietary emulsifiers impact the mouse gut microbiota promoting colitis and metabolic syndrome. Nature 519:92–96. https://doi.org/10. 1038/nature14232 Chauhan NS (2019) Introductory chapter: human and microbes in health and diseases. In: Role of microbes in human health and diseases. IntechOpen, London. https://doi.org/10.5772/ INTECHOPEN.85217 Chevalier C, Stojanović O, Colin DJ et al (2015) Gut microbiota orchestrates energy homeostasis during cold. Cell 163:1360–1374. https://doi.org/10.1016/j.cell.2015.11.004 Chong CW, Ahmad AF, Lim YAL et al (2015) Effect of ethnicity and socioeconomic variation to the gut microbiota composition among pre-adolescent in Malaysia. Sci Rep 5:1–12. https://doi. org/10.1038/srep13338 Chumpitazi BP (2020) The gut microbiome as a predictor of low fermentable oligosaccharides disaccharides monosaccharides and polyols diet efficacy in functional bowel disorders. Curr Opin Gastroenterol 36(2):147–154. https://doi.org/10.1097/MOG.0000000000000608 Copeland JK, Chao G, Vanderhout S et al (2021) The impact of migration on the gut metagenome of South Asian Canadians. Gut Microbes 13:1–29. https://doi.org/10.1080/19490976.2021. 1902705 Cryan JF, O’Mahony SM (2011) The microbiome-gut-brain axis: from bowel to behavior. Neurogastroenterol Motil 23(3):187–192. https://doi.org/10.1111/j.1365-2982.2010.01664.x D’Argenio V, Salvatore F (2015) The role of the gut microbiome in the healthy adult status. Clin Chim Acta 451:97–102. https://doi.org/10.1016/j.cca.2015.01.003 De Filippis F, Ercolini D (2018) Microbiome and diet. In: The gut microbiome in health and disease. Springer International Publishing, Cham, pp 79–88 de Filippo C, Di Paola M, Ramazzotti M et al (2017) Diet, environments, and gut microbiota. A preliminary investigation in children living in rural and urban Burkina Faso and Italy. Front Microbiol 8:1–14. https://doi.org/10.3389/fmicb.2017.01979 De Vadder F, Kovatcheva-Datchary P, Goncalves D et al (2014) Microbiota-generated metabolites promote metabolic benefits via gut-brain neural circuits. Cell 156:84–96. https://doi.org/10. 1016/J.CELL.2013.12.016 Dehingia M, Adak A, Khan MR (2019) Ethnicity-influenced microbiota: a future healthcare perspective. Trends Microbiol 27(3):191–193. https://doi.org/10.1016/j.tim.2019.01.002 Deka P, Mehetre GT, Lalnunmawii E et al (2021) Metagenomic analysis of bacterial diversity in traditional fermented foods reveals food-specific dominance of specific bacterial taxa. Fermentation 7(3):167. https://doi.org/10.3390/fermentation7030167 Dertli E, Çon AH (2017) Microbial diversity of traditional kefir grains and their role on kefir aroma. LWT Food Sci Technol 85:151–157. https://doi.org/10.1016/j.lwt.2017.07.017 Deschasaux M, Bouter KE, Prodan A et al (2018) Depicting the composition of gut microbiota in a population with varied ethnic origins but shared geography. Nat Med 24(10):1526–1531. https://doi.org/10.1038/s41591-018-0160-1 Dhakan DB, Maji A, Sharma AK et al (2019) The unique composition of Indian gut microbiome, gene catalogue, and associated fecal metabolome deciphered using multi-omics approaches. Gigascience 8(3):1–20. https://doi.org/10.1093/gigascience/giz004 Dreyer G, Hull S, Aitken Z et al (2009) The effect of ethnicity on the prevalence of diabetes and associated chronic kidney disease. QJM 102:261–269. https://doi.org/10.1093/qjmed/hcn177 Dubois G, Girard C, Lapointe FJ, Shapiro BJ (2017) The Inuit gut microbiome is dynamic over time and shaped by traditional foods. Microbiome 5:151. https://doi.org/10.1186/s40168-0170370-7 Dwiyanto J, Hussain MH, Reidpath D et al (2021) Ethnicity influences the gut microbiota of individuals sharing a geographical location: a cross-sectional study from a middle-income country. Sci Rep 11:1–10. https://doi.org/10.1038/s41598-021-82311-3

Impact of Dietary Habits, Ethnicity, and Geographical Provenance. . .

23

Eckburg PB, Bik EM, Bernstein CN et al (2005) Diversity of the human intestinal microbial flora. Science 308:1635–1638 Ecklu-Mensah G, Gilbert J, Devkota S (2022) Dietary selection pressures and their impact on the gut microbiome. Cmgh 13:7–18. https://doi.org/10.1016/j.jcmgh.2021.07.009 Ehrlich SD (2016) Le microbiote intestinal humain influe sur la santé et la maladie. Comptes Rendus-Biol 339:319–323. https://doi.org/10.1016/j.crvi.2016.04.008 Ferreira CM, Vieira AT, Vinolo MAR et al (2014) The central role of the gut microbiota in chronic inflammatory diseases. J Immunol Res 2014:1–12. https://doi.org/10.1155/2014/689492 Fijan S, Frauwallner A, Langerholc T et al (2019) Efficacy of using probiotics with antagonistic activity against pathogens of wound infections: an integrative review of literature. Biomed Res Int 2019:1–21. https://doi.org/10.1155/2019/7585486 Findley K, Williams DR, Grice EA, Bonham VL (2016) Health disparities and the microbiome. Trends Microbiol 24(11):847–850. https://doi.org/10.1016/j.tim.2016.08.001 Flint HJ, Scott KP, Duncan SH et al (2012) Microbial degradation of complex carbohydrates in the gut. Gut Microbes 3(4):289–306. https://doi.org/10.4161/gmic.19897 Fontana A, Panebianco C, Picchianti-Diamanti A et al (2019) Gut microbiota profiles differ among individuals depending on their region of origin: an Italian pilot study. Int J Environ Res Public Health 16(21):4065. https://doi.org/10.3390/ijerph16214065 Fortenberry JD (2013) The uses of race and ethnicity in human microbiome research. Trends Microbiol 21(4):165–166. https://doi.org/10.1016/j.tim.2013.01.001 Fragiadakis GK, Smits SA, Sonnenburg ED et al (2019) Links between environment, diet, and the hunter-gatherer microbiome. Gut Microbes 10(2):216–227. https://doi.org/10.1080/19490976. 2018.1494103 Frank DN, St. Amand AL, Feldman RA et al (2007) Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc Natl Acad Sci 104:13780–13785 Franks I (2013) Microbiota: gut microbes might promote intestinal angiogenesis. Nat Rev Gastroenterol Hepatol 10:3. https://doi.org/10.1038/nrgastro.2012.227 Franzosa EA, Huang K, Meadow JF et al (2015) Identifying personal microbiomes using metagenomic codes. Proc Natl Acad Sci 112:E2930–E2938 Gevers D, Knight R, Petrosino JF et al (2012) The human microbiome project: a community resource for the healthy human microbiome. PLoS Biol 10(8):e1001377. https://doi.org/10. 1371/JOURNAL.PBIO.1001377 Gilbert JA, Blaser MJ, Caporaso JG et al (2018) Current understanding of the human microbiome. Nat Med 24(4):392–400. https://doi.org/10.1038/nm.4517 Girard C, Tromas N, Amyot M, Shapiro BJ (2017) Gut microbiome of the Canadian Arctic Inuit. mSphere 2:e00297-16. https://doi.org/10.1128/mSphere.00297-16 Goodrich JK, Waters JL, Poole AC et al (2014) Human genetics shape the gut microbiome. Cell 159(4):789–799. https://doi.org/10.1016/j.cell.2014.09.053 Grice EA, Segre JA (2012) The human microbiome: our second genome. Annu Rev Genomics Hum Genet 13:151–170. https://doi.org/10.1146/annurev-genom-090711-163814 Handajani YS, Turana Y, Yogiara Y et al (2020) Tempeh consumption and cognitive improvement in mild cognitive impairment. Dement Geriatr Cogn Disord 49:497–502. https://doi.org/10. 1159/000510563 Hong SW, Choi YJ, Lee HW et al (2016) Microbial community structure of Korean cabbage kimchi and ingredients with denaturing gradient gel electrophoresis. J Microbiol Biotechnol 26(6): 1057–1062. https://doi.org/10.4014/jmb.1512.12035 Hooper LV (2009) Do symbiotic bacteria subvert host immunity? Nat Rev Microbiol 7(5):367–374. https://doi.org/10.1038/nrmicro2114 Hooper LV, Wong MH, Thelin A et al (2001) Molecular analysis of commensal host-microbial relationships in the intestine. Science 291:881–884. https://doi.org/10.1126/SCIENCE.291. 5505.881

24

P. G. Patel et al.

Hori T, Matsuda K, Oishi K (2020) Probiotics: a dietary factor to modulate the gut microbiome, host immune system, and gut–brain interaction. Microorganisms 8(9):1–24. https://doi.org/10.3390/ microorganisms8091401 Irvine B, Green DG, Mckee M et al (2002) Education and debate: genetics, race, ethnicity, and health. BMJ 325:488 Jandhyala SM, Talukdar R, Subramanyam C et al (2015) Role of the normal gut microbiota. World J Gastroenterol 21(29):8836–8847. https://doi.org/10.3748/WJG.V21.I29.8787 Jiang S, Xie S, Lv D et al (2017) Alteration of the gut microbiota in Chinese population with chronic kidney disease. Sci Rep 7:1–10. https://doi.org/10.1038/s41598-017-02989-2 Joishy TK, Dehingia M, Khan MR (2019) Bacterial diversity and metabolite profiles of curd prepared by natural fermentation of raw milk and back sloping of boiled milk. World J Microbiol Biotechnol 35(7):102. https://doi.org/10.1007/s11274-019-2677-y Kabwe MH, Vikram S, Mulaudzi K et al (2020) The gut mycobiota of rural and urban individuals is shaped by geography. BMC Microbiol 20:1–12. https://doi.org/10.1186/s12866-020-01907-3 Kang Y, Cai Y (2017) Gut microbiota and obesity: implications for fecal microbiota transplantation therapy. Hormones 16:223–234. https://doi.org/10.14310/horm.2002.1742 Karl PJ, Berryman CE, Young AJ et al (2018) Associations between the gut microbiota and host responses to high altitude. Am J Physiol Gastrointest Liver Physiol 315(6):1003–1015. https:// doi.org/10.1152/ajpgi.00253.2018 Karlsson F, Tremaroli V, Nielsen J, Bäckhed F (2013) Assessing the human gut microbiota in metabolic diseases. Diabetes 62(10):3341–3349. https://doi.org/10.2337/DB13-0844 Kau AL, Ahern PP, Griffin NW et al (2011) Human nutrition, the gut microbiome and the immune system. Nature 474:327–336. https://doi.org/10.1038/nature10213 Kennedy PJ, Cryan JF, Dinan TG, Clarke G (2014) Irritable bowel syndrome: a microbiome-gutbrain axis disorder? World J Gastroenterol 20(39):14105. https://doi.org/10.3748/WJG.V20. I39.14105 Keohane DM, Ghosh TS, Jeffery IB et al (2020) Microbiome and health implications for ethnic minorities after enforced lifestyle changes. Nat Med 26(7):1089–1095. https://doi.org/10.1038/ s41591-020-0963-8 Khine WWT, Zhang Y, Goie GJY et al (2019) Gut microbiome of pre-adolescent children of two ethnicities residing in three distant cities. Sci Rep 9:1–10. https://doi.org/10.1038/s41598-01944369-y Kho ZY, Lal SK (2018) The human gut microbiome—a potential controller of wellness and disease. Front Microbiol 9:1–23. https://doi.org/10.3389/fmicb.2018.01835 Lan D, Ji W, Lin B et al (2017) Correlations between gut microbiota community structures of Tibetans and geography. Sci Rep 7:1–9. https://doi.org/10.1038/s41598-017-17194-4 La-ongkham O, Nakphaichit M, Leelavatcharamas V et al (2015) Distinct gut microbiota of healthy children from two different geographic regions of Thailand. Arch Microbiol 197(4):561–573. https://doi.org/10.1007/s00203-015-1089-0 Laursen MF, Bahl MI, Michaelsen KF, Licht TR (2017) First foods and gut microbes. Front Microbiol 8:1–8. https://doi.org/10.3389/fmicb.2017.00356 Le Chatelier E, Nielsen T, Qin J et al (2013) Richness of human gut microbiome correlates with metabolic markers. Nature 500:541–546. https://doi.org/10.1038/nature12506 Li CH, Wang CT, Lin YJ et al (2022) Long-term consumption of the sugar substitute sorbitol alters gut microbiome and induces glucose intolerance in mice. Life Sci 305:120770. https://doi.org/ 10.1016/j.lfs.2022.120770 Lin A, Bik EM, Costello EK et al (2013) Distinct distal gut microbiome diversity and composition in healthy children from Bangladesh and the United States. PLoS One 8:e53838. https://doi.org/ 10.1371/journal.pone.0053838 Liu W, Zhang J, Wu C et al (2016) Unique features of ethnic Mongolian gut microbiome revealed by metagenomic analysis. Sci Rep 6:1–11. https://doi.org/10.1038/srep34826

Impact of Dietary Habits, Ethnicity, and Geographical Provenance. . .

25

Liu K, Zhang Y, Li Q et al (2020) Ethnic differences shape the alpha but not beta diversity of gut microbiota from school children in the absence of environmental differences. Microorganisms 8(2):1–15. https://doi.org/10.3390/microorganisms8020254 Liyanage T, Toyama T, Hockham C et al (2022) Prevalence of chronic kidney disease in Asia: a systematic review and analysis. BMJ Glob Health 7:1–9. https://doi.org/10.1136/bmjgh-2021007525 Low DY, Hejndorf S, Tharmabalan RT et al (2021) Regional diets targeting gut microbial dynamics to support prolonged Healthspan. Front Microbiol 12:1–12. https://doi.org/10.3389/fmicb.2021. 659465 Lozupone CA, Stombaugh JI, Gordon JI et al (2012) Diversity, stability and resilience of the human gut microbiota. Nature 489:220–230. https://doi.org/10.1038/nature11550 Magnúsdóttir S, Ravcheev D, De Crécy-Lagard V, Thiele I (2015) Systematic genome assessment of B-vitamin biosynthesis suggests cooperation among gut microbes. Front Genet 6:148. https:// doi.org/10.3389/fgene.2015.00148 Mar JS, Lamere BJ, Lin DL et al (2016) Disease severity and immune activity relate to distinct interkingdom gut microbiome states in ethnically distinct ulcerative colitis patients. MBio 7(4): 1–11. https://doi.org/10.1128/mBio.01072-16 Markowiak P, Ślizewska K (2017) Effects of probiotics, prebiotics, and synbiotics on human health. Nutrients 9(9):1021. https://doi.org/10.3390/NU9091021 Marsh AJ, O’Sullivan O, Hill C et al (2014) Sequence-based analysis of the bacterial and fungal compositions of multiple kombucha (tea fungus) samples. Food Microbiol 38:171–178. https:// doi.org/10.1016/j.fm.2013.09.003 Martínez I, Stegen JC, Maldonado-Gómez MX et al (2015) The gut microbiota of rural Papua new Guineans: composition, diversity patterns, and ecological processes. Cell Rep 11(4):527–538. https://doi.org/10.1016/j.celrep.2015.03.049 Mathur R, Dreyer G, Yaqoob MM, Hull SA (2018) Ethnic differences in the progression of chronic kidney disease and risk of death in a UK diabetic population: an observational cohort study. BMJ Open 8:1–9. https://doi.org/10.1136/bmjopen-2017-020145 Mazel F (2019) Living the high life: could gut microbiota matter for adaptation to high altitude? Mol Ecol 28(9):2119–2121. https://doi.org/10.1111/mec.15093 Mazidi M, Rezaie P, Kengne AP et al (2016) Gut microbiome and metabolic syndrome. Diabetes Metab Syndr Clin Res Rev 10(2):S150–S157. https://doi.org/10.1016/j.dsx.2016.01.024 Mobeen F, Sharma V, Prakash T (2018) Enterotype variations of the healthy human gut microbiome in different geographical regions. Bioinformation 14(9):560–573. https://doi.org/ 10.6026/97320630014560 Montel MC, Buchin S, Mallet A et al (2014) Traditional cheeses: rich and diverse microbiota with associated benefits. Int J Food Microbiol 177:136–154. https://doi.org/10.1016/J. IJFOODMICRO.2014.02.019 Nagai T (2015) Health benefits of natto. In: Tamang J (ed) Heal benefits of fermented foods and beverages. CRC Press, Boca Raton, pp 433–454 Nallu A, Sharma S, Ramezani A et al (2017) Gut microbiome in chronic kidney disease: challenges and opportunities. Transl Res 179:24–37. https://doi.org/10.1016/j.trsl.2016.04.007 Nettleton JE, Reimer RA, Shearer J (2016) Reshaping the gut microbiota: impact of low calorie sweeteners and the link to insulin resistance? Physiol Behav 164:488–493. https://doi.org/10. 1016/J.PHYSBEH.2016.04.029 Prideaux L, Kang S, Wagner J et al (2013) Impact of ethnicity, geography, and disease on the microbiota in health and inflammatory bowel disease. Inflamm Bowel Dis 19(13):2906–2918. https://doi.org/10.1097/01.MIB.0000435759.05577.12 Qin J, Li R, Raes J et al (2010) A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464:59–65. https://doi.org/10.1038/nature08821 Quin C, Gibson DL (2020) Human behavior, not race or geography, is the strongest predictor of microbial succession in the gut bacteriome of infants. Gut Microbes 11(5):1143–1171

26

P. G. Patel et al.

Rackaityte E, Lynch SV (2020) The human microbiome in the 21st century. Nat Commun 11:19– 21. https://doi.org/10.1038/s41467-020-18983-8 Rothschild D, Weissbrod O, Barkan E et al (2018) Environment dominates over host genetics in shaping human gut microbiota. Nature 555:210–215. https://doi.org/10.1038/nature25973 Ruiz-Ojeda FJ, Plaza-Diaz J, Saez-Lara MJ et al (2019) Effects of sweeteners on the gut microbiota: a review of experimental studies and clinical trials. Adv Nutr 10(31):48. https://doi.org/10.1093/ advances/nmz112 Samuel BS, Shaito A, Motoike T et al (2008) Effects of the gut microbiota on host adiposity are modulated by the short-chain fatty-acid binding G protein-coupled receptor, Gpr41. Proc Natl Acad Sci USA 105:16767–16772 Sankaranarayanan K, Ozga AT, Warinner C et al (2015) Gut microbiome diversity among Cheyenne and Arapaho individuals from Western Oklahoma. Curr Biol 25(24):3161–3169. https:// doi.org/10.1016/j.cub.2015.10.060 Sekirov I, Russell SL, Caetano M, Antunes L, Finlay BB (2010) Gut microbiota in health and disease. Physiol Rev 90(3):859–904. https://doi.org/10.1152/physrev.00045.2009 Senghor B, Sokhna C, Ruimy R, Lagier JC (2018) Gut microbiota diversity according to dietary habits and geographical provenance. Hum Microbiome J 7–8:1–9. https://doi.org/10.1016/j. humic.2018.01.001 Shin JH, Jung S, Kim SA et al (2019) Differential effects of typical Korean versus American-style diets on gut microbial composition and metabolic profile in healthy overweight Koreans: a randomized crossover trial. Nutrients 11(10):2450. https://doi.org/10.3390/nu11102450 Smith M, Kassam Z, Edelstein C et al (2014) OpenBiome remains open to serve the medical community. Nat Biotechnol 32:867. https://doi.org/10.1038/nbt.3006 Sonnenburg J, Sonnenburg E (2018) A microbiota assimilation. Cell Metab 28(5):675–677. https:// doi.org/10.1016/j.cmet.2018.10.010 Stearns JC, Zulyniak MA, de Souza RJ et al (2017) Ethnic and diet-related differences in the healthy infant microbiome. Genome Med 9:1–12. https://doi.org/10.1186/s13073-017-0421-5 Suzuki TA, Worobey M (2014) Geographical variation of human gut microbial composition. Biol Lett 10(2):20131037. https://doi.org/10.1098/rsbl.2013.1037 Tao S, Tao S, Cheng Y et al (2019) Effects of probiotic supplements on the progression of chronic kidney disease: a meta-analysis. Nephrology 24(11):1122–1130. https://doi.org/10.1111/nep. 13549 Tap J, Mondot S, Levenez F et al (2009) Towards the human intestinal microbiota phylogenetic core. Environ Microbiol 11(10):2574–2584. https://doi.org/10.1111/j.1462-2920.2009.01982.x Taur Y, Coyte K, Schluter J et al (2018) Reconstitution of the gut microbiota of antibiotic-treated patients by autologous fecal microbiota transplant. Sci Transl Med 10. https://doi.org/10.1126/ scitranslmed.aap9489 Thursby E, Juge N (2017) Introduction to the human gut microbiota. Biochem J 474(11): 1823–1836. https://doi.org/10.1042/BCJ20160510 United Nations (2017) International migration report 2015 highlights. http://www.un.org/%0Aen/ development/desa/population/migration/publications/migrationreport/docs/%0 AMigrationReport2017_Highlights.pdf%0A Valdes AM, Walter J, Segal E, Spector TD (2018) Role of the gut microbiota in nutrition and health. BMJ 361:36–44. https://doi.org/10.1136/bmj.k2179 van Best N, Hornef MW, Savelkoul PHM, Penders J (2015) On the origin of species: factors shaping the establishment of infant’s gut microbiota. Birth Defects Res Part C Embryo Today Rev 105(4):240–251. https://doi.org/10.1002/bdrc.21113 Vangay P, Johnson AJ, Ward TL et al (2018) US immigration westernizes the human gut microbiome. Cell 175(4):962–972.e10. https://doi.org/10.1016/j.cell.2018.10.029 Wang T, Roest DIM, Smidt H, Zoetendal EG (2019) “We are what we eat”: how diet impacts the gut microbiota in adulthood. In: How fermented foods feed a healthy gut microbiota. Springer International Publishing, Cham, pp 259–283

Impact of Dietary Habits, Ethnicity, and Geographical Provenance. . .

27

Wang B, Liu J, Lei R et al (2022) Cold exposure, gut microbiota, and hypertension: a mechanistic study. Sci Total Environ 833:155199. https://doi.org/10.1016/j.scitotenv.2022.155199 Wu GD, Compher C, Chen EZ et al (2016) Comparative metabolomics in vegans and omnivores reveal constraints on diet-dependent gut microbiota metabolite production. Gut 65:63–72. https://doi.org/10.1136/GUTJNL-2014-308209 Xu J, Lawley B, Wong G et al (2020) Ethnic diversity in infant gut microbiota is apparent before the introduction of complementary diets. Gut Microbes 11(5):1362–1373. https://doi.org/10.1080/ 19490976.2020.1756150 Yatsunenko T, Rey FE, Manary MJ et al (2012) Human gut microbiome viewed across age and geography. Nature 486:222–227. https://doi.org/10.1038/nature11053 Yulandi A, Suwanto A, Waturangi DE, Wahyudi AT (2020) Shotgun metagenomic analysis reveals new insights into bacterial community profiles in tempeh. BMC Res Notes 13:1–7. https://doi. org/10.1186/s13104-020-05406-6 Zabat MA, Sano WH, Wurster JI et al (2018) Microbial community analysis of sauerkraut fermentation reveals a stable and rapidly established community. Foods 7(5):77. https://doi. org/10.3390/foods7050077 Zheng H, Yde CC, Clausen MR et al (2015) Metabolomics investigation to shed light on cheese as a possible piece in the French paradox puzzle. J Agric Food Chem 63(10):2830–2839. https://doi. org/10.1021/JF505878A/SUPPL_FILE/JF505878A_SI_001.PDF Zheng D, Liwinski T, Elinav E (2020) Interaction between microbiota and immunity in health and disease. Cell Res 30(6):492–506. https://doi.org/10.1038/s41422-020-0332-7 Zhu B, Wang X, Li L (2010) Human gut microbiome: the second genome of human. Protein Cell 1(8):718–725. https://doi.org/10.1007/s13238-010-0093-z

Methods Used for Studying Human Microbiome Chinmayi Joshi and Vijay Kothari

Abstract Human microbiome is a complex and dynamic component of the human system. Identifying the members of this vast community and elucidating their functions remains a daunting challenge. Collecting samples from internal body sites under aseptic conditions is the first challenge, and then equally difficult is to identify the microorganisms present in these samples, particularly when most of them are not amenable to conventional laboratory culture. Obligate anaerobes (e.g. many residents of the large intestine) have always been difficult to grow routinely in an average microbiology lab. This chapter describes various sampling methods employed for study of human microbiome and the culture-dependent as well as culture-independent methods for elucidating the taxonomic and functional identity of the microbial symbionts of the human system. Keywords Human microbiome · Symbiont · Sample collection · Metagenomics · Metabolome

1 Introduction ‘Human microbiome’ a well-balanced and extremely environment-specific ecosystem constitutes extraordinarily diverse microbial cells, which exist in correlative associations and reside on or within tissues and biofluids along with the analogous sites of the human body. Microorganisms such as bacteria, archaea, fungi, protists, and viruses can reside in the human body, colonise humans, and form a composite and distinct ecosystem that acclimatises to the specific environment of each niche. A symbiotic relationship between the human body and its naturally occurring

C. Joshi Smt. S.S. Patel Nootan Science and Commerce College, Sankalchand Patel University, Visnagar, Gujarat, India V. Kothari (✉) Institute of Science, Nirma University, Ahmedabad, Gujarat, India e-mail: [email protected] © The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd. 2023 V. Kothari et al. (eds.), Probiotics, Prebiotics, Synbiotics, and Postbiotics, https://doi.org/10.1007/978-981-99-1463-0_2

29

30

C. Joshi and V. Kothari

microbiota begins at childbirth, which plays a crucial role in maintaining overall health. As a result of their biological activities, these organisms are identified as part of the body and result in a variety of alterations from conception to death. In reaction to host factors, the human microbiome is continually changing. Host factors such as age, lifestyle, nutrition, hormonal fluctuations, inherited genes, underlying disease, etc. are key determining factors of the human microbiome. A change in the human microbiota’s composition, a dysbiosis, might cause health problems. Interruptions in human microbiota are being linked to many diseases including inflammatory bowel disease (IBD), diabetes, cancer, cardiovascular diseases, allergic diseases, and antibiotic-resistant infections. Moreover, the human microbiome can also serve as an early detection biomarker and target for curative interface for the treatment of lifethreatening diseases (Castillo et al. 2019; Berg et al. 2020; Ogunrinola et al. 2020). Historically, members of a microbial community were identified by culturedependent methods, which depend on the growth of an organism in the laboratory. Using this approach, researchers did not get the information about the uncultivable members of the microbiota. To overcome this issue, DNA-based methods have been developed in the 1980s. The field of genomics, metagenomics, metatranscriptomics, and modern high-throughput sequencing technologies has contributed to a great extent in identification and characterisation of microorganisms present in microbiota. Additionally, sequencing becomes rapid, easy, and cost-effective, as a result successive characterisation of the human microbiota to explore changes that occur in the human microbiome over time would become possible. Though many questions have been answered using these high-throughput techniques, many questions about human microbiome are yet to be addressed (https://www.ncbi.nlm.nih. gov/books/NBK481559/; Iyer 2016). The different approaches for assessing human microbiome, such as culturedependent or culture-independent methodologies (Fig. 1), have their own advantages and limitations. Studies that include human microbiome are costly and difficult to handle the experiments at different stages, i.e. sample collection, data generation, and data analysis. In addition to sophisticated high-throughput methods, gnotobiotic models and inter-disciplinary approaches are also available for assessing human microbiome. In vitro microbial systems that comprise host cells in the microbial culture are also obtainable and present well-regulated environments for mechanistic and molecular profiling. However, continuous culture of many anaerobic organisms poses difficulties, and in vitro systems are physiologically irrelevant (https://www. ncbi.nlm.nih.gov/books/NBK481559/). This chapter reviews the current approaches and methods used for studying the human microbiome. After describing various sampling methods for accessing microbiome of different human body sites, the chapter further covers the culturedependent in vitro–ex vivo systems, followed by an overview of the high-throughput methods and data analysis approaches. The chapter concludes with a discussion of strengths, weaknesses, and gaps in the technologies.

Methods Used for Studying Human Microbiome

31

Human microbiome

Cultureindependent methods

Culture-dependent methods

Conventional approaches

Molecular approaches

Whole genome sequencing and High-throughput sequencing methods

Isolation Purification Biochemical characterization

Genetic fingerprinting techniques, DNA microarrays, Microautography, Flowcytometry Real-time PCR

Metagenomics Metaproteomics Metatranscriptomics Proteogenomics

Fig. 1 Methods for assessing human microbiome

2 Methods Used for Studying Human Microbiome 2.1

Sample Collection

The human microbiome is the collection of all microbiota that live on different body parts including the skin, gastrointestinal tract, uterus, mammary glands, oral mucosa, seminal fluid, lung, ovarian follicles, conjunctiva, saliva, and biliary tract (Table 1). To study the human microbiome, the first step usually includes the collection of stabilised microbial biomass specimens from specific sites. The following section describes the collection methods for each major body site.

Sample Collection to Study the Skin Microbiome Skin, a body shield, protects the body from the external harms and prevents the evaporation of body fluids. Skin comprises the commensal bacteria such as S. epidermidis, C. acnes, and Corynebacterium spp. that play an important role for skin barrier, immunological reactions, and prevent colonisation of pathogenic bacteria. Kong et al. (2017) reviewed multiple methodologies for skin microbiome sampling, i.e. swabs, surface scrapes, biopsies, cup scrubs, and tape strips. The selection of the sampling method depends on the criteria such as biomass yield, sampling depth, and human DNA contribution. Amongst the sampling methods for

32

C. Joshi and V. Kothari

Table 1 Bacteria present on different body parts and common sample collection methods used for each site Body part Skin

Gastrointestinal tract

Uterus

Mammary glands

Oral mucosa Seminal fluid Conjunctiva

Lung

Ovarian follicles

Common microbial residents Acinetobacter johnsonii, Corynebacterium spp., Cutibacterium acnes, Pseudomonas aeruginosa, Staphylococcus aureus, S. epidermidis, S. warneri, Streptococcus mitis, S. pyogenes Bacteroides, Bifidobacterium, Clostridium, Eubacterium, Fusobacterium, Lactobacillus, Peptococcus, Peptostreptococcus, Ruminococcus, Staphylococcus, Streptococcus Escherichia spp., Fusobacterium nucleatum, Prevotella tannerae, Bacteroides spp., Streptomy ces avermitilis, Mycoplasma spp., Neisseria lactamica, Neisseria polysaccharea, Ureaplasma parvum Staphylococcus, Streptococcus, Corynebacterium, Cutibacterium, Lactobacillus, Lactococcus, and Bifidobacterium Actinomycetes, Bacillus, Firmicutes, Proteobacteria Lactobacillus spp. and Prevotella spp. Acinetobacter, Aquabacterium, Brevundimonas, Corynebacterium, Methylobacterium, Cutibacterium, Bradyrhizobium, Pseudomonas, Sphingomonas, Staphylococci, Streptococcus, Streptophyta Acinetobacter, Fusobacterium, Megasphaera, Prevotella, Pseudomonas, Sphingomonas, Staphylococcus, Streptococcus, Veillonella Actinomyces, Lactobacilli spp., Cutibacterium

Sampling method Swabbing and tape stripping methods

References Ogai et al. (2018)

Faeces, biopsy, luminal brush, laser capture microdissection, catheter aspiration, surgery

Tang et al. (2020)

Cytobrush, Swab

Mitra et al. (2017)

Milk sampling

Taponen et al. (2019)

Mouth-rinsed water, filter paper sampling Semen sample

Jo et al. (2019) Baud et al. (2019) Katzka et al. (2021)

Swabbing, corneal epithelial biopsy

Lung tissue

Carney et al. (2020)

Endocervical mucus, cervical swabs and serum, endometrial biopsy, follicular fluid

Vitale et al. (2021) (continued)

Methods Used for Studying Human Microbiome

33

Table 1 (continued) Body part

Saliva

Biliary tract

Common microbial residents

Campylobacter, Corynebacterium, Cellulosimicrobium, Haemophilus, Porphyromonas, Solobacterium, Streptococcus Proteobacteria and Firmicutes

Sampling method

References

samples and vaginal swab, cotton swab Mouthwash, swabbing, and spitted saliva

Kaan et al. (2022)

Endoscopic retrograde cholangiopancreatography (ERCP), percutaneous biliary drainage, and surgical sampling

Binda et al. (2022)

skin microbiome, premoistened swabbing is the most established sampling method, while dry swabbing has not been extensively employed because of the low biomass collection. Other methods such as tape stripping and scrapes provide a high amount of biomass, but tape stripping is inappropriate for all body sites due to its dimensions and sample attainment time, whereas scrapes could be helpful only for low abundance microbes, i.e. fungi. Cup scrubbing and skin punch biopsies are also the methods which can be useful for microbiome studies. However, these methods are invasive and cannot be used at multiple sites in patients (Chng et al. 2016; Kong et al. 2017). Any method can be used for the study of skin microbiomes depending on the requirement, but it is important to maintain consistency for sample collection throughout the study to reduce confounders and to maximise the ability to identify differences in microbiomes. Additionally, location, sampling frequency, and use of controls are also important aspects of sample collection.

Sample Collection to Study the Gut Microbiome Gut microbiota comprises 1952 uncultured species (Almeida et al. 2019). In humans, the composition of gut microbiota varies between the various regions of gastrointestinal (GI) tract. Gut microbiota play a major role in prevention of infections and promotion of the mature immune system, nutritional assimilation and metabolism, and stimulating anti-cancer functions. Disruption in gut microbiota is associated with various diseases including Clostridium difficile infection, IBD, and irritable bowel syndrome (IBS). We can say that gut microbiota is closely associated with human health, and it is necessary to analyse the association between gut microbiota and disease occurrence, development, and prognosis (Li et al. 2019; Tang et al. 2020). In the previous years, gut microbiome analysis depended on the isolation of anaerobic bacteria that are adequate in the intestine, which affected the precision of the analysis due to the problems in cultivation of anaerobic organisms

34

C. Joshi and V. Kothari

(Lloyd-Price et al. 2019). In current times, the progress of next-generation sequencing (NGS) can precisely evaluate microbial components without culture, has fascinated the research on the gut microbiome. Currently, mucosal biopsy, intestinal aspiration, sample collection from faeces, etc. are the common methods which are being used for sample collection to study the gut microbiome (Tang et al. 2020). Most common method is the sampling from stool. It comprises higher microbial load and minimal human genetic contamination (HMP Consortium 2012a, b) and contains material that can be assayed by using various molecular techniques. This technique can be useful, but preservation of samples, i.e. immediately freezing is required to avoid the change in microbial characteristics due to the environmental changes. Fixatives allow suitable collection and shipping of samples, but they may prevent culture and might not be suitable with accomplishing some molecular assays at afterwards. Other device-based methods such as endoscopy, biopsy, and luminal brushes can also be used to investigate the gut microbiota. Some defects are linked with these methods including invasive procedures, use of laxatives for bowel preparation, and contamination of sampling tools during the time of penetration in the endoscopic channel. Amongst the device-based methods, mucosal biopsy covers a little surface area that may consequence in sampling variation and inaccessibility of rare taxa and may comprise a large amount of contaminated host DNA, which make difficult to analyse the molecular data. Another device-based method is the use of luminal brushing, which is commonly used for the collection of the infectious samples from the lower respiratory tract. This method is appropriate for the analysis of infection associated with lower respiratory tract because the brush specimens are not easily contaminated by microorganisms present in the upper respiratory tract. This method can reduce the bleeding and infection. However, bowel preparation influence and invasion are the similar defects of this method as biopsy. In addition to above sample collection methods, the samples can also be collected using laser capture microdissection (LCM), ingestible sampling devices, capsule device, intestine microbiome aspiration (IMBA). Samples can also be collected using surgery and aspirated intestinal fluid. In spite of the availability of numerous sampling methods, more accurate sampling methods are warranted with reduced invasiveness, avoiding cross-contamination, sampling at fixed points while minimising disturbance to normal physiology of intestine (Song et al. 2016; Tang et al. 2020; https://www.ncbi.nlm.nih.gov/books/NBK481559/).

Sample Collection Methods for Assessment of Microbiome at Various Body Sites To study the respiratory microbiome, samples have been collected from the nasal passages, sinus cavities, oral cavity and pharyngeal region, and the tracheobronchial tree. Swabs, aspirates, sputum, lavage, and brushings are the common methods that are used in respiratory microbiome studies. The respiratory tract has a lower microbial load, and it is crucial to exploit protocols comprising controlled elements to lessen sample contamination by non-target tissue (Lauder et al. 2016). In addition

Methods Used for Studying Human Microbiome

35

to respiratory, skin, and gut microbiome, study of vaginal microbiome is also important. Cytobrush and swab are the common methods, which are used for sampling. Mitra et al. (2017) demonstrated the use of swab and cytobrush to study the compare the vaginal microbiota results at all taxonomic levels and identified unique taxa in cytobrush samples. LefSe analysis identified Proteobacteria, Betaproteobacteria, Burkholderiales, Burkholderiaceae, and Comamonadaceae to be overrepresented in the cytobrush-collected samples. Further, the oral microbiome also has a high biomass and it is also associated with illness. It is associated with the lung microbiome. The oral microbiome served as a promising diagnostic tool for SARS-CoV-2 infection detection and a predictor of disease severity. Several sample collection methods, i.e. raw saliva, oral wash, oral swabs, and scrapings of dental plaque are being used to study oral microbiome. Yano et al. (2020) compared a commercially available OMNIgene ORAL kit to three alternative collection methods including Saccomanno’s fixative, Scope mouthwash, and non-ethanol mouthwash. The results showed clear differences in oral microbial communities between the used oral collection methods. In conclusion, they showed the impact of the sample collection method on oral microbiome analysis. The authors suggested that one consistent oral collection method should be followed for all oral microbiome comparisons. These findings describe that sampling protocols for human microbiome analysis are sensitive to technical methods. Existing microbial communities, their natural features, or environmental conditions can change measured microbial communities. Sample collection and processing can affect the microbiome assays. All these factors should be kept in mind at the time of study design and data analysis (Sinha et al. 2017). Few considerations are necessary for sample collection. First, a sampling device or sampling strategy is determined by factors like clinical facility, staff for sampling, and scientific question behind sampling. After sampling, storage conditions are vital for preserving the samples until further processing. Storage temperature requirement and time duration are important factors. Sample quantity is an important parameter for microbiome analysis. For example, stool samples need little quantity, but consistency of the stool sample is a major contributing factor which affects the downstream microbiome analysis. Bristol scale is required to check the consistency of the stool sample. If the sample requires shipping, then shipping guidelines should be followed and dry ice should be used to preserve the sample during shipping (https://blog.microbiomeinsights.com/considerations-when-choos ing-a-collection-device-for-your-fecal-samples).

2.2

Methods for Taxonomic and Functional Profiling of the Microbiome

Metabolic Profiling to Get Insights of Human Microbiome The vast variety of bacteria that make up the gut microbiota produce a wide range of substances that are essential for both the selection of microbes and the development

36

C. Joshi and V. Kothari

of a metabolic signalling network. Environmental triggers have an impact on microbial activity, resulting in the production of several chemicals that have an impact on the host metabolome and human health. As a result, metabolite profiles associated to the gut microbiota can provide in-depth knowledge about how dietary and lifestyle choices affect both chronic and acute disorders. The host metabolome and its metabolic processes are impacted by the small molecule metabolites. As a result, metabolome research is crucial for understanding how the host and gut microbiota interact. The potential samples for examining host–gut microbiome interactions include faeces, urine, plasma/serum, saliva, exhaled breaths, cerebrospinal fluid (CSF), and tissues from target organs. For metabolome studies, few aspects are important, i.e. the sample types used for experiment, analytical methods to be used for analysis, tools to be used for data processing, etc. For metabolome analysis, careful sample collection and appropriate storage conditions are required. Low temperature should be maintained to preserve the samples. With regard to the extraction of hydrophilic metabolites, it is important to adopt appropriate techniques to enhance the phase transfer of these compounds from a complex biological sample to a clean extract before analysis. The procedures utilised for the global metabolic profile of faeces were evaluated by Deda et al. (2015). Important sample preparation techniques were discussed, including homogenisation, filtration, centrifugation, and solvent extraction. The state of the art in metabolomics research was outlined by Chen et al. (2016), who also provided a more thorough metabolome coverage through advancements in targeted and untargeted methodologies, as well as analytical quality control and calibration methods. Gas chromatography-mass spectrometry (GC-MS), liquid chromatography-mass spectrometry (LC-MS), and capillary electrophoresis-mass spectrometry (CE-MS), three potent technologies that can be used to explore host-gut microbiota interactions. Gas chromatography combined with mass spectrometry, such as electron impactquadrupole (GC-EIMS) or time-of-flight mass spectrometry (GC-TOF MS), has been used to identify metabolites with thermal stability and volatility. GC-MS can also detect non-volatile metabolites. The results of giving microorganisms to animals with IBS were published by Yu et al. in 2018. GC-TOF MS analysis was performed from the faeces samples, which were prepared using organic solvent extraction method. According to their research, giving C. butyricum supplements to IBS mice may have positive effects through altering the metabolism of the host. For their investigation of the biological consequences of faecal microbiota transplantation (FMT) in young patients with ulcerative colitis, Nusbaum et al. (2018) used metagenomics and metabolomics methods. They discovered that the expression of metabolites such short chain fatty acids, xanthine, oleic acid, putrescine, and 5-aminovaleric acid was changed following FMT according to the results of their GC-TOF MS investigation. For the study of gut microbial-host associated co-metabolites in faecal samples, Yin et al. (2017) developed an improved approach based on the gas chromatography/time-of-flight mass spectrometry (GC-TOFMS) platform. For the extraction of certain metabolic pathways of interest, a ratio of chloroform, methanol, and water (W) was utilised. Intestinal microbial metabolite receptors like the pregnane X receptor (PXR) and the aryl hydrocarbon receptor

Methods Used for Studying Human Microbiome

37

(AHR) activity, as well as enzymes like ornithine decarboxylase, have been identified as intestinal microbial metabolite receptors and enzymes that may be affected by host-microbe relationships (ODC). Sixty-two reference standards are used to validate the GC-TOFMS methodology. These illustrations demonstrated the potential of GC-MS as a tool for host-gut microbiota investigations. Liquid chromatographymass spectrometry (LC-MS), in addition to GC-MS, is one of the analytical platforms that is most frequently employed for metabolomics research to examine the hydrophobic and hydrophilic metabolites. The use of LC-MS for host-gut microbiota interactions has been shown in numerous investigations. In their 2017 study, Dodd et al. combined genetics and targeted metabolic profiling. Their findings showed that the bacteria in human guts produce aromatic amino acid metabolites, which build up in the bloodstream of the host and influence intestinal permeability and systemic immunity. To explore tryptophan metabolites in urine, which are connected to gut microbiome metabolism, Pavlova et al. (2017) developed a UHPLC-MS/MS approach. Rusconi et al. (2018) investigated the effects of sphingomyelin metabolism on necrotising enterocolitis in new-borns using broadrange and tailored metabolomics techniques with a focus on ceramides and sphingomyelins. Another crucial analytical technique is capillary electrophoresis (CE), which offers a distinctive mechanism for separation from conventional chromatographic techniques. Ferrer et al. (2017) reported used of CE for phenotyping of the gut microbiota. In order to evaluate the effects of xylitol on the gut microbiota and lipid metabolism, Urbanso et al. (2017) used CE-TOF MS to analyse luminal metabolites (110 targets). The data were combined with bacterial compositions. Mishima et al. (2017) examined the effects of the gut microbiota on uremic solute accumulation and Reno protective effects using CE-TOF MS to analyse mouse metabolites from plasma, urine, and faeces. For metabolite studies employing biological samples, mass spectrometry methods such as matrix-assisted laser desorption ionisation mass spectrometry (MALDI-MS), desorption electrospray ionisation mass spectrometry (DESI-MS), and Mass Spec Pen are also employed (Cameron and Takáts 2018). These cutting-edge MS-based analytical systems could be used for gut microbiome research.

Experimental Methods to Examine Host–Microbiome Interactions In Vitro and Ex Vivo In addition to metabolomics, host–microbiome interactions are being studied using in vitro and ex vivo experimental methods, which improves the management of experimental settings and the ability to explore interactions that are too complex to study in vivo. The primary distinction between in vitro and ex vivo is the origin of the samples used in the investigation. Ex vivo investigations use samples that are directly obtained from a host organism, whereas in vitro research use cell lines or laboratory microbe cultures. Co-cultures of microbes with or without host primary epithelial cells, tissues, or cell lines; microfluidic co-cultures of microorganisms with

38

C. Joshi and V. Kothari

or without engineered tissue, and organoid culture are now being introduced as in vitro and ex vivo approaches to study host–microbiota interactions. These co-culture techniques can be used to investigate the bidirectional signalling between microorganisms, target host tissues or cell types, as well as a body-site microbiome. Additionally, native or immortalised small intestine or colonic cells are planted on the apical face of trans well membranes to form polarised epithelial monolayers. Permeability, transmembrane resistance, active transport, absorption, and excretion can all be assessed to detect changes in the epithelium layer’s quality. A few restrictions of the in vitro and ex vivo experimental systems include the absence of secondary epithelial structures like villi and crypts, the lack of additional epithelialcell subtypes, the absence of mucus layers between host and microbial cells, and the challenge of incorporating realistic multi-organism microbial community components. Gut-on-a-chip technology is employed to get over the constraints of the in vitro and ex vivo experimental methods. This technique investigates the use of microfluidic platforms to cultivate intestinal epithelial cells and replicate the flow of fluids through the gut, which encourages the production of intestinal tissue structures with specialised cell types. Fluids that circulate continuously can support microbial colonisation that lasts over time. Several technology’s constraints include the need for specific chip fabrication, specialised tools and technical know-how, and challenges with adding various microbial components. Chemical exposures, luminal perfusion, and microbial colonisation can all be carefully controlled using ex vivo culture systems. Additionally, it is possible to separate intestinal tissues from model organisms and keep them in ex vivo culture for brief periods of time. Ex vivo methods produce physiological readouts that closely resemble in vivo circumstances. Similar technologies, such as primary airway epithelial cells and cell lines, are well-developed tools to research the host–microbiome interactions in the respiratory tract. It is crucial to research the host–microbiome interactions in the respiratory tract since it is well known that respiratory tract infections (RTIs) are a significant source of morbidity and mortality in children all over the world. The epidemiological evidence relating these connections to mechanistic insights was examined by de Steenhuijsen Piters et al. in 2020. In order to create a three-dimensional model of the human lung, Dye et al. (2015) stimulated human stem cells to produce cell types that later grew into complex tissues in a petri dish. Dye et al. used several signalling pathways that control how organs grow throughout the development of animal embryos to create these lung organoids. Lung-on-a-chip and small-airway-on-a-chip technologies, which are like the gut-on-a-chip platform, were featured by Benam et al. (2016). Animal and human ex vivo lung-perfusion models are being employed in translational research on lung illnesses. Additionally, there are synthetic models for studying the skin microbiota. The model system was created to explore the human stratum corneum by Van der Krieken et al. (2016). The effects of chemical exposure on skin colonisation can be evaluated using a commercial three-dimensional in vitro skin model that is filled with human skin bacteria (Bojar 2015). In order to research how skin

Methods Used for Studying Human Microbiome

39

integration surrounding percutaneous devices protects against bacterial infection, Bolle et al. (2020) created an in vitro reconstructed human skin comparable model. An in vitro mixed infection model containing commensal and pathogenic Staphylococci was established by Kohda et al. in 2021 for the investigation of interspecific interactions and their effects on skin physiology. However, the microbial variety in the context of biochemical conditions on skin is not covered by the microbiological adaptability or modelling accuracy of these synthetic systems. The experimental throughput, physiologic relevance, and experimental control of the in vitro and ex vivo systems used to study host–microbiota interactions are all different. Traditional co-culture with primary epithelial cells or cell lines offers for a moderate amount of precisely controlled and manipulable experimental output.

Use of Model Organisms to Study the Microbiome Microbiome and its interaction with the human host can also be studied using nonhuman model systems. These systems can provide good opportunities to get insights into molecular pathways, physiologic processes, host-specific gut microbiome traits, and biochemical factors such as metabolite concentrations (Davenport et al. 2017). Since animal models provide rigorous control of experimental variables and reproducibility, animal models are widely employed to study the human microbiome. Since humans and other animals share a phylogenetic link with animal models, many genomic, molecular, cellular, and physiologic features have been preserved across animal lineages, allowing for the extrapolation of many findings from animal studies to humans (Turner 2018). Animal models can be utilised to explore microbiomes using a variety of intelligent experimental strategies. The microbiome makeup of animals can be assessed using a variety of factors, including host age, host genotype, host body site, nutrition, and chemical exposure, among others. Animals of the wild type that have been invaded by intricate microbial communities are used in these laboratory investigations. Animals having an indigenous microbiome can be treated with broad-spectrum antibiotics to reduce microbial abundance and change community composition in order to test whether microbiome makeup influences host characteristics. That is a relatively quick and inexpensive technique to disrupt the microbiome, but it has the drawback of not differentiating between the impacts brought on by the direct use of antibiotics, the surviving antibiotic-resistant microbes, or the loss of antibiotic-sensitive microorganisms (Morgun et al. 2015). Gnotobiotic animal models, or germ-free animal models, are being utilised to investigate how the makeup of a microbiota affects a host. To evaluate the effects on the host, these animal models can be colonised with the relevant microbial strains. Strong experimental control can be achieved using gnotobiotic animal models, although these models are relatively expensive, labour-intensive, and have special nutritional needs for gnotobiotic animals as well as developmental, immunologic, and physiologic abnormalities (https://www.ncbi.nlm.nih.gov/books/NBK481559/).

40

C. Joshi and V. Kothari

Animals like zebrafish, fruit flies, Caenorhabditis elegans, and mice are being widely used as model organisms. Choice of the animal model depends on their suitability on the parameters of relative size, microbiome complexity, function, genetic diversity, distance from humans in terms of evolution, etc. (Leulier et al. 2017). For instance, zebrafish is easier to image in vivo due to its optical transparency, its small size permits genetic and chemical screens, and it is also amenable to gnotobiotic methods. Conversely, mice are difficult to image in vivo, but possess good physiologic similarity to humans. Mice also has lesser distance from humans on the evolutionary tree as compared to zebrafish (Hacquard et al. 2015).

Culture-Dependent Methods for Characterisation of Human Microbiome Culture-dependent methods have been polished to study a wide range of organisms such as anaerobes and nonbacterial members. More accurate culture conditions are used to cultivate microbes from the human microbiome. To study interactions of microorganisms, metabolite production from microorganism, chemical influences on the structure and function of the microbiome as well as the kinetics of microorganism-chemical transformations, bioreactors containing microbial cultures are used. Bioreactors offer a novel way to get around some of the drawbacks of traditional culture methods. By simulating the physiological circumstances present in the GI tract, complex microbial communities have been grown and established in bioreactors. Guzman-Rodriguez et al. (2018) reviewed the usefulness of bioreactor systems that are presently available. The ability to explore complicated microbial interactions and perturbations in vitro in a controlled environment without confounding biotic and abiotic factors is made possible by bioreactors. The technique to study the microorganisms without the host conditions offers several advantages including reproducibility and accuracy. The environmental conditions can be controlled depending on the requirement, and metabolites can be precisely identified (Berg et al. 2020). The percentage of host-associated microbes being grown has increased as a result of recent improvements in cultivation techniques. For a culture to be effective, it is necessary to understand the ideal environmental factors, including pH, oxidationreduction potential, temperature, and nutrients for the target microbe. Critical elements for culture-based techniques include cultural context, cultural media, collection, and storage methods. For instance, anaerobic organisms must be grown in an environment without oxygen, in specialised growth chambers, and with the addition of particular nutrients. The organisms can be grown using specialised culture techniques, such as the roll tube method, soft agar plate method, etc. It has been designed to cultivate both abundant and rare species in a microbial community using a microfluidic streak plate platform. These cutting-edge platforms will enable the physiologic characterisation of microbes and aid in understanding the crucial functions of certain microorganisms, including any potential biotransformation pathways (https://www.ncbi.nlm.nih.gov/books/NBK481559/). As previously mentioned, culture-based approaches have some clear advantages but also significant

Methods Used for Studying Human Microbiome

41

drawbacks. As the host is not a part of the investigation, these approaches are unable to give a clear picture of host–microbe interactions. Furthermore, for novel microorganisms of interest, the appropriate growth conditions may not always be known, and they might need more resources and facilities. Microbiologists have revived culture-based approaches by combining them with sophisticated tools, such as culturomics, which involves sample preparations under various growth conditions where only fastidious bacteria can grow, in order to overcome the limitations of conventional culture-based methods. This method works well for identifying the bacteria that interact with the human microbiome. Microculture, microdroplets, and microbial chips are three culture methods that enable a wide range of growing conditions. These techniques are helpful in identifying novel microbial species that are present at different body locations. Culturomics was employed by Lagier et al. (2018) to distinguish between pathogens and commensals. After the initial culture step in culturomics, the targeted samples are put through additional mass spectrometrybased analyses. The material is exposed to NGS-based 16S rRNA metagenomic approaches if the applicable method failed to identify the bacteria based on proteins. Different toxicogenomic principles are employed to categorise new species in phylum or family based on the 16S rRNA gene sequencing.

High-Throughput Methods for Assessing Human Microbiome Uncultivable microorganisms can also be researched using culture-independent approaches, which can overcome the constraints of culture-based techniques. The human microbiome is currently being studied using technologies that enable smallscale proteome and metabolite surveys, as well as nucleotide sequencing to evaluate host and microbial gene expression, taxonomic profiles, and genomes (Wei et al. 2021; Jin et al. 2022). The overview of each technique is presented in the section that follows. Nucleotide sequencing, amplicon sequencing, metagenomics, and metatranscriptomics are being utilised to examine the human microbiome. Amplicon sequencing, which targets a single genomic locus for polymerase chain reaction (PCR) amplification, is one of the most fundamental and widely used procedures. This approach focuses on the universally used 16S rRNA gene for bacterial identification and the universally used 18S rRNA gene for eukaryotic identification. Sequencing the produced PCR products allows for database comparisons with known reference sequences. The methods depend on PCR primer targets that are conserved. Using a wild mammal, Ingala et al. (2018) examined several microbiome sample techniques. Using 16S rRNA amplicon sequencing, researchers compared the microbial communities in 19 species of free-ranging bats from Lamanai, Belize, in their faeces and distal intestine mucosa. The utilisation of 16S sequencing technologies reduced as sequencing techniques advanced. The 16S rRNA gene, however, has served as the cornerstone of sequence-based bacterial investigation. Johnson et al. (2019) evaluated the 16S gene’s potential to offer taxonomic

42

C. Joshi and V. Kothari

resolution at the species and strain level using in silico and sequence-based tests. Targeting 16S variable areas with short-read sequencing technology does not result in taxonomic resolution. This study further demonstrated that full-length sequencing platforms are more accurate to study intragenomic copies of the 16S rRNA gene. Metagenome sequencing is a potent technology since it aids in gaining community-wide information. Billions of sequences read per community can be obtained by metagenome sequencing. Metagenomics is a genomic analysis that is independent of culture and can be utilised as a method for genome-wide shotgun sequencing. Metagenomics not only creates evolutionary profiles but also aids in functional characterisation. The predominant method for metagenomic sequencing today is contemporary NGS, which has taken the role of traditional Sanger sequencing (Bharti and Grimm 2021). Twenty samples of diarrheal faeces were metagenomic sequenced by De et al. (2020) to identify the basic and variable gut microbiota. In order to assess the microbiota and the origin of the antimicrobial resistance genes (ARGs) in the diarrheal stomach, they reported the results of a pilot investigation. The study’s findings showed a pattern in the gut microbiota profile of diarrhoea and identified the abundantly prevalent ARGs and metagenomeassembled genomes (MAGs) that cause AMR. Comparative metagenomic analysis was carried out by Lei et al. in 2021 to examine the impact of vitamin D supplementation in babies. The metagenomics study’s findings showed that baby feeding practises and nutritional intake influence the gut microbiota’s features. Metatranscriptomics, a technique for evaluating the human microbiome like metagenomics, analyses the gene expression profiles of organisms that are not culture dependent. This method is employed to identify the regulation and function of genes in the microbial population. Additionally, metatranscriptomics provides a potent method to investigate the dynamics of energy harvest and chemical cycle, as well as responses to environmental perturbations (Zhang et al. 2021). A subset of 308 men from the Health Professionals Follow-Up Study’s metatranscriptomics of 372 human faeces samples and 929 metagenomes were published by Abu-ali et al. (2018). They discovered a metatranscriptomic ‘core’ that was consistently expressed in all subjects. Reconstruction of an ecological interaction network that remained constant over a 6-month period was made possible using longitudinal metagenomic profiling. According to the study’s findings, the microbial ecology of human faeces may be roughly classified into four categories: core, subject-specific, microorganism-specific, and temporally variable transcription. Metatranscriptomics analysis needs more adaptive and accessible tools for uncharacterised microbial transcripts despite these valuable results (Zhang et al. 2021). Other effective methods for evaluating the human microbiome include proteogenomics and metaproteomics. A variety of OMICs techniques have made significant progress in connecting the microbiome to health and illness. Metaproteomics, also known as proteogenomics, has been developed as an additional method to analyse metagenomic data in order to address the constraints of the mass spectrometry-based tools for proteome analysis. Since protein characterisation is a key component of proteomics, metaproteomic investigations have increasingly relied on advances in molecular separation techniques, mass spectrometry, and

Methods Used for Studying Human Microbiome

43

bioinformatics. Petriz and Franco (2017) evaluated the main drawbacks of metaproteomic investigations in complex microbiota environments and highlighted the drawbacks of metagenomic databases in order to highlight the significance of metaproteomics in the evaluation of the human microbiome. Gouveia et al. (2020) suggested a technique for examining the microbiome of an organism whose genome has not yet been sequenced, which combines high-resolution protein MS with host RNA-seq. To better understand the role and potential involvement of these microbiomes in modulating the effects of toxicants on the host, researchers carried out studies to describe the microbiomes connected to the intestine and hepatopancreatic caeca. Despite recent advancements in computational analysis tools and sequencing methods, a variety of factors could result in biases and inaccuracies. These mistakes could be a reference to the computational and experimental difficulties brought on by poor sample handling, poor experimentation, and poor downstream bioinformatics analysis. Each sample should be pre-processed before being analysed in order to improve such procedures. It is important to properly complete all the procedures, which include sample preparation, sequencing, binning, assembly, and functional annotations. Integrated techniques would reduce variability in the data production and processing phases while also helping to increase the consistency of sequencing results (Bharti and Grimm 2021). Transmission and scanning electron microscopy can be employed in addition to culture-dependent and culture-independent methods to see how microbial communities are organised in fixed samples (Mark Welch et al. 2016).

3 Summary and Future Prospective Numerous experimental-animal systems can be explored to study the human microbiome. Amongst the methods used to study the human microbiome, one method is use of in vitro models. These models are easy to handle, but they do not possess much physiological similarity to humans as they are deficient in host cellular and immune responses. Gnotobiotic animal models can be used to study the effect of microbial community composition on hosts. These models can be advantageous because they can be supplemented with desired microorganisms of known taxonomic identity. In vitro and ex vivo techniques can be practically adapted to understand the diversity among human microbiome members but recognising appropriate culture conditions and models still faces technical difficulties. Additionally, it is difficult to develop a human–microbiome experimental system outside the gut. In culture-dependent genomic methods, bacterial isolation and analysis techniques are relatively well-developed, but for fungi, archaea, and viruses, the techniques are less-developed. Analysis of other organisms may be compromised by the limitation in availability of information about the reference genomes, culture conditions, and adaptability for genetic manipulation. These techniques are cheap and accessible and

44

C. Joshi and V. Kothari

appropriate to study microorganism–microorganism or microorganism–metabolite interaction testing. Additionally, analytical methods are also being used to detect the metabolites produced by gut microbiome, which involves sophisticated methods including MALDI-TOF. Culturomics methods are also helpful in identification of microbes residing in humans, but still, it is challenging to create a strictly artificial environment for cultivation of thousands of microbes (many of whom are viable but not culturable) from the gut. As human microbiome research is a relatively young field and numerous different experimental protocols are being used, it is becoming difficult to compare the results among human–microbiome studies. Sequencing analysis and computational tools face difficulties, i.e. bias and errors in data generation and analysis. Major improvements are needed to use computational methods along with omics technologies. Functional and biochemical characterisation of most microbial genes as well as microbially derived chemicals in the microbiome are yet pending largely, and what fraction of them has been detected is also not clear. Development of novel non-invasive methods for collecting samples from internal body sites will help encourage a greater number of people to volunteer for participation in microbiome studies as sources of samples. Once a larger sample size is available, statistical significance and biological relevance of the output of microbiome studies will also improve. Though the picture of the human gut microbiome is accessible, it is not easy to understand how microbes influence their host and other microbes living in the gut. High-throughput sequencing methods have revolutionised human microbiome research. But analysis of the vast amount of data generated is a big challenge which necessitates the development of new bioinformatics tools and techniques. The availability of inexpensive and adequate raw data has unlocked new opportunities. In future, gut microbiota may be utilised as biomarkers and can be customised to ‘healthy microflora’ on the line of personalised genomics. Consequently, we may be able to cure lifestyle-related diseases by positive manipulation in the composition of gut microbiota using genome editing and synthetic biology.

References Abu-Ali GS, Mehta RS, Lloyd-Price J, Mallick H, Branch T, Ivey KL, Drew DA, DuLong C, Rimm E, Izard J, Chan AT (2018) Metatranscriptome of human faecal microbial communities in a cohort of adult men. Nat Microbiol 3(3):356–366 Almeida A, Mitchell AL, Boland M, Forster SC, Gloor GB, Tarkowska A, Lawley TD, Finn RD (2019) A new genomic blueprint of the human gut microbiota. Nature 568(7753):499–504 Baud D, Pattaroni C, Vulliemoz N, Castella V, Marsland BJ, Stojanov M (2019) Sperm microbiota and its impact on semen parameters. Front Microbiol 10:234 Benam KH, Villenave R, Lucchesi C, Varone A, Hubeau C, Lee HH, Alves SE, Salmon M, Ferrante TC, Weaver JC, Bahinski A, Hamilton GA, Ingber DE (2016) Small airway-on-a-

Methods Used for Studying Human Microbiome

45

chip enables analysis of human lung inflammation and drug responses in vitro. Nat Methods 13(2):151–157 Berg G, Rybakova D, Fischer D, Cernava T, Vergès MCC, Charles T, Chen X, Cocolin L, Eversole K, Corral GH, Kazou M (2020) Microbiome definition re-visited: old concepts and new challenges. Microbiome 8(1):1–22 Bharti R, Grimm DG (2021) Current challenges and best-practice protocols for microbiome analysis. Brief Bioinform 22(1):178–193 Binda C, Gibiino G, Coluccio C, Sbrancia M, Dajti E, Sinagra E, Capurso G, Sambri V, Cucchetti A, Ercolani G, Fabbri C (2022) Biliary diseases from the microbiome perspective: how microorganisms could change the approach to benign and malignant diseases. Microorganisms 10(2):312 Bojar RA (2015) Studying the human skin microbiome using 3D in vitro skin models. Appl In Vitro Toxicol 1(2):165–171 Bolle EC, Verderosa AD, Dhouib R, Parker TJ, Fraser JF, Dargaville TR, Totsika M (2020) An in vitro reconstructed human skin equivalent model to study the role of skin integration around percutaneous devices against bacterial infection. Front Microbiol 11:670 Cameron SJ, Takáts Z (2018) Mass spectrometry approaches to metabolic profiling of microbial communities within the human gastrointestinal tract. Methods 149:13–24 Carney SM, Clemente JC, Cox MJ, Dickson RP, Huang YJ, Kitsios GD, Kloepfer KM, Leung JM, LeVan TD, Molyneaux PL, Moore BB (2020) Methods in lung microbiome research. Am J Respir Cell Mol Biol 62(3):283–299 Castillo DJ, Rifkin RF, Cowan DA, Potgieter M (2019) The healthy human blood microbiome: fact or fiction? Front Cell Infect Microbiol 9:148 Chen Y, Xu J, Zhang R, Abliz Z (2016) Methods used to increase the comprehensive coverage of urinary and plasma metabolomes by MS. Bioanalysis 8(9):981–997 Chng KR, Tay ASL, Li C, Ng AHQ, Wang J, Suri BK, Matta SA, McGovern N, Janela B, Wong XFCC, Sio YY (2016) Whole metagenome profiling reveals skin microbiome-dependent susceptibility to atopic dermatitis flare. Nat Microbiol 1(9):1–10 Davenport ER, Sanders JG, Song SJ, Amato KR, Clark AG, Knight R (2017) The human microbiome in evolution. BMC Biol 15(1):1–12 De R, Mukhopadhyay AK, Dutta S (2020) Metagenomic analysis of gut microbiome and resistome of diarrheal fecal samples from Kolkata, India, reveals the core and variable microbiota including signatures of microbial dark matter. Gut Pathogens 12:1–48 de Steenhuijsen Piters WA, Binkowska J, Bogaert D (2020) Early life microbiota and respiratory tract infections. Cell Host Microbe 28(2):223–232 Deda O, Gika HG, Wilson ID, Theodoridis GA (2015) An overview of fecal sample preparation for global metabolic profiling. J Pharm Biomed Anal 113:137–150 Dodd D, Spitzer MH, Van Treuren W, Merrill BD, Hryckowian AJ, Higginbottom SK et al (2017) A gut bacterial pathway metabolizes aromatic amino acids into nine circulating metabolites. Nature 551(7682):648–652 Dye BR, Hill DR, Ferguson MA, Tsai YH, Nagy MS, Dyal R, Wells JM, Mayhew CN, Nattiv R, Klein OD, White ES (2015) In vitro generation of human pluripotent stem cell derived lung organoids. Elife 4:e05098 Ferrer M, Raczkowska BA, Martínez-Martínez M, Barbas C, Rojo D (2017) Phenotyping of gut microbiota: focus on capillary electrophoresis. Electrophoresis 38(18):2275–2286 Gouveia D, Pible O, Culotta K, Jouffret V, Geffard O, Chaumot A, Degli-Esposti D, Armengaud J (2020) Combining proteogenomics and metaproteomics for deep taxonomic and functional characterization of microbiomes from a non-sequenced host. NPJ Biofilms Microbiomes 6(1): 1–6 Guzman-Rodriguez M, McDonald JA, Hyde R, Allen-Vercoe E, Claud EC, Sheth PM, Petrof EO (2018) Using bioreactors to study the effects of drugs on the human microbiota. Methods 149: 31–41

46

C. Joshi and V. Kothari

Hacquard S, Garrido-Oter R, González A, Spaepen S, Ackermann G, Lebeis S, McHardy AC, Dangl JL, Knight R, Ley R, Schulze-Lefert P (2015) Microbiota and host nutrition across plant and animal kingdoms. Cell Host Microbe 17(5):603–616 HMP Consortium (2012a) Structure, function and diversity of the healthy human microbiome. Nature 486(7402):207–214 HMP Consortium (2012b) A framework for human microbiome research. Nature 486(7402): 215–221 Ingala MR, Simmons NB, Wultsch C, Krampis K, Speer KA, Perkins SL (2018) Comparing microbiome sampling methods in a wild mammal: fecal and intestinal samples record different signals of host ecology, evolution. Front Microbiol 9:803 Iyer N (2016) Methods in microbiome research. Lab Animal 45(9):323–326 Jin J, Yamamoto R, Takeuchi T, Cui G, Miyauchi E, Hojo N, Ikuta K, Ohno H, Shiroguchi K (2022) High-throughput identification and quantification of single bacterial cells in the microbiota. Nat Commun 13(1):1–13 Jo R, Nishimoto Y, Umezawa K, Yama K, Aita Y, Ichiba Y, Murakami S, Kakizawa Y, Kumagai T, Yamada T, Fukuda S (2019) Comparison of oral microbiome profiles in stimulated and unstimulated saliva, tongue, and mouth-rinsed water. Sci Rep 9(1):1–7 Johnson JS, Spakowicz DJ, Hong BY, Petersen LM, Demkowicz P, Chen L, Leopold SR, Hanson BM, Agresta HO, Gerstein M, Sodergren E (2019) Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis. Nat Commun 10(1):5029 Kaan AM, Brandt BW, Buijs MJ, Crielaard W, Keijser BJ, Zaura E (2022) Comparability of microbiota of swabbed and spit saliva. Eur J Oral Sci 130(2):e12858 Katzka W, Dong TS, Luu K, Lagishetty V, Sedighian F, Arias-Jayo N, Jacobs JP, Hsu HY (2021) The ocular microbiome is altered by sampling modality and age. Transl Vis Sci Technol 10(12): 24–24 Kohda K, Li X, Soga N, Nagura R, Duerna T, Nakajima S, Nakagawa I, Ito M, Ikeuchi A (2021) An in vitro mixed infection model with commensal and pathogenic Staphylococci for the exploration of interspecific interactions and their impacts on skin physiology. Front Cell Infect Microbiol 11:712360 Kong HH, Andersson B, Clavel T, Common JE, Jackson SA, Olson ND, Segre JA, TraidlHoffmann C (2017) Performing skin microbiome research: a method to madness. J Investig Dermatol 137(3):561–568 Lagier JC, Dubourg G, Million M, Cadoret F, Bilen M, Fenollar F, Levasseur A, Rolain JM, Fournier PE, Raoult D (2018) Culturing the human microbiota and culturomics. Nat Rev Microbiol 16(9):540–550 Lauder AP, Roche AM, Sherrill-Mix S, Bailey A, Laughlin AL, Bittinger K, Leite R, Elovitz MA, Parry S, Bushman FD (2016) Comparison of placenta samples with contamination controls does not provide evidence for a distinct placenta microbiota. Microbiome 4(1):29 Lei WT, Huang KY, Jhong JH, Chen CH, Weng SL (2021) Metagenomic analysis of the gut microbiome composition associated with vitamin D supplementation in Taiwanese infants. Sci Rep 11(1):1–15 Leulier F, MacNeil LT, Lee WJ, Rawls JF, Cani PD, Schwarzer M, Zhao L, Simpson SJ (2017) Integrative physiology: at the crossroads of nutrition, microbiota, animal physiology, and human health. Cell Metab 25(3):522–534 Li Y, Tinoco R, Elmén L, Segota I, Xian Y, Fujita Y, Sahu A, Zarecki R, Marie K, Feng Y, Khateb A (2019) Gut microbiota-dependent anti-tumor immunity restricts melanoma growth in Rnf5-/- mice. Nat Commun 10(1):1–16 Lloyd-Price J, Arze C, Ananthakrishnan AN, Schirmer M, Avila-Pacheco J, Poon TW, Andrews E, Ajami NJ, Bonham KS, Brislawn CJ, Casero D (2019) Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases. Nature 569(7758):655–662 Mark Welch JL, Rossetti BJ, Rieken CW, Dewhirst FE, Borisy GG (2016) Biogeography of a human oral microbiome at the micron scale. Proc Natl Acad Sci U S A 113(6):E791–E800

Methods Used for Studying Human Microbiome

47

Mishima E, Fukuda S, Mukawa C, Yuri A, Kanemitsu Y, Matsumoto Y, Akiyama Y, Fukuda NN, Tsukamoto H, Asaji K, Shima H (2017) Evaluation of the impact of gut microbiota on uremic solute accumulation by a CE-TOFMS–based metabolomics approach. Kidney Int 92(3): 634–645 Mitra A, MacIntyre DA, Mahajan V, Lee YS, Smith A, Marchesi JR, Lyons D, Bennett PR, Kyrgiou M (2017) Comparison of vaginal microbiota sampling techniques: cytobrush versus swab. Sci Rep 7(1):1–10 Morgun A, Dzutsev A, Dong X, Greer RL, Sexton DJ, Ravel J, Schuster M, Hsiao W, Matzinger P, Shulzhenko N (2015) Uncovering effects of antibiotics on the host and microbiota using transkingdom gene networks. Gut 64(11):1732–1743 Nusbaum DJ, Sun F, Ren J, Zhu Z, Ramsy N, Pervolarakis N, Kunde S, England W, Gao B, Fiehn O, Michail S (2018) Gut microbial and metabolomic profiles after fecal microbiota transplantation in pediatric ulcerative colitis patients. FEMS Microbiol Ecol 94(9):fiy133 Ogai K, Nagase S, Mukai K, Iuchi T, Mori Y, Matsue M, Sugitani K, Sugama J, Okamoto S (2018) A comparison of techniques for collecting skin microbiome samples: swabbing versus tapestripping. Front Microbiol 9:2362. https://doi.org/10.3389/fmicb.2018.02362 Ogunrinola GA, Oyewale JO, Oshamika OO, Olasehinde GI (2020) The human microbiome and its impacts on health. Int J Microbiol 2020:8045646. https://doi.org/10.1155/2020/8045646 Pavlova T, Vidova V, Bienertova-Vasku J, Janku P, Almasi M, Klanova J, Spacil Z (2017) Urinary intermediates of tryptophan as indicators of the gut microbial metabolism. Anal Chim Acta 987: 72–80 Petriz BA, Franco OL (2017) Metaproteomics as a complementary approach to gut microbiota in health and disease. Front Chem 5:4 Rusconi B, Jiang X, Sidhu R, Ory DS, Warner BB, Tarr PI (2018) Gut sphingolipid composition as a prelude to necrotizing enterocolitis. Sci Rep 8(1):1–13 Sinha R, Abu-Ali G, Vogtmann E, Fodor AA, Ren B, Amir A, Schwager E, Crabtree J, Maps, Microbiome Quality Control Project Consortium, Abnet CC, Knight R, White O, Huttenhower C (2017) Assessment of variation in microbial community amplicon sequencing by the Microbiome Quality Control (MBQC) project consortium. Nat Biotechnol 35(11):1077–1086 Song SJ, Amir A, Metcalf JL, Amato KR, Xu ZZ, Humphrey G, Knight R (2016) Preservation methods differ in fecal microbiome stability, affecting suitability for field studies. mSystems 1 Tang Q, Jin G, Wang G, Liu T, Liu X, Wang B, Cao H (2020) Current sampling methods for gut microbiota: a call for more precise devices. Front Cell Infect Microbiol 10:151 Taponen S, McGuinness D, Hiitiö H, Simojoki H, Zadoks R, Pyörälä S (2019) Bovine milk microbiome: a more complex issue than expected. Vet Res 50(1):1–15 Turner PV (2018) The role of the gut microbiota on animal model reproducibility. Animal Model Exp Med 1(2):109–115 Urbanso T, Kano S, Yoshimoto A, Naito C, Shimoneta T, Mawatari K, Takahashi A (2017) Effects of consuming xylitol on gut microbiota and lipid metabolism in mice. Nutrients 9(7):756 van der Krieken DA, Ederveen TH, van Hijum SA, Jansen PA, Melchers WJ, Scheepers PT, Schalkwijk J, Zeeuwen PL (2016) An in vitro model for bacterial growth on human stratum corneum. Acta Derm Venereol 96(7):873–879 Vitale SG, Ferrari F, Ciebiera M, Zgliczyńska M, Rapisarda AMC, Vecchio GM, Pino A, Angelico G, Knafel A, Riemma G, De Franciscis P (2021) The role of genital tract microbiome in fertility: a systematic review. Int J Mol Sci 23(1):180 Wei LQ, Cheong IH, Yang GH, Li XG, Kozlakidis Z, Ding L, Liu NN, Wang H (2021) The application of high-throughput technologies for the study of microbiome and cancer. Front Genet 12:699793

48

C. Joshi and V. Kothari

Yano Y, Hua X, Wan Y, Suman S, Zhu B, Dagnall CL, Hutchinson A, Jones K, Hicks BD, Shi J, Abnet CC (2020) Comparison of oral microbiota collected using multiple methods and recommendations for new epidemiologic studies. mSystems 5(4):e00156-20 Yin S, Guo P, Hai D, Xu L, Shu J, Zhang W, Khan MI, Kurland IJ, Qiu Y, Liu Y (2017) Optimization of GC/TOF MS analysis conditions for assessing host-gut microbiota metabolic interactions: Chinese rhubarb alters fecal aromatic amino acids and phenol metabolism. Anal Chim Acta 995:21–33 Yu LM, Zhao KJ, Wang SS, Wang X, Lu B (2018) Gas chromatography/mass spectrometry based metabolomic study in a murine model of irritable bowel syndrome. World J Gastroenterol 24(8): 894 Zhang Y, Thompson KN, Branch T, Yan Y, Nguyen LH, Franzosa EA, Huttenhower C (2021) Metatranscriptomics for the human microbiome and microbial community functional profiling. Annu Rev Biomed Data Sci 4:279–311

Factors Affecting the Composition of the Human Microbiome Madangchanok Imchen, Simi Asma Salim, Ranjith Kumavath, and Siddhardha Busi

Abstract The microbiome has recently been considered an important component of the host, and its crucial role in maintaining host health is being unveiled. It promotes vitamin synthesis, immune response, colonization resistance, digestion, neurological development, etc. The microbiome begins to develop at birth and continues to mature with age. The meconium microbiome of newborn babies resembles closely to that of the placenta and amniotic microbiome. Infant’s gut microbiome also resemblances the colostrum within a week of breastfeeding. Several other factors influence microbiome development, such as diet, gender, genetics, environment, lifestyle, etc. Fibre-rich vegetables selectively enrich fibre-degrading bacteria, while heavy drinkers are enriched with the genus Neisseria, which has high alcohol dehydrogenase activity, producing acetaldehyde from ethanol. Furthermore, the microbiome of individuals not contacted with western people and from an isolated village exhibits one of the highest microbiome diversities, e.g. individuals from Yanomami Amerindian villages. In addition, significant factors influencing the microbiome are antibiotic treatment, exercise, obesity, age, etc., which directly define the host’s health. In this context, this chapter explores the latest reports on some of the established factors that influence the human microbiome, particularly with regard to diet, smoking, alcohol consumption, environmental factors, antibiotics, age, and BMI. Keywords Microbiome · Dysbiosis · Diet · Health · Microbiome structure

M. Imchen · S. A. Salim · S. Busi (✉) Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, India e-mail: [email protected] R. Kumavath Department of Genomic Science, School of Biological Sciences, Central University of Kerela, Kasaragod, Kerela, India Department of Biotechnology, School of Life Sciences, Pondicherry University, Puducherry, India © The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd. 2023 V. Kothari et al. (eds.), Probiotics, Prebiotics, Synbiotics, and Postbiotics, https://doi.org/10.1007/978-981-99-1463-0_3

49

50

M. Imchen et al.

1 Introduction The human microbiome is a broad term representing the overall microbial community throughout our body. The total number of microbial cells in our body is over ~1012, mostly dominated by Firmicutes and Bacteroidetes, which perform several important metabolic processes and modulate the host’s immunity (Singh et al. 2017; Kumar et al. 2021). Most microbes inhabit the digestive tract and help in the synthesis of vitamins, amino acids, metabolic byproducts, short-chain fatty acids (SCFAs), etc. The microbiome also enhances immunity by promoting toll-like receptor (TLR), CD4+ T cells, and antibody expression (Noverr and Huffnagle 2004; Lundin et al. 2008). The microbiome also resists the colonization of foreign and pathogenic microbes (Karita et al. 2022). Research on the microbiome structure during various disease states has increased exponentially as the cost of next-generation sequencing (NGS) declined substantially. However, an apparent hurdle in microbiome studies is the lack of a definitive catalogue of the healthy microbiome since the microbiome structure varies markedly between healthy individuals (Leeming et al. 2021). Nonetheless, the difference in the microbiome structure between unhealthy individuals varies considerably compared to healthy individuals, a phenomenon known as the Anna Karenina principle (Zaneveld et al. 2017). Hence, a consensus can be drawn through comparative analysis of such cohorts to pinpoint the beneficial and deleterious microbial species. There is also a lack of concrete evidence on the causation of disease due to the dysbiotic microbiome. Yet, recent reports on faecal microbiota transplantation have shown promising results that gut microbiome manipulation alters the host phenotype (De Groot et al. 2017). Such a report provides evidence that characterization of microbiome structure in healthy cohorts is essential to form a baseline of the healthy microbes despite differences at the individual level. Several studies have identified microbes in the meconium, the first stool passed by a newborn baby before feeding, suggesting an initial gut microbiome development before birth (Jiménez et al. 2008; Ardissone et al. 2014). Microbiome from mother to faetus begins prenatally since the placenta and amniotic fluid microbiota resembles infant meconium, and the baby’s microbiome resembles that of colostrum within 5 days of delivery (Collado et al. 2016). The microbiome at an early age is a critical window period that shapes the microbiome in later life. The development of the microbiome is characterized by increased diversity and abundance. This change in the microbiome is further accelerated with the introduction of solid food (Zimmermann and Curtis 2018). In adults, the microbiome is shaped by various factors such as food habits, sex, genetic makeup, environment, lifestyle, etc. (Table 1). Microbiome in healthy individuals is shaped by a number of factors, particularly diet (Gupta et al. 2017). Variations in dietary habits such as a polysaccharide-rich diet or non-digestible carbohydrates can enrich Bacteroidetes or SCFAs producing microbes, respectively (Tan et al. 2014; De Filippo et al. 2017). Hence, variation in dietary habits, from fibre-rich vegetables to fast food or a westernized lifestyle, is causing selective depletion of fibre-degrading bacteria (De Filippo et al. 2017).

Factors Affecting the Composition of the Human Microbiome

51

Table 1 List of microbes that are significantly enriched in various body sites based on diet and environmental factors Factors Vegan diet

Non-vegetarians diet

Modern Paleolithic diet

Obesity Smoking

Alcohol consumption

Area of living (urban) Age (old)

Enrichment Neisseria subflava Haemophilus parainfluenzae Rothia mucilaginosa Capnocytophaga spp. Prevotella copri Bifidobacterium Lactobacillus Akkermansia Alistipes, Bacteroides Parabacteroides Bacteroides Faecalibacterium Prevotella melaninogenica Streptococcus Sutterella Odoribacter Bilophila Akkermansia Veillonellaceae Coriobacteriia Atopobium Bifidobacterium Lactobacillus Streptococcus Catenibacterium Slackia Collinsella Coriobacteriia Bacteroides Pseudomonas Actinomyces Aggregatibacter Actinomyces, kingella Leptotrichia Cardiobacterium Prevotella Neisseria Sutterella Clostridium Holdemania Trabulsiella Enhydrobacter

Body site Mouth

References Hansen et al. (2018)

Gut

Ruengsomwong et al. (2016) Bai et al. (2019)

Gut

Ruengsomwong et al. (2016) Bai et al. (2019)

Mouth

Hansen et al. (2018)

Gut

Barone et al. (2019)

Gut Mouth

Borgo et al. (2018) Wu et al. (2016)

Gut

Nolan-Kenney et al. (2020)

Intestine

Lin et al. (2020)

Mouth

Fan et al. (2018)

Gut

Bjørkhaug et al. (2019)

Skin

Ying et al. (2015)

Skin

52

M. Imchen et al.

Furthermore, the female mucosal microbiome has higher dominance of phylum Actinobacteria and Bifidobacterium adolescentis, while Gemmiger formicilis and Veillonellaceae are associated with males indicating the role of gender-based microbiome differences (Borgo et al. 2018). The microbiome is highly sensitive to various factors, including alcohol consumption and smoking, age, antibiotic treatment, body mass index (BMI), etc. Hence, this chapter aims to explore the recent reports of microbiome dysbiosis under the influence of such variables through metagenomic approaches.

2 Influence of Diet on the Saliva and Gut Microbiome Research on the gut microbiome is an intense area of research. It is partly due to its central role in digestion and immunity, which profoundly affect blood-sugar levels, response to medical treatments, neurological development, etc. (Fig. 1) (Valdes et al. 2018). The central role of the gut microbiome for maintaining a healthy system warrants the necessity to understand how the microbiome originates and develops in newborn babies and how it matures with the age of the host. A study on the effects of delivery mode and diet pattern (breastfed and formula-fed) in the shaping of gut microbiota of newborn babies (n = 24) for the first 4 months identified that phylum Bacteroidetes was absent in all caesarean section delivered infants, irrespective of

Fig. 1 A schematic representation of the beneficial functions mediated by the gut microbiome in humans

Factors Affecting the Composition of the Human Microbiome

53

their breastfeeding status, while Proteobacteria members were present in all infants although in low abundance. The genera Escherichia and Shigella were also underrepresented in caesarean section delivered infants. The authors concluded that formula-fed infants had more species richness and a higher abundance of Clostridium difficile than breastfed infants (Azad et al. 2013). Children following a vegetarian diet are enriched with SCFA producing Bifidobacterium, Lactobacillus, and Eubacterium (Bai et al. 2019). Thus, the initial environmental exposure and the dietary patterns shape our microbiome long before adolescence. The dietary patterns continue to exert differential enrichment on the healthy adult microbiome. A large study of healthy adults (n = 160) with vegan and omnivore dietary habits reported that the saliva microbiome differed significantly between the two diet groups. The vegans had a higher abundance of commensal like Neisseria subflava, Haemophilus parainfluenzae, Rothia mucilaginosa, and Capnocytophaga sp. Furthermore, the vegans also had a higher abundance of anaerobic periodontal opportunistic pathogens such as Campylobacter rectus and Porphyromonas endodontalis. The omnivore group was predominated by Prevotella melaninogenica and Streptococcus species. Interestingly, both diet patterns had a shared core microbiome mainly composed of Prevotella, Veillonella, Neisseria, and Streptococcus (Hansen et al. 2018). Similarly, Neisseria and Prevotella as dominant members of oral microbiome were also persistent in healthy Indian individuals (n = 54), probably due to its ability to degrade complex plant polysaccharides present in the plant-rich Indian diet and their all-round metabolic functions required for a healthy oral cavity (Bhute et al. 2016; Chaudhari et al. 2020). The influence of dietary habits greatly determines the structure of gut microbiome. The gut microbiome dominant genera in vegans (n = 36) and non-vegetarians (n = 36) are Prevotella and Bacteroides. Individuals with a vegan diet, compared to non-vegetarians, are enriched with Prevotella and Klebsiella. In contrast, the gut microbiota of non-vegetarians was enriched with Faecalibacterium prausnitzii, which is known for its anti-inflammatory properties. The gut microbiome also harbours genera specific to each diet group, i.e. Acinetobacter, Bulleidia, Caldimonas, and Elusimicrobium were exclusive to the vegetarian group, while Acidaminococcus, Pediococcus, Peptoniphilus, Succinivibrio, and Turicibacter were detected only in the non-vegetarian gut microbiome. Furthermore, the authors also noted that the vegans were significantly enriched with the pathogen K. pneumoniae, while the non-vegetarians were enriched ( p < 0.05) with Bilophila wadsworthia and E. hermannii (Ruengsomwong et al. 2016). In another study, omnivorous diet enriched bile resistant bacteria like Bacteroides and Faecalibacterium (Bai et al. 2019). However, the difference in the gut microbiome between individuals could be greater than the effect of short-term changes in dietary habits. For instance, change in gut microbiome after 4 weeks of a gluten-free diet was less prominent than the difference between the subjects. Yet, modulation in certain microbial groups was prominent during the gluten-free diet period: depletion of lactose fermenting bacteria Veillonellaceae, resistant-starch degradation bacteria Ruminococcus bromii, enrichment of Victivallaceae, Clostridiaceae, Coriobacteriaceae, and genus Slackia (Bonder et al. 2016).

54

M. Imchen et al.

3 Dysbiosis Based on Smoking and Alcohol Consumption Globally there are ~650 million smokers, causing over five million annual death globally, particularly common in low-middle-income countries (LMIC) (Francis 2017). Smoking-related diseases continue to be one of the highest preventable diseases. A report on the adult gut microbiome dysbiosis (n = 249) due to smoking in Bangladesh identified significant enrichment of Slackia, Collinsella, and Erysipelotrichia-to-Catenibacterium among current smokers compared to people who never practised smoking (Nolan-Kenney et al. 2020). Large-scale studies from developed countries have also reported similar influence of smoking habits on microbiome. For instance, U.S. adults (n = 1204) with smoking habits have profound dysbiosis in the oral microbiome, particularly the current smokers, characterized by lower abundance of Proteobacteria but increased abundance of Actinobacteria and Firmicutes. Several genera were found to be enriched in the current smokers, such as Neisseria, Haemophilus, Aggregatibacter, Capnocytophaga, Corynebacterium, Porphyromonas, Prevotella, Leptotrichia, Peptostreptococcus, Abiotrophia, Selenomonas, etc. The authors also report the enrichment of facultative or obligate anaerobic and acid-tolerant genus Streptococcus in current smokers (Wu et al. 2016). Similarly, dysbiosis in the gut microbiota of healthy South Korean male soldiers (n = 100) was observed, with Bifidobacterium genera and Negativicutes class being significantly decreased and increased in current smokers, respectively (Yoon et al. 2021). However, confounding variables could also lead to inconsistencies in determining the alteration of the microbiome. For instance, contrasting observations in the enrichment of Proteobacteria among current smokers have been reported (Wu et al. 2016; Yoon et al. 2021). Certain genera exhibit a dose-dependent response to smoking. Genera Slackia and Collinsella exhibit a dose-dependent increase in their abundance (Nolan-Kenney et al. 2020), while the genus Flavobacteriia is negatively associated with the number of cigarettes smoking/day (Wu et al. 2016). Furthermore, cigarette smoking associated microbiome dysbiosis can be long term on selected bacterial groups and continue to persist after the cessation of smoking, e.g., higher prevalence of Erysipelotrichaceae in former smokers compared to never-smokers (Nolan-Kenney et al. 2020). However, such a prolonged effect could depend on the lifestyle, diet, and the time gap after quitting smoking since significant differences were not observed when compared between the oral microbial structure of former and never-smokers, indicating that smoking-related alterations are not permanent (Wu et al. 2016). Alcohol consumption is more common than smoking in the present day, with over two billion consumers globally (Engen et al. 2015). Although alcohol consumption in moderation could have a positive effect, excessive consumption has serious health complications. Alcohol consumption is among the most common cause of premature adult death (Lim et al. 2012). Alcohol consumption leads to enrichment of the microbiome favourable for metabolizing ethanol. For instance, heavy drinkers are enriched with the acetaldehyde producing genus Neisseria, which

Factors Affecting the Composition of the Human Microbiome

55

has high alcohol dehydrogenase activity (Fan et al. 2018). The dysbiosis includes depletion of beneficial microbes and enrichment of opportunistic pathogens. The oral microbiome (n = 1044) of heavy drinkers, compared to non-drinkers, has higher species richness, depletion of order Lactobacillales which is a beneficial commensal bacteria known for its probiotic effect in carbohydrate fermentation, increased abundance of human opportunistic pathogenic and cardiogenic pathogens Prevotella. Aggregatibacter, Kingella, Cardiobacterium, and Leptotrichia (Fan et al. 2018). Similar gut microbiome dysbiosis of alcohol consumers (n = 24 alcohol over-consumers and 18 control subjects) was identified with a higher abundance of Proteobacteria. The abundance of Faecalibacterium genus, which is important in maintaining a healthy gut, was significantly decreased in alcohol over-consumers compared to control subjects. In contrary, alcohol over-consumers were significantly enriched with Sutterella, Clostridium, and Holdemania (Bjørkhaug et al. 2019). In line with these studies, microbiome profiles of colonic mucosa samples from heavy drinkers (n = 34) suggested depletion of Verrucomicrobia and an enrichment of Proteobacteria. Never drinkers had a higher relative abundance of Faecalibacterium, Subdoligranulum, Sutterella, Alistipes, and Roseburia, while heavy drinkers had the lowest abundance of these genera (Gurwara et al. 2020). These microbial changes might pave the way for alcohol-related diseases, including periodontal, head, neck, and digestive tract cancer (Fan et al. 2018). Individuals that consume alcohol are often smokers as well. ~80 of the alcohol consumers are also smokers (Romberger and Grant 2004). The combined effect of alcohol consumption and smoking can have additive health risks. A study of alcohol consumption and smoking among healthy males (n = 116) found that the smokingonly and drinking-smoking groups had a lower occurrence of Firmicutes. Surprisingly, no significant microbial dysbiosis was reported for the drinking–smoking group compared to the drinking-only and smoking-only groups. Moreover, smoking-only group had higher microbial dysbiosis than the drinking-only group (Lin et al. 2020). Despite the strong evidence on the detrimental effects of smoking and alcohol consumption, a sharp decline in the number of consumers is yet to be witnessed. Moreover, the dysbiotic microbiome in such addicts could be involved in reward-seeking behaviours that might lead to anxiety and psychiatric disorders (Hillemacher et al. 2018).

4 Influence of Environmental Factors The role of genetic and environmental variables in determining the microbiome composition has attracted intense study across the globe (Goodrich et al. 2017). Individuals living in rural areas have a significantly distinct microbiome than those in urban areas. The differences have also been observed between nationalities (Hospodsky et al. 2014). The underlying factors influencing such microbiome differences could stem from several factors, including genetics, diet, hygiene, environment, and geography. The microbiome of individuals living in isolated

56

M. Imchen et al.

locations, away from modern society, harbours a significantly different microbiome. For instance, the microbiome of individuals (n = 34) from Yanomami Amerindian village who have never been in contact with the western societies has the highest microbiome diversity (faecal and skin) reported so far from human microbiome studies, which could be due to the consistent environmental exposure. The uniqueness of the Yanomami samples was the enrichment of genera Prevotella, Fusobacterium, Gemella and depletion of Rothia, Stenotrophomonas, Acinetobacter, and Pseudomonas. The skin microbiome of the Yanomami individuals varied substantially between individuals and was dominated by Knoellia and Solibacteraceae, while U.S. individuals were dominated by Staphylococcus, Corynebacterium, Neisseriaceae and Propionibacterium (Clemente et al. 2015). Similarly a comparative study of Venezuelan Amerindians and U.S. (New York and Colorado) cutaneous microbiome (n = 112) identified that Propionibacterium was more dominant in U.S. individuals. Among the Amerindians, the individuals were grouped into two clusters—one of them dominated by Staphylococcus resembled the U.S. group, while the other cluster was significantly more diverse and dominated by Proteobacteria (Pseudomonas, Xanthomonadaceae, and Methylophilus). The differences observed between the two cohorts suggest the influence of ethnicity and that the difference observed between Amerindians could be based on lifestyle (Blaser et al. 2013). In adults, the microbiome can remain stable for several months despite the change in geographical locations. For instance, the microbiome of Chinese (n = 12) and Pakistanis (n = 12) living in the same locality for more than 1 year had a unique microbiome associated with nationality and body sites (forehead, cheek, jaw, opisthenar, and palm). Compared to the Pakistanis, the Chinese subjects’ forehead, opisthenar, jaw, and cheeks had higher Staphylococcus aureus abundance. The Pakistani subjects were dominated with Proteobacteria, while the Chinese were dominated with Firmicutes, Spirochaetes, Thermi, Acidobacteria, and Bacteroidetes. The authors suggest that the higher abundance of Proteobacteria could be because Proteobacteria is a common member of soil that the Pakistani subjects are more commonly exposed to (Wang et al. 2021). In another similar study, immigrants in the USA (n = 1674) that were relocated to the USA from Latin America during their adulthood exhibited contrasting microbiome features compared to subjects moving in at an early age—higher diversity of microbes and Prevotella-to-Bacteroides ratios for the former (Kaplan et al. 2019). It is alarming since obesity is associated with lowering microbiome diversity and has become a major public health issue (Davis 2016). The variation in the microbiome among the immigrants, despite the similarity in nationality or place of origin, may be partly due to the initial microbiome. Recent reports have shown that microbiome dysbiosis can be predicted to a certain extent based on the initial microbiome structure (Imchen et al. 2020).

Factors Affecting the Composition of the Human Microbiome

57

5 Influence of Antibiotics, Age, and BMI Antimicrobial usage is one of the most efficient and rapid means for altering microbiome. This holds true for narrow as well as wide spectrum antibiotics since most antibiotics can inhibit the growth of untargeted microbes. The application of antibiotics is necessary at an early stage of life for most medical treatments despite the fact that disruption of the microbiome at an early age can lead to microbiome instability and disease development at a later stage of life (Yassour et al. 2016; Gaufin et al. 2018). Ampicillin and gentamycin administration in preterm infants (n = 74) reduces gastrointestinal microbial diversity within days after administration, and the microbiome did not restore over the span of a 3-week study. The antibiotic-treated infants had an increased abundance of Enterobacter (47%) and Enterococcus (35%) compared to the non-treated group (36% and 17%, respectively) (Greenwood et al. 2014). Another long term study on the effect of antibiotics in infant (n = 39) gut microbiome, collected monthly over a 3 year period, reported that species and strain level diversity was lesser among the antibiotic-treated children compared to non-treated subjects. In many cases, the identified species (e.g., E. coli, F. prausnitzii, B. fragilis, and Haemophilus parainfluenzae) in the antibiotic-treated group were majorly represented by a single strain which explains the lower microbial diversity and enrichment of antibioticresistant strains (Yassour et al. 2016). Although most studies target stool samples for gut microbiome studies, it is worth mentioning that the gut microbiome, from the point of microbial community stability, differs significantly between the lumen and mucosal environment. In the mucosal microbiome, the overall microbial diversity is higher and enriched with aerotolerant and fermentative microbes such as phylum Proteobacteria, Streptococcus, and Clostridia. The lumen profile, however, has a higher occurrence of genera Bacteroides, Prevotella and Oscillospira, possibly because of their ability to degrade complex biopolymers and thereby help in digestion (Borgo et al. 2018). The other important factors in shaping the microbiome are age, physical activity, and BMI. The microbiome continues to mature and increase its diversity with the host’s age (Odamaki et al. 2016). Veillonella and Corynebacterium have a positive correlation with age, while Aggregatibacter exhibits a negative correlation (Freire et al. 2020). Microbiome maturation can also be influenced by brushing and physical activity. For instance, it was also found that Streptococcus abundance decreased when brushing frequency increased among twins (Freire et al. 2020). Enrichment of Firmicutes phylum, SCFA and butyrate-producing genera Clostridiales, Lachnospiraceae, and Erysipelotrichaceae were associated with exercise frequency (Bai et al. 2019). Similarly, the influence of Body Mass Index (BMI) and lifestyle variants such as diet and exercise in the gut microbiome (n = 267; aged 7–18 years) identified a higher microbial diversity among overweight and normal BMI subjects compared to underweight subjects (Bai et al. 2019). Higher BMI levels were associated with Lactobacillus and Bifidobacterium. Obese individuals are also depleted of important butyrate-producing species Faecalibacterium prausnitzii and

58

M. Imchen et al.

Flavonifractor plautii (Borgo et al. 2018). The abundance of phylum Proteobacteria, Fusobacteria, and genus Bacteroides in the gut or oral cavity increases with age (Odamaki et al. 2016; Chaudhari et al. 2020). The increase in Proteobacteria with age could be an indication of weaker immunity in older individuals since several opportunistic bacteria belong to Proteobacteria (Chaudhari et al. 2020).

6 Restoration of the Microbiome for Disease Treatment The dysbiotic microbiome in diseased individuals can be recalibrated to a certain extent by administrating probiotics, postbiotics, prebiotics, or faecal microbiome transplantation. The well-known substrates used as prebiotics are non-digestible dietary fibres, e.g., pectin, fructo-oligosaccharides, and inulin (Mindt and DiGiandomenico 2022). The fibres are metabolized by the gut microbiome and converted to SCFAs. Recent reports have indicated that depletion of SCFAgenerating bacteria is associated with lung function and deterioration of pulmonary function (Mindt and DiGiandomenico 2022). The important SCFAs are butyrate, propionate, and acetate. The importance of these SCFAs includes promotion of intestinal barrier integrity, haematopoiesis of immune cells in the bone marrow, stimulation of lung immunity, anti-inflammatory, immunomodulatory, and more functions are being unveiled regularly (Le Poul et al. 2003; Smith et al. 2013; Chuang et al. 2012; Parada Venegas et al. 2019). Microbiome modulation can also be considered a combinatory treatment for COVID-19 patients. Clinical trials have shown promising potential in subduing the severity and disease duration of COVID19 patients (Xavier-Santos et al. 2022). Probiotics have been used for infants with low-birth-weight and acute gastroenteritis (Preidis et al. 2020; Su et al. 2020). Probiotics such as Lactobacillus sporogenes, Bacillus coagulans, and Bifidobacterium are efficient in irritable bowel syndrome (IBS), diarrhoea, and type 2 diabetes (Asemi et al. 2014; Islek et al. 2014; Gulliver et al. 2022). Similar to faecal microbiome transplantation, research on vaginal microbiome transplantation (VMT) has also shown promising potential in treating bacterial vaginosis (Lev-Sagie et al. 2019; Vieira-Baptista et al. 2022). Despite such immense potential of microbiome transplantation, care should be taken to avoid the unintended transfer of pathogens and multidrug-resistant microbes. Hence, stringent screening methods are required to minimize the risks.

7 Conclusion The importance of the microbiome is well documented. However, a clear-cut solution to deciphering the factors that influence the microbiome structure is complicated since every aspect of the host–environment interaction redefines the microbiome composition. Nonetheless, environmental factors have a more profound

Factors Affecting the Composition of the Human Microbiome

59

effect in shaping the microbiome compared to the host’s genetics. The recent reports on the influence of unhealthy diet, smoking, drinking, and lack of physical exercise on the microbiome are conclusive that it negatively impacts the gut and oral microbiome. Hence, treatment of secondary infections and diseases should also be focused on gut microbiome restoration, such as through prebiotics, probiotics, and faecal microbiome transplantation. Further research should be focused on the mechanistic action of the host immune cells and microbiome interaction. Efforts should also be put into the development of affordable, efficient organ chips to serve as a platform for drug–microbiome interactions and to accelerate microbiome-based therapeutics. Acknowledgments The authors thank the research facilities support of Pondicherry University and Central University of Kerala, M.I. thanks to DBT-RA Program in Biotechnology and Life Sciences. Declarations Funding: Not Applicable. Conflicts of Interest The authors hereby declare no conflict of interest. Ethical Approval Not applicable. Availability of Data and Material Not applicable. Author Contributions M.I., S.A.S., and S.B. contributed in preparing the draft of the manuscript and preparing the figures. R.K. and S.B. contributed in critically refining and revising the manuscript. All the authors read and approved the manuscript.

References Ardissone AN, de la Cruz DM, Davis-Richardson AG, Rechcigl KT, Li N, Drew JC, MurgasTorrazza R, Sharma R, Hudak ML, Triplett EW, Neu J (2014) Meconium microbiome analysis identifies bacteria correlated with premature birth. PLoS One 9(3):e90784. https://doi.org/10. 1371/journal.pone.0090784 Asemi Z, Khorrami-Rad A, Alizadeh SA, Shakeri H, Esmaillzadeh A (2014) Effects of synbiotic food consumption on metabolic status of diabetic patients: a double-blind randomized crossover controlled clinical trial. Clin Nutr 33(2):198–203. https://doi.org/10.1016/j.clnu.2013. 05.015 Azad MB, Konya T, Maughan H, Guttman DS, Field CJ, Chari RS, Sears MR, Becker AB, Scott JA, Kozyrskyj AL (2013) Gut microbiota of healthy Canadian infants: profiles by mode of delivery and infant diet at 4 months. CMAJ 185(5):385–394. https://doi.org/10.1503/cmaj. 121189 Bai J, Hu Y, Bruner DW (2019) Composition of gut microbiota and its association with body mass index and lifestyle factors in a cohort of 7–18 years old children from the American gut project. Pediatr Obes 14(4):e12480. https://doi.org/10.1111/ijpo.12480 Barone M, Turroni S, Rampelli S, Soverini M, D’Amico F, Biagi E, Brigidi P, Troiani E, Candela M (2019) Gut microbiome response to a modern Paleolithic diet in a Western lifestyle context. PLoS One 14(8):e0220619. https://doi.org/10.1371/journal.pone.0220619

60

M. Imchen et al.

Bhute S, Pande P, Shetty SA, Shelar R, Mane S, Kumbhare SV, Gawali A, Makhani H, Navandar M, Dhotre D, Lubree H (2016) Molecular characterization and meta-analysis of gut microbial communities illustrate enrichment of Prevotella and Megasphaera in Indian subjects. Front Microbiol 7:660. https://doi.org/10.3389/fmicb.2016.00660 Bjørkhaug ST, Aanes H, Neupane SP, Bramness JG, Malvik S, Henriksen C, Skar V, Medhus AW, Valeur J (2019) Characterization of gut microbiota composition and functions in patients with chronic alcohol overconsumption. Gut Microbes 10(6):663–675. https://doi.org/10.1080/ 19490976.2019.1580097 Blaser MJ, Dominguez-Bello MG, Contreras M, Magris M, Hidalgo G, Estrada I, Gao Z, Clemente JC, Costello EK, Knight R (2013) Distinct cutaneous bacterial assemblages in a sampling of South American Amerindians and US residents. ISME J 7(1):85–95. https://doi.org/10.1038/ ismej.2012.81 Bonder MJ, Tigchelaar EF, Cai X, Trynka G, Cenit MC, Hrdlickova B, Zhong H, Vatanen T, Gevers D, Wijmenga C, Wang Y (2016) The influence of a short-term gluten-free diet on the human gut microbiome. Genome Med 8(1):1–1. https://doi.org/10.1186/s13073-016-0295-y Borgo F, Garbossa S, Riva A, Severgnini M, Luigiano C, Benetti A, Pontiroli AE, Morace G, Borghi E (2018) Body mass index and sex affect diverse microbial niches within the gut. Front Microbiol 9:213. https://doi.org/10.3389/fmicb.2018.00213 Chaudhari DS, Dhotre DP, Agarwal DM, Gaike AH, Bhalerao D, Jadhav P, Mongad D, Lubree H, Sinkar VP, Patil UK, Salvi S (2020) Gut, oral and skin microbiome of Indian patrilineal families reveal perceptible association with age. Sci Rep 10(1):1–3. https://doi.org/10.1038/s41598-02062195-5 Chuang SC, Norat T, Murphy N, Olsen A, Tjønneland A, Overvad K, Boutron-Ruault MC, Perquier F, Dartois L, Kaaks R, Teucher B (2012) Fiber intake and total and cause-specific mortality in the European prospective investigation into cancer and nutrition cohort. Am J Clin Nutr 96(1):164–174. https://doi.org/10.3945/ajcn.111.028415 Clemente JC, Pehrsson EC, Blaser MJ, Sandhu K, Gao Z, Wang B, Magris M, Hidalgo G, Contreras M, Noya-Alarcón Ó, Lander O (2015) The microbiome of uncontacted Amerindians. Sci Adv 1(3):e1500183. https://doi.org/10.1126/sciadv.1500183 Collado MC, Rautava S, Aakko J, Isolauri E, Salminen S (2016) Human gut colonization may be initiated in utero by distinct microbial communities in the placenta and amniotic fluid. Sci Rep 6(1):1–3. https://doi.org/10.1038/srep23129 Davis CD (2016) The gut microbiome and its role in obesity. Nutr Today 51(4):167. https://doi.org/ 10.1097/NT.0000000000000167 De Filippo C, Di Paola M, Ramazzotti M, Albanese D, Pieraccini G, Banci E, Miglietta F, Cavalieri D, Lionetti P (2017) Diet, environments, and gut microbiota. A preliminary investigation in children living in rural and urban Burkina Faso and Italy. Front Microbiol 8:1979. https://doi.org/10.3389/fmicb.2017.01979 De Groot PF, Frissen MN, De Clercq NC, Nieuwdorp M (2017) Fecal microbiota transplantation in metabolic syndrome: history, present and future. Gut Microbes 8(3):253–267. https://doi.org/ 10.1080/19490976.2017.1293224 Engen PA, Green SJ, Voigt RM, Forsyth CB, Keshavarzian A (2015) The gastrointestinal microbiome: alcohol effects on the composition of intestinal microbiota. Alcohol Res 37(2):223 Fan X, Peters BA, Jacobs EJ, Gapstur SM, Purdue MP, Freedman ND, Alekseyenko AV, Wu J, Yang L, Pei Z, Hayes RB (2018) Drinking alcohol is associated with variation in the human oral microbiome in a large study of American adults. Microbiome 6(1):1–5. https://doi.org/10.1186/ s40168-018-0448-x Francis DL (2017) P1. 01-008 knowledge, attitudes, and smoking behaviors among dental and medical students in Chennai, Tamil Nadu, India: topic: tobacco, radon, air pollution, other risk factors. J Thorac Oncol 12(1):S452–S453. https://doi.org/10.1016/j.jtho.2016.11.532 Freire M, Moustafa A, Harkins DM, Torralba MG, Zhang Y, Leong P, Saffery R, Bockmann M, Kuelbs C, Hughes T, Craig JM (2020) Longitudinal study of oral microbiome variation in twins. Sci Rep 10(1):7954. https://doi.org/10.1038/s41598-020-64747-1

Factors Affecting the Composition of the Human Microbiome

61

Gaufin T, Tobin NH, Aldrovandi GM (2018) The importance of the microbiome in pediatrics and pediatric infectious diseases. Curr Opin Pediatr 30(1):117. https://doi.org/10.1097/MOP. 0000000000000576 Goodrich JK, Davenport ER, Clark AG, Ley RE (2017) The relationship between the human genome and microbiome comes into view. Annu Rev Genet 51:413–433. https://doi.org/10. 1146/annurev-genet-110711-155532 Greenwood C, Morrow AL, Lagomarcino AJ, Altaye M, Taft DH, Yu Z, Newburg DS, Ward DV, Schibler KR (2014) Early empiric antibiotic use in preterm infants is associated with lower bacterial diversity and higher relative abundance of Enterobacter. J Pediatr 165(1):23–29. https://doi.org/10.1016/j.jpeds.2014.01.010 Gulliver EL, Young RB, Chonwerawong M, D’Adamo GL, Thomason T, Widdop JT, Rutten EL, Rossetto Marcelino V, Bryant RV, Costello SP, O’Brien CL (2022) The future of microbiomebased therapeutics. Aliment Pharmacol Ther 56:192. https://doi.org/10.1111/apt.17049 Gupta VK, Paul S, Dutta C (2017) Geography, ethnicity or subsistence-specific variations in human microbiome composition and diversity. Front Microbiol 8:1162. https://doi.org/10.3389/fmicb. 2017.01162 Gurwara S, Dai A, Ajami NJ, Graham DY, White DL, Chen L, Jang A, Chen E, El-Serag HB, Petrosino JF, Jiao L (2020) Alcohol use alters the colonic mucosa-associated gut microbiota in humans. Nutr Res 83:119–128. https://doi.org/10.1016/j.nutres.2020.09.004 Hansen TH, Kern T, Bak EG, Kashani A, Allin KH, Nielsen T, Hansen T, Pedersen O (2018) Impact of a vegan diet on the human salivary microbiota. Sci Rep 8(1):5847. https://doi.org/10. 1038/s41598-018-24207-3 Hillemacher T, Bachmann O, Kahl KG, Frieling H (2018) Alcohol, microbiome, and their effect on psychiatric disorders. Prog Neuro-Psychopharmacol Biol Psychiatry 85:105–115. https://doi. org/10.1016/j.pnpbp.2018.04.015 Hospodsky D, Pickering AJ, Julian TR, Miller D, Gorthala S, Boehm AB, Peccia J (2014) Hand bacterial communities vary across two different human populations. Microbiology 160(6): 1144–1152. https://doi.org/10.1099/mic.0.075390-0 Imchen M, Moopantakath J, Kumavath R, Barh D, Tiwari S, Ghosh P, Azevedo V (2020) Current trends in experimental and computational approaches to combat antimicrobial resistance. Front Genet 11:563975. https://doi.org/10.3389/fgene.2020.563975 Islek A, Sayar E, Yilmaz A, Baysan BO, Mutlu D, Artan R (2014) The role of Bifidobacterium lactis B94 plus inulin in the treatment of acute infectious diarrhea in children. Turk J Gastroenterol 25(6):628–633. https://doi.org/10.5152/tjg.2014.14022 Jiménez E, Marín ML, Martín R, Odriozola JM, Olivares M, Xaus J, Fernández L, Rodríguez JM (2008) Is meconium from healthy newborns actually sterile? Res Microbiol 159(3):187–193. https://doi.org/10.1016/j.resmic.2007.12.007 Kaplan RC, Wang Z, Usyk M, Sotres-Alvarez D, Daviglus ML, Schneiderman N, Talavera GA, Gellman MD, Thyagarajan B, Moon JY, Vázquez-Baeza Y (2019) Gut microbiome composition in the Hispanic community health study/study of Latinos is shaped by geographic relocation, environmental factors, and obesity. Genome Biol 20(1):1–21. https://doi.org/10.1186/ s13059-019-1831-z Karita Y, Limmer DT, Hallatschek O (2022) Scale-dependent tipping points of bacterial colonization resistance. PNAS 119(7):e2115496119. https://doi.org/10.1073/pnas.2115496119 Kumar P, Lee JH, Lee J (2021) Diverse roles of microbial indole compounds in eukaryotic systems. Biol Rev 96(6):2522–2545 Le Poul E, Loison C, Struyf S, Springael JY, Lannoy V, Decobecq ME, Brezillon S, Dupriez V, Vassart G, Van Damme J, Parmentier M (2003) Functional characterization of human receptors for short chain fatty acids and their role in polymorphonuclear cell activation. J Biol Chem 278(28):25481–25489. https://doi.org/10.1074/jbc.m301403200 Leeming ER, Louca P, Gibson R, Menni C, Spector TD, Le Roy CI (2021) The complexities of the diet-microbiome relationship: advances and perspectives. Genome Med 13(1):1–4. https://doi. org/10.1186/s13073-020-00813-7

62

M. Imchen et al.

Lev-Sagie A, Goldman-Wohl D, Cohen Y, Dori-Bachash M, Leshem A, Mor U, Strahilevitz J, Moses AE, Shapiro H, Yagel S, Elinav E (2019) Vaginal microbiome transplantation in women with intractable bacterial vaginosis. Nat Med 25(10):1500–1504. https://doi.org/10.1038/ s41591-019-0600-6 Lim SS, Vos T, Flaxman AD, Danaei G, Shibuya K, Adair-Rohani H, AlMazroa MA, Amann M, Anderson HR, Andrews KG, Aryee M (2012) A comparative risk assessment of burden of disease and injury attributable to 67 risk factors and risk factor clusters in 21 regions, 1990–2010: a systematic analysis for the global burden of disease study 2010. Lancet 380(9859):2224–2260. https://doi.org/10.1016/s0140-6736(12)61766-8 Lin R, Zhang Y, Chen L, Qi Y, He J, Hu M, Zhang Y, Fan L, Yang T, Wang L, Si M (2020) The effects of cigarettes and alcohol on intestinal microbiota in healthy men. J Microbiol 58(11): 926–937. https://doi.org/10.1007/s12275-020-0006-7 Lundin A, Bok CM, Aronsson L, Björkholm B, Gustafsson JÅ, Pott S, Arulampalam V, Hibberd M, Rafter J, Pettersson S (2008) Gut flora, toll-like receptors and nuclear receptors: a tripartite communication that tunes innate immunity in large intestine. Cell Microbiol 10(5):1093–1103. https://doi.org/10.1111/j.1462-5822.2007.01108.x Mindt BC, DiGiandomenico A (2022) Microbiome modulation as a novel strategy to treat and prevent respiratory infections. Antibiotics 11(4):474. https://doi.org/10.3390/ antibiotics11040474 Nolan-Kenney R, Wu F, Hu J, Yang L, Kelly D, Li H, Jasmine F, Kibriya MG, Parvez F, Shaheen I, Sarwar G (2020) The association between smoking and gut microbiome in Bangladesh. Nicotine Tob Res 22(8):1339–1346. https://doi.org/10.1093/ntr/ntz220 Noverr MC, Huffnagle GB (2004) Does the microbiota regulate immune responses outside the gut? Trends Microbiol 12(12):562–568. https://doi.org/10.1016/j.tim.2004.10.008 Odamaki T, Kato K, Sugahara H, Hashikura N, Takahashi S, Xiao JZ, Abe F, Osawa R (2016) Age-related changes in gut microbiota composition from newborn to centenarian: a crosssectional study. BMC Microbiol 16(1):1–2. https://doi.org/10.1186/s12866-016-0708-5 Parada Venegas D, De la Fuente MK, Landskron G, González MJ, Quera R, Dijkstra G, Harmsen HJ, Faber KN, Hermoso MA (2019) Short chain fatty acids (SCFAs)-mediated gut epithelial and immune regulation and its relevance for inflammatory bowel diseases. Front Immunol 10:277. https://doi.org/10.3389/fimmu.2019.00277 Preidis GA, Weizman AV, Kashyap PC, Morgan RL (2020) AGA technical review on the role of probiotics in the management of gastrointestinal disorders. Gastroenterology 159(2):708–738. e4. https://doi.org/10.1053/j.gastro.2020.05.060 Romberger DJ, Grant K (2004) Alcohol consumption and smoking status: the role of smoking cessation. Biomed Pharmacother 58(2):77–83. https://doi.org/10.1016/j.biopha.2003.12.002 Ruengsomwong S, La-Ongkham O, Jiang J, Wannissorn B, Nakayama J, Nitisinprasert S (2016) Microbial community of healthy Thai vegetarians and non-vegetarians, their core gut microbiota, and pathogen risk. J Microbiol Biotechnol 26(10):1723–1735. https://doi.org/10. 4014/jmb.1603.03057 Singh RK, Chang HW, Yan DI, Lee KM, Ucmak D, Wong K, Abrouk M, Farahnik B, Nakamura M, Zhu TH, Bhutani T (2017) Influence of diet on the gut microbiome and implications for human health. J Transl Med 15(1):1–7. https://doi.org/10.1186/s12967-0171175-y Smith PM, Howitt MR, Panikov N, Michaud M, Gallini CA, Bohlooly-y M, Glickman JN, Garrett WS (2013) The microbial metabolites, short-chain fatty acids, regulate colonic Treg cell homeostasis. Science 341(6145):569–573. https://doi.org/10.1126/science.1241165 Su GL, Ko CW, Bercik P, Falck-Ytter Y, Sultan S, Weizman AV et al (2020) AGA clinical practice guidelines on the role of probiotics in the management of gastrointestinal disorders. Gastroenterology 159(2):697–705. https://doi.org/10.1053/j.gastro.2020.05.059 Tan J, McKenzie C, Potamitis M, Thorburn AN, Mackay CR, Macia L (2014) The role of shortchain fatty acids in health and disease. Adv Immunol 121:91–119. https://doi.org/10.1016/ b978-0-12-800100-4.00003-9

Factors Affecting the Composition of the Human Microbiome

63

Valdes AM, Walter J, Segal E, Spector TD (2018) Role of the gut microbiota in nutrition and health. BMJ 361:k2179. https://doi.org/10.1136/bmj.k2179 Vieira-Baptista P, De Seta F, Verstraelen H, Ventolini G, Lonnee-Hoffmann R, Lev-Sagie A (2022) The vaginal microbiome: V. Therapeutic modalities of vaginal microbiome engineering and research challenges. J Low Genit Tract Dis 26(1):99–104. https://doi.org/10.1097/lgt. 0000000000000647 Wang Y, Yu Q, Zhou R, Feng T, Hilal MG, Li H (2021) Nationality and body location alter human skin microbiome. Appl Microbiol Biotechnol 105(12):5241–5256. https://doi.org/10.1007/ s00253-021-11387-8 Wu J, Peters BA, Dominianni C, Zhang Y, Pei Z, Yang L, Ma Y, Purdue MP, Jacobs EJ, Gapstur SM, Li H (2016) Cigarette smoking and the oral microbiome in a large study of American adults. ISME J 10(10):2435–2446. https://doi.org/10.1038/ismej.2016.37 Xavier-Santos D, Padilha M, Fabiano GA, Vinderola G, da Cruz AG, Sivieri K, Antunes AE (2022) Evidences and perspectives of the use of probiotics, prebiotics, synbiotics, and postbiotics as adjuvants for prevention and treatment of COVID-19: a bibliometric analysis and systematic review. Trends Food Sci Technol 120:174. https://doi.org/10.1016/j.tifs.2021.12.033 Yassour M, Vatanen T, Siljander H, Hämäläinen AM, Härkönen T, Ryhänen SJ, Franzosa EA, Vlamakis H, Huttenhower C, Gevers D, Lander ES (2016) Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability. Sci Transl Med 8(343):343ra81. https://doi.org/10.1126/scitranslmed.aad0917 Ying S, Zeng DN, Chi L, Tan Y, Galzote C, Cardona C, Lax S, Gilbert J, Quan ZX (2015) The influence of age and gender on skin-associated microbial communities in urban and rural human populations. PLoS One 10(10):e0141842. https://doi.org/10.1371/journal.pone.0141842 Yoon H, Lee DH, Lee JH, Kwon JE, Shin CM, Yang SJ, Park SH, Lee JH, Kang SW, Lee JS, Kim BY (2021) Characteristics of the gut microbiome of healthy young male soldiers in South Korea: the effects of smoking. Gut Liver 15(2):243. https://doi.org/10.5009/gnl19354 Zaneveld JR, McMinds R, Vega Thurber R (2017) Stress and stability: applying the Anna Karenina principle to animal microbiomes. Nat Microbiol 2(9):1–8 Zimmermann P, Curtis N (2018) Factors influencing the intestinal microbiome during the first year of life. Pediatr Infect Dis J 37(12):e315–e335. https://doi.org/10.1097/inf.0000000000002103

Part II

Correlation of the Human Microbiome to Specific Health/Disease Conditions

Mapping the Microbial Metabolites in Metabolic Disorder with Special Reference to Type-2 Diabetes Sunny Kumar, Zeel Bhatia, and Sriram Seshadri

Abstract The drastic increase in metabolic disorders has now became a major global health concern. Metabolic disease and disorders include obesity, liver cirrhosis, dyslipidaemia, hypolipidemia, inflammatory bowel disease (IBD), type-2 diabetes (T2D), etc. There are various gut derived metabolites produced inside the host such as branched chain amino acids (BCAAs), short chain fatty acid (SCFA), branched chain fatty acids (BCFA), long chain fatty acid (LCFA), medium chain fatty acids (MCFA), and trimethyamine (TMA). These metabolites are majorly associated with metabolic complication. Role of gut microbiota is highlighted as connecting link between obesity, inflammation, and T2D and it is mainly affected by lifestyle, food habits, and medication; however, other factors such stress, genetic components are also responsible. The substantial research indicates that the alterations of gut barrier could be responsible for the metabolic endotoxemia which further leads to inflammation and T2D. In this chapter we have highlighted some of the key microbial metabolites that contribute to progression of T2D along with how this alteration in metabolites regulates pathogensis and progression of metabolic disorders. Mapping of this microbial ratio and metabolites level at various stage of disease and disorder progression could be used as promising hope to develop potential biomarkers, early stage diagnosis and treatment. The gut microbiota restoration and metabolites mapping can be used for early stage detection and safe therapeutic development. Keywords Gut microbiota · Metabolic disorders · Type 2 diabetes · Bacterial metabolites · Prebiotics · Postbiotics

S. Kumar · Z. Bhatia · S. Seshadri (✉) Institute of Science, Nirma University, Ahmedabad, Gujarat, India e-mail: [email protected]; [email protected]; [email protected] © The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd. 2023 V. Kothari et al. (eds.), Probiotics, Prebiotics, Synbiotics, and Postbiotics, https://doi.org/10.1007/978-981-99-1463-0_4

67

68

S. Kumar et al.

1 Introduction Gut microbiota is a collection of different community of microbes that resides in our body, which lives in a symbiotic state with their host in normal conditions. The microbial diversity and population vary from species to species. The mammalian gut microbiota, their abundance differ at different taxonomic levels; however, there are major reported phyla such as Bacteroidetes, Firmicutes, Proteobacteria, and Actinobacteria which are dominantly present (Brown et al. 2012). Their diversity may differ from organ to organ and from one species to other, the major predominant species Proteobacteria, Verrucobacteria, Actinobacteria, Bacteroidetes, and Firmicutes are established in various studies (Fig. 1). Microbial colonization starts at the time of birth from mother as major donor. In the early stage of life newborn intestines are believed to be sterile or have a very low level of population at the time of delivery. The gastrointestinal tract (GIT) starts colonizing rapidly between the timeframe of before and after delivery. While the neonate passes through the birth canal of mother where they get major exposure to the microbial population of the mother’s vagina, it shows similar microbial diversity to the vaginal microbiota of their mother at that time at the time of delivery. The human body consists of trillion of microbial population that is higher than tenfold of cells that is close to the total human body; it means that our cells composed of 10% human and 90% microbes. Gut is very rich in bacterial population and diversity at different locations starting from stomach to different parts of intestine (Table 1). Gut microbiota are key players that regulate the metabolic system of host body by ensuring energy balance, regulating low grade inflammation and glucose Fig. 1 The predominant taxonomic group of the human colonic microbiota (Chassard and Lacroix 2013)

Firmicutes

Bacteroidetes

Actinobacteriaa

Verrncobacteria

Proteobacteria

Mapping the Microbial Metabolites in Metabolic Disorder with. . .

69

Table 1 Gastrointestinal tract distribution of microflora and their region specific CFU count Digestive area Stomach Small intestine: Duodenum Small intestine: Jejunum Small intestine: Ileum Colon

Major rich flora Lactobacillus; Candida; Streptococcus; Helicobacter pylori; Peptostreptococcus Lactobacillus; Streptococcus

Reported CFU number 0–102 101–102

Lactobacillus; Streptococcus

101–102

Streptococcus; Lactobacillus

102–103

Bacteroidetes; Bifidobacterium; Enterobacteriaceae; Clostridium groups IV and XIV

1011–1012

metabolism. Gram negative bacteria composed of lipopolysaccharides (LPS) is a major component of their cell wall. This gut derived LPS plays crucial role in progression of metabolic diseases and inflammation (Cani et al. 2012). Along with common metabolic disorder T2D and obesity, gut microbiota alteration deciphers different disease and gastrointestinal (GI) conditions such as IBD and irritable bowel syndrome (Bull and Plummer 2014). The composition and luminal numbers of dominant microbial species in the human GIT are depicted in Table 1 (Sartor and Mazmanian 2012). The microbes present in gastrointestinal (GI) tract are very important site for the host, they help the host in process which includes breakdown of various carbohydrates, dietary fibbers, SCFA production and synthesis of vitamins in major. They also help their host in determining the susceptibility to GI infection. They endorsed for their functional role in production of molecules that modulate neuro-immuno-endocrine signalling, immunological activity, their differentiation of cell and glucose uptake as well as in lipid metabolism (Ghosh and Pramanik 2021). The gut microbiota also protects the organism from pathogenic bacteria by outcompeting the pathogens by using available nutrients in abundance on that site and maintains pH level of intestine as well as prevents their attachment via colonization resistance (Stecher and Hardt 2011). Liver and gut are very closely connected via portal system, receiving the blood content from the gut, which activates the liver functions. Intestinal microbiota forms a very complex ecological system that requires optimal physiological conditions, to produce and meet the demands of vitamins, digestion of nutrients, degradation of bile acids (BA). This is also essential for common immunological activity on daily basis (Cesaro et al. 2011).

70

S. Kumar et al.

2 The Gut Derived Microbial Metabolites Gut microbiota derived metabolites are generated with the help of diverse group of bacteria that resides inside the host gut. They act as molecular mediators between the microbiota and host that maintain and guard the metabolic balance. It exerts diverse effects on host physiology. There are classes of microbial derived metabolites such as SCFAs, BCAA, MCFA, TMA, LCFA, BCFA that are very crucial for metabolic homeostasis and reported to be altered in various diseases as well as disorders likeT2D, obesity, CVD, etc. (Fig. 2). The metabolites such as SCFAs, MCFAs, LCFAs and others are detectable in biological sample like serum, urine, cerebral fluids, and faecal sample. The mapping of these metabolites will serve as an indicator of pathophysiological condition, which is crucial to detect disease at an early stage and can be further explored as a future targets for precision therapeutic applications and probable modulation. Metabolites individually and in coordination with other gut derived metabolites act as balancing role in disease progression such as higher BCAA availability interfering with insulin activity and mood of actions. The activation of downstream mediator such as mTOR SK61 results in downregulation of insulin receptor substrate (IRS), respectively, IRS1 and IRS2. In vitro study has shown that BCAAs trigger mTOR signalling in skeletal muscle that ends with a decreased glucose uptake. Prolong mTOR (mechanistic target of rapamycin) activation due to high load of chronic BCAA may interfere in insulin activity and therefore contribute to insulin resistance (Gojda and Cahova 2021). Fig. 2 List of major microbial metabolites which play crucial role in metabolic disorders: BCAA, SCFA BCFA LCFA MCFA, TMA

Mapping the Microbial Metabolites in Metabolic Disorder with. . .

2.1

71

Short Chain Fatty Acid (SCFAs)

SCFAs are those fatty acids which consist of one to six carbons with aliphatic tails. Three major SCFAs produced from fermentation such as acetate (C2), propionate (C3), and butyrate (C4) contribute close to 95% of total SCFAs (Table 2). The caecum and proximal colon are major site for SCFA production, where majority of activity occurs. The SCFAs, butyrate, propionate and acetate are present in the ratio of 1:1:2 respectively (Cummings et al. 1987). In the process to produce SCFA gut microbiota convert prebiotics to produce different SCFA via fermentation, which is cucial for healthy functional gut barrier integrity. Also this is required for key metabolic activity of host such as metabolism of glucose, lipid. The inflammatory response and immune system also modulated by gut derived SCFA (Esgalhado et al. 2017). SCFA regulates blood glucose in the form of indole saturated SCFA that’s indole-3-propionic acid and improve insulin activity. It negatively affects liver lipid synthesis and inflammatory response and maintains the intestinal barrier that prevents endotoxin to pass and prevent low grade inflammation (Zhang et al. 2022). SCFA plays a vital activity in energy homeostasis and metabolism. These SCFA positively inhance the adipose tissue, liver and skeletal muscle associated function which ends with an improve condition for better glucose homeostasis as well as insulin activity. Collectively this inflammation associated complication regulated by SCFA (Vinolo et al. 2011b). As an extracellular and an intracellular signalling molecules, they act on outside of the cell, where they work as agonists for different G-protein-coupled receptors (GPCRs) such as the free fatty acid receptors 2 (FFAR2, also known as GPR43) and GPR41. Butyrate one of the key SCFA can also activate the hydroxycarboxylic acid receptor 2 (HCAR2 or GPR109A). Expressed by different cell types such as epithelial cells of intestinal and immune cells. SCFAs regulate production of cytokines, eicosanoides, and chemokines. These leukocytes migrate to the foci of inflammation and destroy microbial pathogens (Vinolo et al. 2011a). Acetate reduces LPS induced TNF-α production in human and mice mononuclear cells via FFAR activation (Masui et al. 2013). Propionate reduces inflammatory mediators such as IL-4, IL-5, and IL-17A in allergic mice in FFAR3 dependent manner (Trompette et al. 2014). Propionate and butyrate attenuate NF-kB activation and prevent inflammation by inhibiting expression level of pro-inflammatory cytokines. In airway inflammation, SCFAs reduce IL-8 mediated inflammation by activation of Table 2 SCFAs, their formula and molecular formula (Zhang et al. 2021)

SCFA Acetic acid Butyric acid Formic acid Isobutyric acid Isovaleric acid Propionic acid Valeric acid

Molecular formula C2H4O2 C4H8O2 CH2O2 C4H8O2 C5H10O2 C3H6O2 C5H10O2

Structural formula CH3COOH CH3(CH2)2COOH HCOOH (CH3)2CHCOOH (CH3)2CHCH2COOH CH3CH2COOH CH3(CH2)3COOH

72

S. Kumar et al.

Fig. 3 Schematic representation on the involvement of SCFA role in liver gluconeogenesis and de novo lipogenesis. SCFA, propionate acts as a precursor, via inhibition of fatty acid synthase (FAS) expression. (Adapted and modified from Canfora et al. 2015)

FFAR2 and FFAR3 on macrophages and neutrophils (Halnes et al. 2017). SCFAs prevent activation of microglial cells by HDAC inhibition and prevention of inflammatory mediators involved in various neurodegenerative diseases like Alzheimer and Parkinson’s disease (Vinolo et al. 2011a). SCFAs collectively play vital role for metabolic function of T2D such as gluconeogenesis and de novo lipogenesis (Fig. 3). This whole activity moves with higher AMP to ATP ratio, the upregulation of PPARα approches target genes, thereby increasing FA oxidation and glycogen storage. This activity mediated with the help of GPR41 and GPR43-dependent cascade mechanism. Acetate and butyrate might directly upregulate hepatic AMPK phosphorylation and biological function that require in this condition.

Mapping the Microbial Metabolites in Metabolic Disorder with. . .

2.2

73

Medium Chain Fatty Acids (MCFAs)

MCFAs are fatty acids that range between 6 and 12 carbon chain in their lengths, such as hexanoate having six carbons, octanoate with eight carbons, and decanoate having 10 carbons in their chain. The common MCFAs include: caprylic acid having 8 carbons, capricacid with 10 carbons, and lauric acid having 12 carbon chain. However large amounts of MCFAs are present in MCT (medium chain triglycerides) form. MCFAs upon entry into the cell and mitochondrial matrix, improves oxidative capacity which may directly contribute to its effects on insulin sensitivity specific to tissue (Fig. 4). In case of metabolic disorders such as T2D and obesity MCFAs act by modulating glucose homeostasis, followed by fat metabolism, and hormone secretion that are involved in maintaing the energy homeostasis. MCFA generated via microbes in the form of microbial metabolites activates the PPARγ pathway. MCFA also plays role in inflammatory cytokines release via GPR84 (Huang et al. 2021).

2.3

Long Chain Fatty Acid (LCFAs)

LCFAs are fatty acids having 16 or more cabon chain, they are also known as free fatty acids (FFA). The most common LCFA are arachidonic acid, linoleic acid, oleic acid, palmitic acid, stearic acid, etc. Many of these metabolites have been quantified from bacterial strain such as E. coli phylogenic group. Study shows that in neonatal maternal separation (NMS), LCFAs present prominantly in higher amount in the

Fig. 4 MCFA binds with intracellular receptors and trigger core secondry messenger molecules, further they activate the PPARγ pathway. This result in Adipocytes remodelling, improve insulin sensitivity, increase lipid metabolism and mitochondria oxidative capacity

74

S. Kumar et al.

colon lumen and in the faeces of NMS rat model. Once they get confirmation from their stimulatory activity on colon motility, function-based metagenomic analysis suggests high level synthesis of LCFAs inside the GIT which is mediated by the gut microbiota residing in NMS rats (Zhao et al. 2018). Interestingly, while intake of the diet that contains fat in higher amount is correlated with LCFA level. The ratio of Firmicutes to Bacteroidetes significantly decreases, while a downregulation in the relative abundance of Proteobacteria may attribute for the lowering host body weight (Zhou et al. 2017). Which contribute further to diabetic complication. LCFA in the form of FFA (free fatty acids) with different form of PUFA which is generated after biosynthesis as active signalling molecule which modulate the insulin signalling pathway by triggering the level of reactive oxygen species (ROS), protein kinase C (PKC), and diacylglycerol (DAG). They are core components that take this cascade to increase the insulin receptor substrate-1 (IRS-1) level, serine phosphorylation and decrease IRS-1 tyrosine phosphorylation, thereby inhibiting the activity of PI3K. Together this triggered cascade creates disturbance in fragile balance between β-cell function along with peripheral insulin resistance. These processes are further responsible for metabolic disorders, clinical manifestation of T2D and associated complications.

2.4

Branched Chain Fatty Acids (BCFAs)

BCFAs are mostly fatty acids having one or more than one methyl group present on carbon chain, mostly they fall under sarurated form. BCFAs such as sobutyrate, methylbutyrate, isovalerate, and isocaproate mainly generate after the degradation of the amino acids such as isoleucine, leucine, and valine. The presence of these compounds in faeces is comparatively lower than that of SCFA (Rios-Covian et al. 2020). The synthesis of BCFA start from branched-chain acyl-CoA (BCA-CoA) primers along with malonyl-CoA as their extender chain. The BCA-CoA primer synthesized from two different types of primer sources, one which include a-ketoacids a-ketoisocaproic acid (KIC), a-ketoisovaleric acid (KIV), while the other primer source with a-keto-b-methylvaleric acid (KMV) (Fig. 5). These a-ketoacids are generated as end product after the catabolism of the BCAAs such as leucine, valine, and isoleucine. They influence GIT (gastrointestinal tract) and participate in host physiology. BCFAs are major components that are responsible for gut colonization in newborn (Ran-Ressler et al. 2008). As it is a major component of meconium and vernix. These two components meconinum and vernix which are rich in BCFA represent broad range of faetal exposure in early stage. Also it is rich source of metabolites and other component that is required for gut micrbiota in early stage (Houghteling and Walker 2015).

Mapping the Microbial Metabolites in Metabolic Disorder with. . .

75

Fig. 5 Main pathways of BCAA catabolism and their associated components; ALA alanine; branched-chain-amino-acid aminotransferase (BCAT); branched-chain α-keto acid dehydrogenase (BCKD); GLN glutamine, GLU glutamate, HMG-CoA 3-hydroxy-3-methylglutaryl-CoA, HMB β-hydroxy-β-methylbutyrate, KIC α-ketoisocaproate (ketoleucine), KIV α-ketoisovalerate (ketovaline), KMV α-keto-β-methylvalerate (ketoisoleucine), α-KG α-ketoglutarate. 1,3 KIC dioxygenase (Holeček 2018)

2.5

Branched Chain Amino Acid (BCAA)

Isoleucine, leucine, and valine are the most common BCFA present inside host, having protein anabolic properties and are essential to the body. Role of BCAA has been firmly known for their activity in insulin resistance and their further metabolic progression. Amino acid at first hand interrupts insulin signalling in skeletal muscle and it negatively affects the glucose uptake. BCAAs have been implicated in regulation of insulin secretion by pancreatic beta cells starting from a short to a long-term depending on availability, it also prohibits function of beta cells by inducing hyper secretion, one of the main reported hallmarks of T2D. The metabolism of BCAA broadly relies on the gut intestinal flora (GIF). This GIF is very crucial for the host due to its wide range of associated activity including their enzymatic functions which require in triggering BCAA biosynthesis. BCAA, subsequently, is adsorbed and enters inside the human circulation. Catabolism of BCAA is especially very active in adipose as well as in hepatic tissues of the host body. The elevated level of BCAA and insulin resistance was interlinked with dysbiosis of host gut microbiota. BCAAs act as both signalling molecule and important energy substrate which is crucial for mRNA translation. BCAA passes signal to mTOR, promoting protein

76

S. Kumar et al.

synthesis and cell growth. Additionally, BCAA signalling downregulates insulin cascade activity, followed by reduced insulin-dependent substrate uptake when present in excess amounts. This shift is denoted with an increased level of biosynthesis of BCAA and reduced bacterial inward transporters for amino acids. This leads to an increased production as well as their availability for absorbance in the intestine via intestinal wall. This is mainly mediated by Prevotella copri and Bacteroides vulgatus. BCAA acts as key component to trigger the energy generation for the host via TCA cycle, glycogenesis, ketogenesis, etc. In the animal model it has been shown that administration of Prevotella copri increased serum levels of BCAA and led to insulin resistance (Fig. 6).

Fig. 6 Major intracellular BCAA metabolic and signalling pathways, highlighting their role in insulin signalling and glycogenesis. BCAT (branched-chain amino acid aminotransferase), BCFA AcCoA (acetyl, coenzyme A), and TCA (tricarboxylic acid cycle) and their interplay role with BCAA

Mapping the Microbial Metabolites in Metabolic Disorder with. . .

2.6

77

Trimethylamine (TMA)

TMA appears as small colourless compound having amine oxide, which is generated via microbial metabolism inside the gut using compounds such as choline, betaine, and carnitine. Level of TMA changes with different factor compostion of diet that an individual take, gut micrbiota their abundance and diversity, presence of drug inside the body, and enzymatic activity of monooxygenase inside the liver (Janeiro et al. 2018). TMA enters by gut micrbiota-dependent conversion of dietary sources of individual such as choline, carnitine (Fig. 7). Further it get oxidized by monooxygenase that convert TMA to trimethylamine N-oxide (TMAO). Which accumulated as oxidized form, primarily this accumulation is oberved in the marine animals. Activity such as protein-destabilizing effects of urea is being protected due to high level of TMAO in the host. Diet with high content of fat increases the level of TMAO in plasma. Under normal circumstances, TMA is converted to TMAO by flavin monooxygenases. During T2D or following oral intake of broad spectrum Fig. 7 TMA biosynthesis from dietary sources via enzymatic conversion of anaerobic bacteria (Herrema and Niess 2020)

78

S. Kumar et al.

antibiotics, dysbiosis of intestinal microbiota alters the production of TMAO. Additionally, dietary supplementation of choline and carnitine acts as a prebiotic in modulating microflora to increase the production of TMA.

3 Mapping Microbiota and Their Metabolites Currently, mapping of microbial metabolites for the diagnostic purpose is currently under the developing stage. However, the metagenomic and metabolomic studies are now well established for research purpose and being widely used. The mapping of key gut derived microbial metabolites would open a new doorway towards precise preventive and therapeutics approach. The abovementioned key metabolites present in serum, urine, and faecal samples along with gut microbiota dysbiosis and their relation with altered metabolites can be further explored as early diagnostic marker and further used for precise, safe, and effective personalized medication (Fig. 8). These mapping insights would open newer avenues of health supplementation of nutrients, metabolites that require restoring healthy condition of the host. Metabolites and gut microbiota, together, may become a viable tool in management and treatment of various diseases highlighted earlier. Furthermore, in-depth

Fig. 8 Schematic outline for mapping microbiota and their metabolites from serum, urine, and faecal sample

Mapping the Microbial Metabolites in Metabolic Disorder with. . .

79

studies about the co-relation between host gut microbiota (specific microbes or microbial communities) which produce the specialized metabolites can depict the physiological and pathophysiological state of the host.

4 Conclusion and Way Forward Emerging study strongly highlight the crucial role of microbes and their metabolites that broadly shape host responses and development of the metabolic syndrome like T2D. Prior to work on such fascinating research idea go to clinical practice for diagnostics and treatment, we strongly recomand the following frontiers that can be considered for further studies. Establishing a connecting link between an altered gut microbiome and its metabolites, their association with metabolic disorders. Significant progress has been made in this area in the rodent models; however, a comprehensive study is required for their possible alternative conncetion with early stage of T2D as well as other physiological function and its associated complication needs to be addressed. How different microbes or metabolites shift from a healthy condition to pre-diabtic stage and contribute to the metabolic imbalnce and end up in T2D condition needs to be understood. A deep dive scientific understanding is required to unfold the more crytal clear link between gut microbiota, its metabolites and their role in host phsiology and metabolism, which needs to be explored more. This will take scientific dicovery and further appropiate investigation to the next level for the therapeutic development of various metabolic disorders.

References Brown K, DeCoffe D, Molcan E, Gibson DL (2012) Correction: Brown K., et al. Diet-induced dysbiosis of the intestinal microbiota and the effects on immunity and disease. Nutrients 2012, 4, 1095–1119. Nutrients 4(11):1552–1553 Bull MJ, Plummer NT (2014) Part 1: the human gut microbiome in health and disease. Integr Med 13(6):17 Canfora EE, Jocken JW, Blaak EE (2015) Short-chain fatty acids in control of body weight and insulin sensitivity. Nat Rev Endocrinol 11(10):577–591 Cani PD, Osto M, Geurts L, Everard A (2012) Involvement of gut microbiota in the development of low-grade inflammation and type 2 diabetes associated with obesity. Gut Microbes 3(4): 279–288 Cesaro C, Tiso A, Del Prete A, Cariello R, Tuccillo C, Cotticelli G, del Vecchio Blanco C, Loguercio C (2011) Gut microbiota and probiotics in chronic liver diseases. Dig Liver Dis 43(6):431–438 Chassard C, Lacroix C (2013) Carbohydrates and the human gut microbiota. Curr Opin Clin Nutr Metab Care 16(4):453–460 Cummings J, Pomare EW, Branch WJ, Naylor CP, Mac Farlane G (1987) Short chain fatty acids in human large intestine, portal, hepatic and venous blood. Gut 28(10):1221–1227

80

S. Kumar et al.

Esgalhado M, Kemp JA, Damasceno NR, Fouque D, Mafra D (2017) Short-chain fatty acids: a link between prebiotics and microbiota in chronic kidney disease. Future Microbiol 12(15): 1413–1425 Ghosh S, Pramanik S (2021) Structural diversity, functional aspects and future therapeutic applications of human gut microbiome. Arch Microbiol 203(9):5281–5308 Gojda J, Cahova M (2021) Gut microbiota as the link between elevated BCAA serum levels and insulin resistance. Biomol Ther 11(10):1414 Halnes I, Baines KJ, Berthon BS, MacDonald-Wicks LK, Gibson PG, Wood LG (2017) Soluble fibre meal challenge reduces airway inflammation and expression of GPR43 and GPR41 in asthma. Nutrients 9(1):57 Herrema H, Niess JH (2020) Intestinal microbial metabolites in human metabolism and type 2 diabetes. Diabetologia 63(12):2533–2547 Holeček M (2018) Branched-chain amino acids in health and disease: metabolism, alterations in blood plasma, and as supplements. Nutr Metab 15(1):1 Houghteling PD, Walker WA (2015) Why is initial bacterial colonization of the intestine important to the infant’s and child’s health? J Pediatr Gastroenterol Nutr 60(3):294 Huang L, Gao L, Chen C (2021) Role of medium-chain fatty acids in healthy metabolism: a clinical perspective. Trends Endocrinol Metab 32(6):351–366 Janeiro MH, Ramírez MJ, Milagro FI, Martínez JA, Solas M (2018) Implication of trimethylamine N-oxide (TMAO) in disease: potential biomarker or new therapeutic target. Nutrients 10(10): 1398 Masui R, Sasaki M, Funaki Y, Ogasawara N, Mizuno M, Iida A, Izawa S, Kondo Y, Ito Y, Tamura Y, Yanamoto K (2013) G protein-coupled receptor 43 moderates gut inflammation through cytokine regulation from mononuclear cells. Inflamm Bowel Dis 19(13):2848–2856 Ran-Ressler RR, Devapatla S, Lawrence P, Brenna JT (2008) Branched chain fatty acids are constituents of the normal healthy newborn gastrointestinal tract. Pediatr Res 64(6):605–609 Rios-Covian D, González S, Nogacka AM, Arboleya S, Salazar N, Gueimonde M, de Los ReyesGavilán CG (2020) An overview on fecal branched short-chain fatty acids along human life and as related with body mass index: associated dietary and anthropometric factors. Front Microbiol 11:973 Sartor RB, Mazmanian SK (2012) Intestinal microbes in inflammatory bowel diseases. Am J Gastroenterol Suppl 1(1):15 Stecher B, Hardt WD (2011) Mechanisms controlling pathogen colonization of the gut. Curr Opin Microbiol 14(1):82–91 Trompette A, Gollwitzer ES, Yadava K, Sichelstiel AK, Sprenger N, Ngom-Bru C, Blanchard C, Junt T, Nicod LP, Harris NL, Marsland BJ (2014) Gut microbiota metabolism of dietary fiber influences allergic airway disease and hematopoiesis. Nat Med 20(2):159–166 Vinolo MA, Rodrigues HG, Hatanaka E, Sato FT, Sampaio SC, Curi R (2011a) Suppressive effect of short-chain fatty acids on production of proinflammatory mediators by neutrophils. J Nutr Biochem 22(9):849–855 Vinolo MA, Rodrigues HG, Nachbar RT, Curi R (2011b) Regulation of inflammation by short chain fatty acids. Nutrients 3(10):858–876 Zhang M, Wang Y, Zhao X, Liu C, Wang B, Zhou J (2021) Mechanistic basis and preliminary practice of butyric acid and butyrate sodium to mitigate gut inflammatory diseases: a comprehensive review. Nutr Res 95:1–18 Zhang B, Jiang M, Zhao J, Song Y, Du W, Shi J (2022) The mechanism underlying the influence of indole-3-propionic acid: a relevance to metabolic disorders. Front Endocrinol 13:841703 Zhao L, Huang Y, Lu L, Yang W, Huang T, Lin Z, Lin C, Kwan H, Wong HLX, Chen Y, Sun S (2018) Saturated long-chain fatty acid-producing bacteria contribute to enhanced colonic motility in rats. Microbiome 6(1):1–16 Zhou S, Wang Y, Jacoby JJ, Jiang Y, Zhang Y, Yu LL (2017) Effects of medium-and long-chain triacylglycerols on lipid metabolism and gut microbiota composition in C57BL/6J mice. J Agric Food Chem 65(31):6599–6607

Human Microbiome in Malnutrition Mehul Chauhan, Priya Mori, and Vijay Kumar

Abstract Human gut microbiota is resilient in nature, so it can be easily modified by diet. The resilient nature of gut microflora can contribute to prevent metabolic syndromes in the human body by changing the diet and lifestyle. The outcome as a result of the interaction of gut microflora with the host, which is further influenced by the food consumed, is a widely explored area in the present time. Malnutrition is a wide terminology that includes a variety of nutritional deficiencies, including undernutrition and obesity. It is characterized by unevenness between energy intake and expenditure. Children who survive malnutrition are more likely to have delayed cognitive and motor development, obesity, and non-communicable illnesses later in their life. Obesity and undernutrition have a common biological feature: changes in the configuration and diversity of the gut microbiota as compared to healthy people. In the recent scenario, obesity is a major health problem worldwide. Metabolic disorders like obesity have characteristic composition of gut microflora that arises as a result of microflora dysbiosis. Probiotics play a very important role in managing the gut microbiota of humans. Thus, they can help to restore our gut microbiota. Studies have shown that gastrointestinal microbiota can change two factors: energy utilization from the feeding materials and secretion of the metabolites that regulate the genes responsible for energy utilization as well as its storage in the human body. Another aspect to modulate the gut microbiota is providence of probiotics, prebiotics, synbiotics, and fecal microbiota transplant (FMT). In this chapter, the factors affecting the gut microbiota and possible treatment for malnutrition and obesity will be discussed in detail. Keywords Genetics · Gut microbiota · Malnutrition · Obesity · Prebiotics · Probiotics · Synbiotics

M. Chauhan · P. Mori · V. Kumar (✉) Postbiotics and Foodomics Lab, Department of Microbiology, School of Science, RK University, Rajkot, Gujarat, India e-mail: [email protected] © The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd. 2023 V. Kothari et al. (eds.), Probiotics, Prebiotics, Synbiotics, and Postbiotics, https://doi.org/10.1007/978-981-99-1463-0_5

81

82

M. Chauhan et al.

1 Introduction Malnutrition is a wide terminology that includes a variety of nutritional deficiencies, including undernutrition and obesity. It is characterized by unevenness between energy absorption and expense (de Clercq et al. 2016). Prolonged malnutrition gives rise to two major health conditions, i.e. underweight and overweight which have consequences on human health. Overweight and obesity are defined as irregular or excessive fat accumulation that may impair health (WHO 2016). Children who survive malnutrition are more likely to have delayed cognitive and motor development, obesity, and non-communicable illnesses later in their life (Black et al. 2013). Thus, the etiology of children’s malnutrition, as well as preventative and treatment measures, is of great activity, and the gut microbiota may be a promising purpose for the detriment and treatment of childhood malnutrition (Pekmez et al. 2019). World Health Organization (WHO) in its National Family Health Survey (NFHS-5), for India, issued in the year 2020 revealed the global scenario which says that 149 million children under the age of 5 are predicted to be stunted (too short for age), 45 million wasted (too thin for height), and 38.9 million were overweight or obese. According to the previous data from World Health Organization (WHO 2016), more than 1.9 billion individuals aged 18 and above are overweight with a higher prevalence among males. This makes up approximately 39% of the world’s adult overweight population; over 650 million comes under the category of “obese” (an average of 13%). The same report also reveals that approximately 2.8 million deaths occur as an outcome of being overweight or obese. Another combined survey conducted by WHO, the United Nations Children’s Fund (UNICEF), and the World Bank Group found that 150.8 million (22.2%) youngsters under the age of 5 were stunted globally in 2017, with waste endangering the lives of 7.5% (50.5 million) of children (Iddrisu et al. 2021). Malnutrition in children under the age of five, continues to be a serious problem in underdeveloped countries. When we look for the data from Indian states, National Family Health Survey (NFHS-5), India, 2019–2021 of Ministry of Health and Family Welfare, Govt. of India based on a survey conducted among the rural and urban population, between 2019 and 2021, states that in India, 3.4% children below 5 years of age and 24% adult female and 22.9% adult male are obese (BMI ≥ 25 kg/m2), while 32.1% children under 5 years age are malnourished. This data says a lot about the malnutrition status in urban as well as rural areas of the Indian subcontinent. Various research centers on exploring the diversity of the human gut microbiome have reached a common consensus that the adult human gut contains between 10 and 100 billion bacterial cells; among them, the majority are concentrated in the colon. Such a huge population of microbes makes around 1.5 kg of the average body weight (about the same as liver weight), with the microbes holding 150–200 times more genes than the whole human genome. This equates to around 3.3 million genes that comprise the microbiome vs approximately 23,000 genes reported from the human genome. Unlike our Homo sapiens-derived fixed and inert DNA, the microbiome

Human Microbiome in Malnutrition

83

Fig. 1 Influencing factors on the makeup of the gut microbiota

genome is more flexible, and it adapts to age, food, antibiotic usage, and other variables (Fig. 1). The relationship between gut microbiota and food is a widely explored area in the present time. Obesity and undernutrition have a common biological feature in this regard: modulation in the composition and diversity of the gut microbiota as compared to healthy people. Dysbiosis, or disruption in microbial composition, has been linked to changes in body weight and fat accumulation. Improved knowledge of how the gut microbiota affects energy balance and appetite control might lead to innovative therapies like probiotics and fecal microbiota transplantation (FMT) that modify the gut microbiota more rapidly than existing therapeutic options (de Clercq et al. 2016). Undernutrition leads to poorly established gut flora as well as compromised immunological and metabolic development. For example, in germ-free mice, malnutrition leads to growth hormone resistance, whereas microbiota colonization boosts tissue insulin-growth factor (Hou et al. 2020). Growing clinical evidence as an outcome of extensive exploratory research carried out worldwide suggests that calorie-dense diets have resulted in higher rates of obesity and overweight, which acts as a potential trigger for a variety of diseases, including cardiovascular disease, diabetes, and even some types of cancers (Razzoli et al. 2017). A high-fat diet (HFD) has been linked to extreme lipid metabolic disorders in previous studies (Saad et al. 2016; Tulipani et al. 2016). Furthermore, it has also been established that high-fat diet is strongly linked to dysbiosis in gut microbiota profiles, microbial products, and the loss or disappearance of certain members of normal microflora and thus contributes to the development of obesity (Bianchi et al. 2019; Greenhill 2017; Hou et al. 2020). Various dysbiosis centered researches carried out on the human population have not come up with strong evidence in support of correlation between the gut microbiota and disease state. This may be due to being statistically underpowered since they use limited human sample sizes. Duvallet (2018) advocates for metaanalyses of extensive research carried out to date for dysbiosis to account for these limitations. A meta-analysis will improve the statistical strength of several small studies. A series of consistent findings through independent studies or the refutation

84

M. Chauhan et al.

of false correlations is major benefit of meta-analysis. A few valuable researchers have established gut microbiota’s connection to obesity (Brüssow 2020).

2 Early Life Factors and Gut Microbiota The framework of gut microflora of any individual begins even before his or her birth and depends on various factors. It is anticipated that the microbiota of newborns would expand both during nursing and upon delivery when neonates pass through the vaginal canal and are exposed to the mother’s microbes (Hildebrandt et al. 2009). According to several studies, it is important to pay attention to conserving the gastrointestinal tract’s microbial ecology while it is still forming, or prenatally, in expectant mothers and fetuses after delivery. The most recent research findings reveal that colonization of bacteria could start even before birth since certain live microbes cross the placenta, highlighting the need of nourishing the gut throughout prenatal and pregnancy period (Aagaard et al. 2014). Humans are thought to develop their entire microbiota within the first 100 days of life (Robertson et al. 2019; Soderborg et al. 2016; Nielsen et al. 2014). This may include good nutrition and breastfeeding during pregnancy, as well as avoiding antibiotics and cesarean sections wherever possible (Robertson et al. 2019; Gilbert et al. 2018; Mischke and Plösch 2013; Nauta et al. 2013). Various studies find a strong association between cesarean section and body mass in childhood and adolescence (Blustein et al. 2013) and its manifestation into the risk of overweight and obesity among preschool children (Rutayisire et al. 2016). Studies have established that neonates that are exposed to antibiotics due to their health conditions are vulnerable to altered body mass in the long run of their life. Evidences suggest that antibiotics can forever alter fetal metabolic patterns by alternating epigenetic pathways or the protective microbiota (Saari et al. 2015; Azad et al. 2017). The newborn of malnourished parents (either overfed or underfed) is at greater risk of onset of type 1 or type 2 diabetes, and/or obesity, due to alterations in the gut flora and epigenetic markers (Nielsen et al. 2014; Canani et al. 2011; Austvoll et al. 2020).

3 Birth Pattern Has Its Impact on the Development of Malnutrition Cesarean section delivery is consistently connected to a higher threat of obesity in the future (Blustein et al. 2013; Rutayisire et al. 2016; Mueller et al. 2015; Keag et al. 2018). When the baby is born through cesarean section, his/her exposure to the mother’s vaginal and fecal microbiota during delivery is minimized. As a result, they remain unexposed to this natural source of bacterial colonization. According to one study, cesarean-delivered children had a nearly doubled chance of becoming

Human Microbiome in Malnutrition

85

overweight or obese by the age of 11, compared to children born to ordinary-weight moms. This relationship was stronger and prolonged among children born to overweight or obese mothers (Blustein et al. 2013). This contradicts the association between the usage of antibiotics and the mother’s weight (Ajslev et al. 2011). For both scheduled and emergency cesarean section deliveries, the risk estimate was identical (Mueller et al. 2015). The degree to which cesarean section is linked to changes in the microbiota needs to be investigated further (Austvoll et al. 2020).

4 Gut Microbiota Under Malnutrition Condition Until recently, the two frequently identified causes of malnutrition are inadequate to diet intake and disease conditions, but enteric infections such as diarrhea also contribute significantly to global malnutrition cases in children (Brown 2003), implying a link among diarrhea and undernourishment modulation of gut microbial composition (Fig. 2). Diarrhea sickness can cause malnutrition due to decreased nutritional absorption and mucosal injury, along with nutrient deficiency due to each bout of diarrhea. Several studies (Youmans et al. 2015; Hsiao et al. 2014) have observed drastic modifications in the gut microbiota during and following diarrhea infections. In the fecal microbiome of diarrheal children (1–6 years old), for instance, sustained

Fig. 2 Impairment in the gut microbiome and its correlation with malnutrition

86

M. Chauhan et al.

increases of Fusobacterium mortiferum, Escherichia coli, and oral bacteria have been documented (The et al. 2018). There are abundant scientific findings supporting and establishing the role of microbiota in modulating malnutrition. Various studies conducted in animal models like mice revealed that a low-nutrient diet in combination with gut microbiome with high differential abundances of Bilophila wadsworthia and Clostridioides innocuum increased malnutrition (Smith et al. 2013). It is necessary to highlight that there are modest differences in the gut microbiota exchange across the different groups including Bifidobacterium spp., Lactobacillus spp., Ruminococcus spp., and Faecalibacterium prausnitzii and other bacterial species that are consistently reported to be lost during malnutrition, whereas Bacteroidetes, Clostridioides innocuum, Streptococcus spp., and Escherichia spp. have been consistently found to increase (Iddrisu et al. 2021).

5 Dietary Fats and the Gut Microbiota The amount and consistency of dietary fat consumed on a daily basis have an effect on the composition of the gut microbiota (Candido et al. 2018). Fatty acids consumed daily via various sources can be classified as saturated fatty acids (SFAs), monounsaturated fatty acids (MUFAs), or polyunsaturated fatty acids (PUFAs) based on double bonds between carbon molecules. Mammalian products are rich source saturated fatty acids. Several animal trial-based researches have found that the gut composition among mice fed on saturated fatty acid rich high-fat diet (HFD) had fewer Bacteroidetes and Bacillus bifidus levels while increasing the count of Firmicutes and Proteobacteria. Surprisingly, these changes can be reversed over time with a standard chow and pellets (Hildebrandt et al. 2009; Wu et al. 2011; Zhang et al. 2012). Intestinal dysbiosis can arise due to frequent and higher consumption of SFAs, as reported by several studies. In addition, high-fat diet induced imbalance in gut microbes can change the intestinal barrier integrity. Sulfate-reducing bacteria (SRB) such as Bilophila wadsworthia are found in higher numbers in hosts that consume high-fat diets, for example, milk fat (Ijssennagger et al. 2016; Johansson et al. 2008). The large concentration of sulfide generated by these sulfate-reducing bacteria has the potential to reduce disulfide bonds present in epithelial cells of the mucosal lining resulting in a deficient mucus layer. This leads to disruption of the MUC2 mediated network of polymeric protein produced by goblet cells which otherwise maintains the mucus layer stability. Consumption of a high-SFA diet promotes the population of sulfate-reducing bacteria and increased gut inflammation, colitis scores, and IBD (Devkota et al. 2012; Gruber et al. 2013; Devkota and Chang 2015). The biochemical composition of the diet we consume has a great impact on the body physiology, metabolism as well as microbial diversity. For instance, monounsaturated fatty acids, like the oleic acid contained in extra virgin olive oil (EVOO), are an essential part of the “Mediterranean diet.” Consuming extra virgin olive oil

Human Microbiome in Malnutrition

87

has been demonstrated to maintain the bulk of the cardioprotective effects of the Mediterranean diet and is strongly advised for reducing the risk of coronary heart disease (Colica et al. 2017). It has been found that the phenolic contents of extra virgin olive oil are majorly responsible for its anti-inflammatory and antioxidant properties rather than its monounsaturated fatty acid content (Bulotta et al. 2014). In yet another systematic review conducted by Wolters et al. (2019), they have reported that high-monounsaturated fatty acid diets have no effect on the Bacteroidetes-toFirmicutes ratio, phylum distribution, or richness/diversity indexes. While some other findings suggest that monounsaturated fatty acids-rich diets promote the population of Parabacteroides, Prevotella, and Turicibacter genera and the Enterobacteriaceae family, while they cause decrease in the number of Bifidobacterium genus at the family and genus level. Wolter and colleagues also highlight that the presence of phylum Tenericutes was positively correlated with lower triglyceride levels, while it was inversely linked with monounsaturated fatty acids metabolites. Conversely, the excess of Blautia spp. in individuals with a high body mass index (BMI) was reported to be proportionally linked with monounsaturated fatty acids serum metabolites. Sunflowers, soybean, corn oil, nuts, and seeds are rich in polyunsaturated fatty acids that are essential for cell metabolism but cannot be produced by our own cells, hence categorized as “essential fatty acids.” Polyunsaturated fatty acids are classified as omega-3 and omega-6 polyunsaturated fatty acids. Fish-derived omega-3 polyunsaturated fatty acids are beneficial for health as they restore the balance between microbiota makeup and boosting anti-inflammatory compounds. The conjugated linoleic acids (CLAs) are a distinct class of polyunsaturated fatty acids, the most abundant of which are 18:2cis-9, trans-11 (9,11 conjugated linoleic acid, or rumenic acid) and 18:2 trans-10, cis-12 CLAs (10,12 CLA). These polyunsaturated fatty acids are produced by ruminative bacteria that express linoleic acid isomerase and bio-hydrogenated linoleic acid. Foods made from ruminative animals like lamb, beef, butter, and dairy products include conjugated linoleic acids. The Food and Drug Administration (FDA) classifies conjugated linoleic acids as “Generally Regarded as Safe (GRAS)” since numerous lines of research have demonstrated that they have anti-atherosclerotic, anti-obesogenic, and anti-cancer characteristics (den Hartigh 2019). The impact of conjugated linoleic acids on the composition of the gut microbiota can be used to explain some of their positive qualities. Based on studies carried out in murine model, dietary supplementation with 10,12 conjugated linoleic acid has been shown to boost the presence of Bacteroidetes, Butyrivibrio, Roseburia, and Lactobacillus significantly while bring about decrease in Firmicutes. This alteration causes a major increase in the shortchain fatty acids butyrate in feces and acetate in plasma (Marques et al. 2015; den Hartigh et al. 2018). Scientific findings support the fact that omega-3 polyunsaturated fatty acids can increase Lachnospiraceae taxa and restore the Firmicutes/ Bacteroidetes ratio, both of which are linked to the elevated synthesis of antiinflammatory short-chain fatty acids butyrate (Watson et al. 2018; Noriega et al. 2016; Menni et al. 2017).

88

M. Chauhan et al.

The western diet is known to have a high omega-6/omega-3 polyunsaturated fatty acids ratio, which has been related to increased metabolic endotoxemia and intestinal barrier permeability (Kaliannan et al. 2015). This dietary shift has resulted in the conversion of cardiovascular and chronic diseases into epidemics (Simopoulos 2008; Kang 2011). Restoring this ratio by significant uptake of omega-3 polyunsaturated fatty acids may improve the composition of the gut microbiota, as a result, minimize metabolic endotoxemia (Rinninella et al. 2019a, b).

6 Gut Microbiota Modulation by Diet and Its Relation with Malnutrition The study conducted by Gehrig et al. (2019) indicates that intestinal microbiota in infants with severe acute malnutrition (SAM) had a more immature microbial distribution pattern in its regular chronologic development when matched to children suffering from moderate acute malnutrition (MAM) as well as healthy children of the same age (Fukuda et al. 2011). This conclusion is consistent with earlier research that establishes the connection between a developing enteric microbiota and malnutrition, and an immature abdominal microbiota has been linked to lower amounts of lean body mass expansion, metabolic deformity, and bone development disturbances (Guo et al. 2017). The effects of severe acute malnutrition were sustained even when the subjects’ nutritional intake was changed (Fukuda et al. 2011; Valentine et al. 2020). Therefore, food intake and the development of the gut microbiome are inextricably connected, and a reduction in nutrient absorption, such as that seen in malnourished situations, is directly related to an immature enteric microbiota. This immature gut microbiota enhances the host’s undernutrition by favorably modifying growth mediators. However, these negative effects are lessened when the intestinal microbiota is the focus of microbiota-directed diets, illustrating the constantly interconnected and linked relationship between one’s nutritional status and the intestinal microbiome (Valentine et al. 2020).

7 Gut Microbiota Modulation by Prebiotics and Its Relation with Obesity Glenn R. Gibson and Marcel B. Roberfroid coined the term “prebiotics” in 1995. They defined “Prebiotics” as “a non-digestible food ingredient” that, on consumption, confers constructive effects to the host by selectively stimulating the growth and/or activity of a finite number of bacteria in the gut, thus improving the host’s health. Gibson and Roberfroid also set some parameters to categorize the food fibers

Human Microbiome in Malnutrition

89

as prebiotics. As per them, a food ingredient can be considered a prebiotic only if those criteria are met. These criteria include 1. The food ingredient shall neither be hydrolyzed nor absorbed in the upper part of the gastrointestinal tract. 2. It should act as a selective substrate for beneficial bacterial microflora residing in the colon, thus stimulating their growth and/or metabolite production by them. 3. It shall be able to positively alter the colonic bacterial formation. 4. It shall activate luminal or systematic effects that are useful to host health. In addition to the above-mentioned criteria, the food ingredient, to be considered as prebiotics, shall also be resistant to the acidic pH of the stomach and shall be easily fermented by intestinal bacterial consortia. The definition of prebiotic proposed by Gibson and Roberfroid is still considered valid. In 2008, the International Scientific Association of Probiotics and Prebiotics (ISAPP), during its sixth meeting, took into consideration the research works carried out and their key findings and redefined the “dietary prebiotics” as “a selectively fermented ingredient that results in specific changes in the composition and/or activity of the gastrointestinal microbiota, thus conferring benefit(s) upon host health.” Foods like whole grains, vegetables, fruits, nuts, and legumes are high in fiber and thus are potential sources of various prebiotics (Gibson et al. 2004). As per the criteria defined for any compound to be considered as prebiotic, only a few substances qualify that included short and long chain β-fructans like fructo-oligosaccharides (FOS) and inulin, lactulose, and galacto-oligosaccharides (GOS). Additionally, carbohydrates that are made available as prebiotics for the gut microbiota to metabolize through short-chain fatty acids are known as microbiota-accessible carbohydrates (MACs). These MACs cannot be digested by the host’s metabolic pathway. Intestinal mucus glycans are degraded by Bacteroides thetaiotaomicron bacteria, according to Sonnenburg et al. (2016). Presently, in addition to those previously mentioned, many other carbohydrates and non-carbohydrate compounds like raffinose family oligosaccharides, resistant starch, polydextrose, pectin-oligosaccharides, and cocoa-derived flavanols are considered prebiotics. When dietary MACs are scarce, these bacteria can use host mucus glycans, causing a thinning of the intestinal barrier (Mu et al. 2017). In a study conducted by Singh et al. (2018), it was reported that alteration in the fecal microbiota among high-fat-diet male rats due to dose-dependent administration of inulin can mask the number of Firmicutes (Roseburia, Clostridium clusters I, IV, and XIV) and enhancing the number of Bifidobacterium spp. and Bacteroidetes (Singh et al. 2018). Vandeputte et al. (2017) investigated the impact of inulin absorption on stool recurrence in healthy individuals with moderate constipation. They observed a decline in Bilophila abundance subsequently after inulin intake, evident by softer stools, and a positive improvement in constipation-specific qualityof-life measures. They came up with the conclusion that insulin induces improvements in the relative abundances of Anaerostipes, Bilophila, and Bifidobacterium (Vandeputte et al. 2017). These findings suggest that the effects of dietary prebiotics on the colon microbiota pose a promising new target for mechanistic study.

90

M. Chauhan et al.

Human milk oligosaccharides (HMO), which are primarily unique, are an essential origin of prebiotics in early life (Bode et al. 2016). Human milk’s HMO composition is highly variable, with over 200 distinct constituents comprising monomers such as glucose, galactose, N-acetylglucosamine, fucose, and sialic acid (Ninonuevo and Lebrilla 2009). Although the use of human milk oligosaccharides varies depending on the strain, in vitro studies show that the early gut microbiota, which includes Bifidobacterium and Bacteroides spp., may ferment the components in human milk oligosaccharides (Jost et al. 2015). The heterogeneity and uniformity of the human milk oligosaccharides configuration are linked to development and body composition among healthy infants for the first 180 days of life (Alderete et al. 2015). The onset of microbiota-dependent malnutrition in newborn infants has been connected to sialylated milk oligosaccharides (Charbonneau et al. 2016). In a meta study conducted by Pekmez et al. (2019) and Rinninella et al. (2019a, b) in order to create compositional profiling of breast milk of Malawian mothers with healthy and acutely stunted infants, it was revealed that nonsecretor moms with extremely stunted children have reduced total fucosylated and sialylated human milk oligosaccharides concentrations in their breast milk than nonsecretor mothers with healthy infants. Moreover, fecal microbiota transplantation from stunted underweight neonates to Germ-free and gnotobiotic mice, followed by sialylated human milk oligosaccharides supplementation, enhanced bone development, body weight, and lean body mass increase, as well as metabolic changes in the liver, muscle, and brain.

8 Treating Obesity with the Help of Probiotics The human’s gut microbiota consists of more than 1000 diverse species of bacteria, yeasts, and viruses. The bacterial diversity can be divided into six phyla: Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria, Fusobacteria, and Verrucomicrobia. Among these, Firmicutes and Bacteroidetes are the most prevalent, accounting for 90% of the gut microbiota (Rinninella et al. 2019a, b). Probiotics, as per the World Health Organization, are living microorganisms that, when given in sufficient proportions, can provide health advantages to the host. Probiotics, which may be found in meals or supplements, can affect the gut microbiome and help people lose weight. However, not all probiotics are treated equally, and some might even cause weight gain, causing obesity. Probiotics from the genera Lactobacillus and Bacillus, as well as yeasts from the species Saccharomyces, have been shown to reduce Firmicutes/Bacteroidetes (F/B) ratio and obesity. Firmicutes and Bacteroidetes, which are the most significant bacterial phyla in the gastrointestinal system, have gotten a lot of attention in recent years. Probiotics can possibly cure a variety of disorders (Hemarajata and Versalovic 2013) and have anti-obesity and anti-inflammatory properties (Abenavoli et al. 2019) by altering the microbiota. Probiotics affect the Firmicutes/Bacteroidetes ratio, regulating host adiposity or intestinal inflammation. Thus it can be administered to modulate the gut microbiota by diverse dietary supplementation (Fig. 3) to prevent obesity and reverse dysbiosis.

Human Microbiome in Malnutrition

91

Fig. 3 Obesity and inflammatory bowel illness can be caused by an imbalance in the Firmicutes/ Bacteroidetes ratio

Fig. 4 Advantages of using probiotics

The Firmicutes/Bacteroidetes ratio is thought to play a significant role in maintaining good intestinal homeostasis. Dysbiosis is defined as an increase or reduction in the Firmicutes/Bacteroidetes ratio, with the former being associated with obesity and then with inflammatory bowel illness (IBD). When provided in sufficient proportions, probiotics can provide health advantages to the host (Fig. 4). There is a lot of evidence that probiotics have nutritional and immunosuppressive

92

M. Chauhan et al.

qualities, including studies that link them to the Firmicutes/Bacteroidetes ratio, obesity, and IBD (Stojanov et al. 2020). In obese mice, Lactobacillus rhamnosus GG and Lactobacillus sakei NR28 were administered which resulted in a significant decrease in the Firmicutes/Bacteroidetes ratio. In addition, the administration of these consortia lowered the epididymal fat mass, acetyl-CoA carboxylase, fatty acid synthase, and stearoyl-CoA desaturase-1 (Ji et al. 2012). In another investigation, Lactobacillus rhamnosus GG supplementation combined with a high-fat diet may help in weight gain and reduce the Firmicutes/Bacteroidetes ratio in a C57BL/6J mouse model (Ji et al. 2018).

9 Probiotics and Their Relation with Malnutrition A consortium of probiotics tends to be more beneficial than single strains based on a small number of trials (Chapman et al. 2011). Saccharomyces boulardii, Bacillus coagulans, Lactobacillus, and Bifidobacteria are widely used alone or in mixtures (Pandey et al. 2015). A blend of 12 Firmicutes, Bacteroidetes, and Actinobacteria species was recently expected as a promising probiotic therapy to restore the lost microbiota of Kwashiorkor children from Niger and Senegal. However, the usefulness of this combo on Kwashiorkor development results has to be determined (Tidjani Alou et al. 2017; Pekmez et al. 2019). Furthermore, probiotics may influence satiety through the interaction of shortchain fatty acids and intestinal peptides. In cell culture and animal models based experimentation, probiotic therapy was reported to increase glucagon-like peptide-1 (GLP-1) release in a butyrate-dependent way, followed by less food intake and enhanced glucose tolerance (Yadav et al. 2013). Certain animal models showed reduced bowel wall atrophy with probiotic therapy, regeneration of colonic goblet cells and colon wall stratum, higher systemic immune response, and better recovery from malnutrition (Azevedo et al. 2014). It appears that probiotics and prebiotics can improve growth outcomes, lower morbidity in undernourished children, and decrease overweight and obesity in pediatric populations. To ascertain how, when, and which probiotics and prebiotics should be used in adolescent obesity and malnutrition (Fig. 5), further clinical trials must be conducted.

10

Genetics and Nutrient Deficiency in Malnutrition

Consumption of macronutrients protein, carbohydrates, and fat is a statistic that is closely connected to food consumption and is generally steady. Although there is a significant amount of inter-individual variance, heredity can range from 11% to 65%

Human Microbiome in Malnutrition

93

Fig. 5 Relationship between enteric microbiome with malnutrition and obesity

(Rankinen and Bouchard 2006). Chu et al. (2013) identified genetic areas associated with the quantity of high-calorie consumption for proteins and carbs utilizing a population-based cohort in a genome-wide association meta-analysis of macronutrients. After adjusting for body mass index, they discovered a sizable single-nucleotide polymorphism (SNP) in the FGF21 region that was associated with lower protein, higher carbohydrate, and lower fat intake. Genetic research has been done on micronutrients found in serum or blood, such as trace elements like zinc, and genes governing or regulating these nutrients have been found. Potential therapeutic targets for these genes include increasing vitamin intake and lowering malnutrition. A lack of zinc causes oxidative stress and decreased intracellular signaling. Zinc absorption in the stomach requires transporters for uptake and subsequent release into the circulation. The carbonic anhydrase genes (Table 1), SCAMP5/PPCDC, and KLF8/ZXDA/ZXDB are three gene regions on the X chromosome that have been connected to zinc concentrations, according to Evans et al. (2013). Investigations into vitamin A or serum retinol have also uncovered SNPs in the retinol transportrelated genes RBP4 and TTR. Similar to zinc, vitamin A serves a range of purposes and has been connected to a number of health consequences, including malnutrition. It is crucial to identify common genetic changes that may affect the population’s variability in blood levels of these important micronutrients as well as the heterogeneity in serum levels.

94

M. Chauhan et al.

Table 1 Significant areas of the genome linked to diarrhea and macro- or micronutrients Outcome Having diarrhea by the age of one Protein macronutrient Carbohydrate macronutrient Zinc trace elements in blood Retinol levels Breast milk fatty acid FADS1, FAD2, FADS

Nearest reported gene(s) NTN5, FUT2, SEC1P FUT1, IZUMO1, FGF21, RASIP1, FUT2 TANK SCAMP5, PPCDC, KLF8, ZXDA, CA1, CA2, CA3, CA13, MAX, FNTB, ZXDB BP4, TTR FADS1, FADS3, FAD2

References Bustamante et al. (2016) Chu et al. (2013) Chu et al. (2013) Evans et al. (2013), Ng et al. (2015) Mondul et al. (2011) Mychaleckyj et al. (2018)

NTN5 (netrin-5 gene), SEC1P (secretory blood group 1 pseudogene), FUT2 (fucosyltransferase 2), FUT1 (fucosyltransferase 1), IZUMO1 (izumo sperm-egg fusion 1), FGF21 (fibroblast growth factor 21), RASIP1 (ras interacting protein 1), TANK (TRAF family member-associated NF-kappaB activator), SCAMP5 (secretory carrier membrane protein 5), PPCDC (phosphopantothenoylcysteine decarboxylase), KLF8 (Kruppel like factor 8), ZXDA (zinc finger X-linked duplicated A), ZXDB (zinc finger X-linked duplicated B), CA1 (carbonic anhydrase 1), CA2 (carbonic anhydrase 2), CA3 (carbonic anhydrase 3), CA13 (carbonic anhydrase 13), MAX (MYC associated factor X), FNTB (farnesyltransferase CAAX box), BP4 (blood pressure QTL 4), TTR (transthyretin), FADS1 (fatty acid desaturase 1), FAD2 (fatty acid desaturase 2), FADS3 (fatty acid desaturase 3)

11

The Genetics of Obesity

The technique used to find genes connected to obesity varies according to the type of obesity and the genotyping technology available at the time. Monogenic and polygenic obesity are the two basic types of obesity. “Monogenic obesity is caused by either modest or large chromosomal deletions or single-gene abnormalities, is inherited in a Mendelian pattern, and is often rare, early-onset, and severe.” A prevalent type of obesity that arises in some disorders and leads to polymorphism is called polygenic obesity. In mice with severe hyperphagia and obesity, such as the obese and diabetic mouse lines, a number of suspected genes and the mechanisms underlying them that regulate body weight were first identified. After the cloning of the ob gene, the db gene was used to identify and clone the leptin receptor (LEPR). Antagonizing the relationship between melanocortin 1 and 4 receptors (MC1R and MC4R), these two genes, and melanocortin with body weight control has been found, exposing a plethora of novel obesity candidate genes. Hundreds of genes were investigated as possible targets in the last 15 years, but only six, ADRB3, BDNF, CNR1, MC4R, PCSK1, and PPAR-Gamma, established a consistent link with obesity onset (Table 2). According to genome-wide association studies (GWAS) published in 2007, the FTO locus gene and body mass index are linked. The most frequent single-gene abnormality, MC4R gene mutations lead to hyperphagia and obesity. Till 5% of instances of severe childhood obesity had pathogenic

Human Microbiome in Malnutrition

95

Table 2 Genes responsible for severe and early-onset obesity Gene symbol and name ADRB3 (β-3 adrenergic receptor gene) BDNF (brain-derived neurotrophic factor) CNR1 (cannabinoid receptor 1) MC4R (melanocortin-4 receptor) PCSK1 (proprotein convertase subtilisin/Kexin type 1) PPAR-G (peroxisome proliferatoractivated receptor γ)

Role in body weight regulation ADRB3 Trp64Arg variant is linked in BMI

References Kurokawa et al. (2008)

Brain-derived neurotrophic factor (BDNF) and BMI Val66Met polymorphism

Shugart et al. (2009)

Endocannabinoid receptor 1 gene variations raise the risk for obesity and may change body mass index in European populations The MC4R V103I polymorphism is linked to obesity

Benzinou et al. (2008)

Contribution of common non-synonymous variants in PCSK1 to body mass index variation and risk of obesity Peroxisome proliferator-activated receptor gamma Pro12Ala polymorphism and prediabetic characteristics

Wang et al. (2010) Nead et al. (2015) Tonjes et al. (2006)

mutations in the MC4R gene. In the current status, one billion adults will have obesity by 2025 (Loos and Yeo 2022).

12

Conclusion

Human gut microbiota can be easily imbalanced due to alteration in living style, food habits, and antibiotic consumption. The condition of malnutrition and obesity is strongly correlated with human gut microbiota, thus this disease’s condition can be controlled and ameliorated by altering the gut microflora. It is easily modified by changing diet and lifestyle. Some of the diseases are because of a long-term dysbiosis of good gut microbiota and then some good microbiota helps in the modulation of our gut microbiota.

References Aagaard K, Ma J, Antony KM, Ganu R, Petrosino J, Versalovic J (2014) The placenta harbors a unique microbiome. Sci Transl Med 6(237):237ra65. https://doi.org/10.1126/scitranslmed. 3008599 Abenavoli L, Scarpellini E, Colica C, Boccuto L, Salehi B, Sharifi-Rad J, Aiello V, Romano B, De Lorenzo A, Izzo AA, Capasso R (2019) Gut microbiota and obesity: a role for probiotics. Nutrients 11(11):2690

96

M. Chauhan et al.

Ajslev TA, Andersen CS, Gamborg M, Sørensen TIA, Jess T (2011) Childhood overweight after establishment of the gut microbiota: the role of delivery mode, pre-pregnancy weight and early administration of antibiotics. Int J Obes 35(4):522–529 Alderete TL, Autran C, Brekke BE, Knight R, Bode L, Goran MI, Fields DA (2015) Associations between human milk oligosaccharides and infant body composition in the first 6 mo of life. Am J Clin Nutr 102(6):1381–1388 Austvoll CT, Gallo V, Montag D (2020) Health impact of the Anthropocene: the complex relationship between gut microbiota, epigenetics, and human health, using obesity as an example. Glob Health Epidemiol Genom 5:e2 Azad MB, Moossavi S, Owora A, Sepehri S (2017) Early-life antibiotic exposure, gut microbiota development, and predisposition to obesity. Nestle Nutr Inst Workshop Ser 88:67–80 Azevedo JF, Hermes-Uliana C, Lima DP, Sant’Ana DM, Alves G, Araujo EJ (2014) Probiotics protect the intestinal wall of morphological changes caused by malnutrition. An Acad Bras Cienc 86:1303–1314 Benzinou M, Chevre JC, Ward KJ, Lecoeur C, Dina C, Lobbens S, Durand E, Delplanque J, Horber FF, Heude B, Balkau B (2008) Endocannabinoid receptor 1 gene variations increase risk for obesity and modulate body mass index in European populations. Hum Mol Genet 17(13): 1916–1921 Bianchi F, Duque ALRF, Saad SMI, Sivieri K (2019) Gut microbiome approaches to treat obesity in humans. Appl Microbiol Biotechnol 103(3):1081–1094 Black RE, Victora CG, Walker SP, Bhutta ZA, Christian P, De Onis M, Ezzati M, GranthamMcGregor S, Katz J, Martorell R, Uauy R (2013) Maternal and child undernutrition and overweight in low-income and middle-income countries. Lancet 382(9890):427–451 Blustein J, Attina T, Liu M, Ryan AM, Cox LM, Blaser MJ, Trasande L (2013) Association of cesarean delivery with child adiposity from age 6 weeks to 15 years. Int J Obes 37(7):900–906 Bode L, Contractor N, Barile D, Pohl N, Prudden AR, Boons GJ, Jin YS, Jennewein S (2016) Overcoming the limited availability of human milk oligosaccharides: challenges and opportunities for research and application. Nutr Rev 74(10):635–644 Brown KH (2003) Diarrhea and malnutrition. J Nutr 133(1):328S–332S Brüssow H (2020) Problems with the concept of gut microbiota dysbiosis. Microb Biotechnol 13 (2):423–434 Bulotta S, Celano M, Lepore SM, Montalcini T, Pujia A, Russo D (2014) Beneficial effects of the olive oil phenolic components oleuropein and hydroxytyrosol: focus on protection against cardiovascular and metabolic diseases. J Transl Med 12(1):1–9 Bustamante M, Standl M, Bassat Q, Vilor-Tejedor N, Medina-Gomez C, Bonilla C, Ahluwalia TS, Bacelis J, Bradfield JP, Tiesler CM, Rivadeneira F (2016) A genome-wide association metaanalysis of diarrhoeal disease in young children identifies FUT2 locus and provides plausible biological pathways. Hum Mol Genet 25(18):4127–4142 Canani RB, Di Costanzo M, Leone L, Bedogni G, Brambilla P, Cianfarani S, Nobili V, Pietrobelli A, Agostoni C (2011) Epigenetic mechanisms elicited by nutrition in early life. Nutr Res Rev 24(2):198–205 Candido FG, Valente FX, Grześkowiak ŁM, Moreira APB, Rocha DMUP, Alfenas RDCG (2018) Impact of dietary fat on gut microbiota and low-grade systemic inflammation: mechanisms and clinical implications on obesity. Int J Food Sci Nutr 69(2):125–143 Chapman CMC, Gibson GR, Rowland I (2011) Health benefits of probiotics: are mixtures more effective than single strains? Eur J Nutr 50(1):1–17 Charbonneau MR, O’Donnell D, Blanton LV, Totten SM, Davis JC, Barratt MJ, Cheng J, Guruge J, Talcott M, Bain JR, Muehlbauer MJ (2016) Sialylated milk oligosaccharides promote microbiota-dependent growth in models of infant undernutrition. Cell 164(5):859–871 Chu AY, Workalemahu T, Paynter NP, Rose LM, Giulianini F, Tanaka T, Ngwa JS, CHARGE Nutrition Working Group, Qi Q, Curhan GC, Rimm EB (2013) Novel locus including FGF21 is associated with dietary macronutrient intake. Hum Mol Genet 22(9):1895–1902

Human Microbiome in Malnutrition

97

Colica C, Di Renzo L, Trombetta D, Smeriglio A, Bernardini S, Cioccoloni G, Costa de Miranda R, Gualtieri P, Sinibaldi Salimei P, De Lorenzo A (2017) Antioxidant effects of a hydroxytyrosolbased pharmaceutical formulation on body composition, metabolic state, and gene expression: a randomized double-blinded, placebo-controlled crossover trial. Oxid Med Cell Longev 2017: 2473495 de Clercq NC, Groen AK, Romijn JA, Nieuwdorp M (2016) Gut microbiota in obesity and undernutrition. Adv Nutr 7(6):1080–1089 den Hartigh LJ (2019) Conjugated linoleic acid effects on cancer, obesity, and atherosclerosis: a review of pre-clinical and human trials with current perspectives. Nutrients 11(2):370 den Hartigh LJ, Gao Z, Goodspeed L, Wang S, Das AK, Burant CF et al (2018) Obese mice losing weight due to trans-10, cis-12 conjugated linoleic acid supplementation or food restriction harbor distinct gut microbiota. J Nutr 148(4):562–572 Devkota S, Chang EB (2015) Interactions between diet, bile acid metabolism, gut microbiota, and inflammatory bowel diseases. Dig Dis 33(3):351–356 Devkota S, Wang Y, Musch MW, Leone V, Fehlner-Peach H, Nadimpalli A, Antonopoulos DA, Jabri B, Chang EB (2012) Dietary-fat-induced taurocholic acid promotes pathobiont expansion and colitis in Il10-/- mice. Nature 487(7405):104–108 Duvallet C (2018) Meta-analysis generates and prioritizes hypotheses for translational microbiome research. Microb Biotechnol 11(2):273 Evans DM, Zhu G, Dy V, Heath AC, Madden PA, Kemp JP, McMahon G, St Pourcain B, Timpson NJ, Golding J, Lawlor DA (2013) Genome-wide association study identifies loci affecting blood copper, selenium and zinc. Hum Mol Genet 22(19):3998–4006 Fukuda S, Toh H, Hase K, Oshima K, Nakanishi Y, Yoshimura K, Tobe T, Clarke JM, Topping DL, Suzuki T, Taylor TD (2011) Bifidobacteria can protect from enteropathogenic infection through production of acetate. Nature 469(7331):543–547 Gehrig JL, Venkatesh S, Chang HW, Hibberd MC, Kung VL, Cheng J, Chen RY, Subramanian S, Cowardin CA, Meier MF, O’Donnell D (2019) Effects of microbiota-directed foods in gnotobiotic animals and undernourished children. Science 365(6449):eaau4732 Gibson GR, Probert HM, Van Loo J, Rastall RA, Roberfroid MB (2004) Dietary modulation of the human colonic microbiota: updating the concept of prebiotics. Nutr Res Rev 17(2):259–275 Gilbert JA, Blaser MJ, Caporaso JG, Jansson JK, Lynch SV, Knight R (2018) Current understanding of the human microbiome. Nat Med 24(4):392–400 Greenhill C (2017) Gut microbiome and serum metabolome changes. Nat Rev Endocrinol 13 (9):501–501 Gruber L, Kisling S, Lichti P, Martin FP, May S, Klingenspor M, Lichtenegger M, Rychlik M, Haller D (2013) High fat diet accelerates pathogenesis of murine Crohn’s disease-like ileitis independently of obesity. PLoS One 8(8):e71661 Guo S, Gillingham T, Guo Y, Meng D, Zhu W, Walker WA, Ganguli K (2017) Secretions of Bifidobacterium infantis and Lactobacillus acidophilus protect intestinal epithelial barrier function. J Pediatr Gastroenterol Nutr 64(3):404–412 Hemarajata P, Versalovic J (2013) Effects of probiotics on gut microbiota: mechanisms of intestinal immunomodulation and neuromodulation. Ther Adv Gastroenterol 6(1):39–51 Hildebrandt MA, Hoffmann C, Sherrill-Mix SA, Keilbaugh SA, Hamady M, Chen YY, Knight R, Ahima RS, Bushman F, Wu GD (2009) High-fat diet determines the composition of the murine gut microbiome independently of obesity. Gastroenterology 137(5):1716–1724 Hou D, Zhao Q, Yousaf L, Khan J, Xue Y, Shen Q (2020) Consumption of mung bean (Vigna radiata L.) attenuates obesity, ameliorates lipid metabolic disorders and modifies the gut microbiota composition in mice fed a high-fat diet. J Funct Foods 64:103687 Hsiao A, Ahmed AM, Subramanian S, Griffin NW, Drewry LL, Petri WA, Haque R, Ahmed T, Gordon JI (2014) Members of the human gut microbiota involved in recovery from Vibrio cholerae infection. Nature 515(7527):423–426 Iddrisu I, Monteagudo-Mera A, Poveda C, Pyle S, Shahzad M, Andrews S, Walton GE (2021) Malnutrition and gut microbiota in children. Nutrients 13(8):2727

98

M. Chauhan et al.

Ijssennagger N, van der Meer R, van Mil SW (2016) Sulfide as a mucus barrier-breaker in inflammatory bowel disease? Trends Mol Med 22(3):190–199 International Institute for Population Sciences (IIPS) and ICF (2021) National family health survey (NFHS-5), India. 2019–2021. International Institute for Population Sciences (IIPS) and ICF, Deonar Ji Y, Kim H, Park H, Lee J, Yeo S, Yang J, Park S, Yoon H, Cho G, Franz CMAP, Bomba A (2012) Modulation of the murine microbiome with a concomitant anti-obesity effect by Lactobacillus rhamnosus GG and Lactobacillus sakei NR28. Benef Microbes 3(1):13–22 Ji Y, Park S, Park H, Hwang E, Shin H, Pot B, Holzapfel WH (2018) Modulation of active gut microbiota by Lactobacillus rhamnosus GG in a diet induced obesity murine model. Front Microbiol 9:710 Johansson ME, Phillipson M, Petersson J, Velcich A, Holm L, Hansson GC (2008) The inner of the two Muc2 mucin-dependent mucus layers in colon is devoid of bacteria. Proc Natl Acad Sci 105(39):15064–15069 Jost T, Lacroix C, Braegger C, Chassard C (2015) Impact of human milk bacteria and oligosaccharides on neonatal gut microbiota establishment and gut health. Nutr Rev 73(7):426–437 Kaliannan K, Wang B, Li XY, Kim KJ, Kang JX (2015) A host-microbiome interaction mediates the opposing effects of omega-6 and omega-3 fatty acids on metabolic endotoxemia. Sci Rep 5(1):1–17 Kang JX (2011) The omega-6/omega-3 fatty acid ratio in chronic diseases: animal models and molecular aspects. In: Healthy agriculture, healthy nutrition, healthy people, vol 102. Karger Publishers, Basel, pp 22–29 Keag OE, Norman JE, Stock SJ (2018) Long-term risks and benefits associated with cesarean delivery for mother, baby, and subsequent pregnancies: systematic review and meta-analysis. PLoS Med 15(1):e1002494 Kurokawa N, Young EH, Oka Y, Satoh H, Wareham NJ, Sandhu MS, Loos RJ (2008) The ADRB3 Trp64Arg variant and BMI: a meta-analysis of 44 833 individuals. Int J Obes 32(8):1240–1249 Loos RJ, Yeo GS (2022) The genetics of obesity: from discovery to biology. Nat Rev Genet 23(2): 120–133 Marques TM, Wall R, O'Sullivan O, Fitzgerald GF, Shanahan F, Quigley EM, Cotter PD, Cryan JF, Dinan TG, Ross RP, Stanton C (2015) Dietary trans-10, cis-12-conjugated linoleic acid alters fatty acid metabolism and microbiota composition in mice. Br J Nutr 113(5):728–738 Menni C, Zierer J, Pallister T, Jackson MA, Long T, Mohney RP, Steves CJ, Spector TD, Valdes AM (2017) Omega-3 fatty acids correlate with gut microbiome diversity and production of N-carbamylglutamate in middle aged and elderly women. Sci Rep 7(1):1–11 Mischke M, Plösch T (2013) More than just a gut instinct—the potential interplay between a baby’s nutrition, its gut microbiome, and the epigenome. Am J Phys Regul Integr Comp Phys 304(12): R1065–R1069 Mondul AM, Yu K, Wheeler W, Zhang H, Weinstein SJ, Major JM et al (2011) Genome-wide association study of circulating retinol levels. Hum Mol Genet 20(23):4724–4731 Mu Q, Kirby J, Reilly CM, Luo XM (2017) Leaky gut as a danger signal for autoimmune diseases. Front Immunol 8:598 Mueller NT, Whyatt R, Hoepner L, Oberfield S, Dominguez-Bello MG, Widen EM, Hassoun A, Perera F, Rundle A (2015) Prenatal exposure to antibiotics, cesarean section and risk of childhood obesity. Int J Obes 39(4):665–670 Mychaleckyj JC, Nayak U, Colgate ER, Zhang D, Carstensen T, Ahmed S, Ahmed T, Mentzer AJ, Alam M, Kirkpatrick BD, Haque R (2018) Multiplex genome wide association analysis of breast milk fatty acid composition extends the phenotypic association and potential selection of FADS1 variants to arachidonic acid, a critical infant micronutrient. J Med Genet 55(7):459–468 Nauta AJ, Ben Amor K, Knol J, Garssen J, Van der Beek EM (2013) Relevance of pre-and postnatal nutrition to development and interplay between the microbiota and metabolic and immune systems. Am J Clin Nutr 98(2):586S–593S

Human Microbiome in Malnutrition

99

Nead KT, Li A, Wehner MR, Neupane B, Gustafsson S, Butterworth A, Engert JC, Davis AD, Hegele RA, Miller R, den Hoed M (2015) Contribution of common non-synonymous variants in PCSK1 to body mass index variation and risk of obesity: a systematic review and meta-analysis with evidence from up to 331 175 individuals. Hum Mol Genet 24(12):3582–3594 Ng E, Lind PM, Lindgren C, Ingelsson E, Mahajan A, Morris A, Lind L (2015) Genome-wide association study of toxic metals and trace elements reveals novel associations. Hum Mol Genet 24(16):4739–4745 Nielsen JH, Haase TN, Jaksch C, Nalla A, Søstrup B, Nalla AA, Larsen L, Rasmussen M, Dalgaard LT, Gaarn LW, Thams P (2014) Impact of fetal and neonatal environment on beta cell function and development of diabetes. Acta obstetricia et gynecologica. Scandinavica 93(11):1109–1122 Ninonuevo MR, Lebrilla CB (2009) Mass spectrometric methods for analysis of oligosaccharides in human milk. Nutr Rev 67(suppl_2):S216–S226 Noriega BS, Sanchez-Gonzalez MA, Salyakina D, Coffman J (2016) Understanding the impact of omega-3 rich diet on the gut microbiota. Case Rep Med 2016:1 Pandey K, Naik S, Vakil B (2015) Probiotics, prebiotics and synbiotics—a review. J Food Sci Technol 52(12):7577–7587 Pekmez CT, Dragsted LO, Brahe LK (2019) Gut microbiota alterations and dietary modulation in childhood malnutrition—the role of short chain fatty acids. Clin Nutr 38(2):615–630 Rankinen T, Bouchard C (2006) Genetics of food intake and eating behavior phenotypes in humans. Annu Rev Nutr 26:413–434 Razzoli M, Pearson C, Crow S, Bartolomucci A (2017) Stress, overeating, and obesity: insights from human studies and preclinical models. Neurosci Biobehav Rev 76:154–162 Rinninella E, Cintoni M, Raoul P, Lopetuso LR, Scaldaferri F, Pulcini G, Miggiano GAD, Gasbarrini A, Mele MC (2019a) Food components and dietary habits: keys for a healthy gut microbiota composition. Nutrients 11(10):2393 Rinninella E, Raoul P, Cintoni M, Franceschi F, Miggiano GAD, Gasbarrini A, Mele MC (2019b) What is the healthy gut microbiota composition? A changing ecosystem across age, environment, diet, and diseases. Microorganisms 7(1):14 Robertson RC, Manges AR, Finlay BB, Prendergast AJ (2019) The human microbiome and child growth—first 1000 days and beyond. Trends Microbiol 27(2):131–147 Rutayisire E, Wu X, Huang K, Tao S, Chen Y, Tao F (2016) Cesarean section may increase the risk of both overweight and obesity in preschool children. BMC Pregnancy Childbirth 16(1):1–8 Saad MJA, Santos A, Prada PO (2016) Linking gut microbiota and inflammation to obesity and insulin resistance. Physiology 31:283 Saari A, Virta LJ, Sankilampi U, Dunkel L, Saxen H (2015) Antibiotic exposure in infancy and risk of being overweight in the first 24 months of life. Pediatrics 135(4):617–626 Shugart YY, Chen L, Day IN, Lewis SJ, Timpson NJ, Yuan W, Abdollahi MR, Ring SM, Ebrahim S, Golding J, Lawlor DA (2009) Two British women studies replicated the association between the Val66Met polymorphism in the brain-derived neurotrophic factor (BDNF) and BMI. Eur J Hum Genet 17(8):1050–1055 Simopoulos AP (2008) The importance of the omega-6/omega-3 fatty acid ratio in cardiovascular disease and other chronic diseases. Exp Biol Med 233(6):674–688 Singh A, Zapata RC, Pezeshki A, Reidelberger RD, Chelikani PK (2018) Inulin fiber dosedependently modulates energy balance, glucose tolerance, gut microbiota, hormones and diet preference in high-fat-fed male rats. J Nutr Biochem 59:142–152 Smith MI, Yatsunenko T, Manary MJ, Trehan I, Mkakosya R, Cheng J, Kau AL, Rich SS, Concannon P, Mychaleckyj JC, Liu J (2013) Gut microbiomes of Malawian twin pairs discordant for kwashiorkor. Science 339(6119):548–554 Soderborg TK, Borengasser SJ, Barbour LA, Friedman JE (2016) Microbial transmission from mothers with obesity or diabetes to infants: an innovative opportunity to interrupt a vicious cycle. Diabetologia 59(5):895–906

100

M. Chauhan et al.

Sonnenburg ED, Smits SA, Tikhonov M, Higginbottom SK, Wingreen NS, Sonnenburg JL (2016) Diet-induced extinctions in the gut microbiota compound over generations. Nature 529(7585): 212–215 Stojanov S, Berlec A, Štrukelj B (2020) The influence of probiotics on the firmicutes/bacteroidetes ratio in the treatment of obesity and inflammatory bowel disease. Microorganisms 8(11):1715 The HC, Florez de Sessions P, Jie S, Pham Thanh D, Thompson CN, Nguyen Ngoc Minh C, Chu CW, Tran TA, Thomson NR, Thwaites GE, Rabaa MA (2018) Assessing gut microbiota perturbations during the early phase of infectious diarrhea in Vietnamese children. Gut Microbes 9(1):38–54 Tidjani Alou M, Million M, Traore SI, Mouelhi D, Khelaifia S, Bachar D et al (2017) Gut bacteria missing in severe acute malnutrition, can we identify potential probiotics by culturomics? Front Microbiol 8:899 Tonjes ANKE, Scholz M, Loeffler M, Stumvoll M (2006) Association of Pro12Ala polymorphism in peroxisome proliferator–activated receptor γ with pre-diabetic phenotypes: meta-analysis of 57 studies on nondiabetic individuals. Diabetes Care 29(11):2489–2497 Tulipani S, Palau-Rodriguez M, Alonso AM, Cardona F, Marco-Ramell A, Zonja B et al (2016) Biomarkers of morbid obesity and prediabetes by metabolomic profiling of human discordant phenotypes. Clin Chim Acta 463:53–61 Valentine GC, Hair AB, Martin CR (2020) Microbiome and pediatric obesity, malnutrition, and nutrition. Dev Microbiome:157–181 Vandeputte D, Falony G, Vieira-Silva S, Wang J, Sailer M, Theis S, Verbeke K, Raes J (2017) Prebiotic inulin-type fructans induce specific changes in the human gut microbiota. Gut 66(11): 1968–1974 Wang D, Ma J, Zhang S, Hinney A, Hebebrand J, Wang Y, Wang HJ (2010) Association of the MC4R V103I polymorphism with obesity: a Chinese case–control study and meta-analysis in 55, 195 individuals. Obesity 18(3):573–579 Watson H, Mitra S, Croden FC, Taylor M, Wood HM, Perry SL, Spencer JA, Quirke P, Toogood GJ, Lawton CL, Dye L (2018) A randomised trial of the effect of omega-3 polyunsaturated fatty acid supplements on the human intestinal microbiota. Gut 67(11):1974–1983 Wolters M, Ahrens J, Romaní-Pérez M, Watkins C, Sanz Y, Benítez-Páez A, Stanton C, Günther K (2019) Dietary fat, the gut microbiota, and metabolic health—a systematic review conducted within the MyNewGut project. Clin Nutr 38(6):2504–2520 World Health Organization: WHO (2016) Obesity and overweight. https://www.who.int/newsroom/fact-sheets/detail/obesity-and-overweight Wu GD, Chen J, Hoffmann C, Bittinger K, Chen YY, Keilbaugh SA, Bewtra M, Knights D, Walters WA, Knight R, Sinha R (2011) Linking long-term dietary patterns with gut microbial enterotypes. Science 334(6052):105–108 Yadav H, Lee JH, Lloyd J, Walter P, Rane SG (2013) Beneficial metabolic effects of a probiotic via butyrate-induced GLP-1 hormone secretion. J Biol Chem 288(35):25088–25097 Youmans BP, Ajami NJ, Jiang ZD, Campbell F, Wadsworth WD, Petrosino JF, DuPont HL, Highlander SK (2015) Characterization of the human gut microbiome during travelers’ diarrhea. Gut Microbes 6(2):110–119 Zhang C, Zhang M, Pang X, Zhao Y, Wang L, Zhao L (2012) Structural resilience of the gut microbiota in adult mice under high-fat dietary perturbations. ISME J 6(10):1848–1857

Association of Probiotics and Prebiotics with Human Microbiome and the Functioning of Immune System Pia Dey, Samir Kumar Mukherjee, and Debaprasad Parai

Abstract The evolution of mutualism and homeostasis between mammals and their commensal microorganisms makes sense from an ecological perspective. Microbiota and the immune system play a multifaceted role in the development and function of mammalian bodies. Many research studies have described the innate and adaptive immune system’s interactions with the trillions of microbes living in the gastrointestinal tracts of the human body. A dynamic multispecies community of bacteria, fungi, protozoa, and archaea is the key maker of gut microbiota which plays a fundamental role in triggering, training, and sustaining the human body’s immunity. The pathogenesis of many immune-mediated disorders is believed to be influenced by imbalances in microbiota–immunity interactions in genetically susceptible hosts. Environmental intrusions (such as diet, antibiotic use, or geographical changes) may alter the gut microbiome, impair host–microbiome interfaces, or alter the immune system, resulting in systemic dispersal of commensal microorganisms, pathogenic invasion, and divergent immune responses. This chapter aims to summarize the features of microbiota–immunity crosstalk, their game-changing roles in the establishment of disease, and the impact of metabolism, micronutrients, and environmental factors that orchestrate these interactions in different immune organs. Keywords Gut microbiome · Innate immunity · Adaptive immunity · Micronutrients · Probiotics · Metabolites

P. Dey · S. K. Mukherjee Department of Microbiology, University of Kalyani, Kalyani, West Bengal, India D. Parai (✉) ICMR-Regional Medical Research Centre, Bhubaneswar, Odisha, India © The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd. 2023 V. Kothari et al. (eds.), Probiotics, Prebiotics, Synbiotics, and Postbiotics, https://doi.org/10.1007/978-981-99-1463-0_6

101

102

P. Dey et al.

1 Introduction The human body harbours an array of organisms such as bacteria, fungi, archaea, viruses, protists, and microscopic animals which establish themselves in almost every part of the body including the gut, skin, and other mucosal environments, thereby collectively forming an ecosystem within the body and is known by the name of “microbiome”. The past two decades witnessed vigorous research regarding the genomic composition of the various organisms of the microbiome along with the development of culture-independent genomics techniques (Integrative HMP Research Network Consortium 2019). The outcome of such studies reported that the microbiota does not act as a passive bystander but actively influences a wide range of host functions such as nutritional responses, circadian rhythmicity, metabolism, and immunity (Hacquard et al. 2015; Lynch and Hsiao 2019). The evolution of human microbiota is directly linked with the immune system, which is evident by the fact that the microbiota accomplishes various biological functions at each site where it is present and is important for maintaining human health (Belkaid and Hand 2014). Likewise, any alteration of the components of indigenous microflora can contribute to disease development, known as dysbiosis (Petersen and Round 2014). The microbiome is a complex concoction of several interactions, which is not constant in every human being and hence, it is an area of research which is rapidly evolving. Such vivid research across the globe led to the foundation of the International Human Microbiome Consortium (IHMC) in 2005, which aims to understand the influence of microbes on human health and disease (Peterson et al. 2009). The National Institutes of Health (NIH) launched the Human Microbiome Project (HMP) in 2007, which is in line with a global initiative for biomedical research to examine the average microbial composition present in four sites of the human body, viz. the gastrointestinal tract, the mouth, the vagina, and the skin (Turnbaugh et al. 2007; Peterson et al. 2009). Adaptive and innate components of the mammalian immune system play an essential role in defending the host against potentially harmful organisms. It is now established from the ecological perspective that mammals and commensal microorganisms inside them have developed mutualism and have established homeostasis (Dethlefsen et al. 2007). However, there is tight regulation at each step which monitors the proper functioning of host immunity and prevents overexploitation of host resources by commensals as long as innocuous stimuli are tolerated by the immune system (Macpherson et al. 2005; Chu and Mazmanian 2013). The delicate balance of such interaction between the commensal and the host is broken only when the microbiome is disrupted or the equilibrium is disturbed by environmental factors such as antibiotic use, dietary changes, geographical changes, aberrant immune responses, host-microbiome impairment, remodelling of the immune system, etc. Complex and dynamic interactions exist between the microbiome and host immunity based on the resources available that further regulate the host’s physiological outcome (Belkaid and Hand 2014).

Association of Probiotics and Prebiotics with Human Microbiome and. . .

103

2 Innate Immune System The innate and adaptive immune systems are the two primary components of a body’s immune response (Parkin and Cohen 2001). Innate immunity is regarded as the first line of defence in the immune system of any organism. Hence, it is assigned to provide non-specific protection through several strata of physical and chemical barriers along with innate immune cells. The physical barrier includes the skin and the mucous membranes, whereas the chemical barriers contain antimicrobial proteins and enzymes. The immune cells comprise granulocytes, macrophages, and natural killer cells (Hillion et al. 2020). Conversely, in adaptive immune system, various functions like antigen recognition and specific response generation are carried out by the B- and T-lymphocytes. The T-cells regulate the B cells’ functioning, which in turn secrete antigen-specific antibodies and proteins (Wiertsema et al. 2021). T-cells are known to provide cellular immunity through the direct involvement of the cells for imparting immunity, whereby it recognizes the infectious agents that have invaded the host cells. Likewise, B cells are known to provide humoral immunity through the involvement of humour or body fluids, as antibodies circulate through it (Bonilla and Oettgen 2010). It has been two decades since the first report of close inter-relation between the innate immune system and the human microbiota was established (Thaiss et al. 2016). By shaping the microflora community and ecology in a way that is acceptable to the host and beneficial for its metabolic processes, the innate immune system plays a crucial role in shaping the community and ecology of gut microflora (Thaiss et al. 2016). Conversely, the indigenous microflora influences multiple facets of host homeostasis by integrating into the host physiology and eventually affecting their innate immune system. Various cellular components like the epithelial cells, myeloid cells, and innate lymphoid cells provide direct evidence of the interdependence between the innate immune system and the microbiota, which acts in a closed and orchestrated sequential manner (Thaiss et al. 2014). It is the fine equilibrium between the innate immune system and the human microbiota that influences the overall physiology of an individual.

3 Effect of Innate Immune System on Human Microbiota Various research studies have established that the composition of the human microbiota within the human body is directly linked with the development and functioning of the immune system. The innate immune system communicates signals to the host after receiving information about the microbiota’s metabolic state (Fig. 1). This aids to adapt with tissue-level physiology, which further modulates the composition and function of the microbiota (Thaiss et al. 2016). The variation in microbiota composition with respect to different individuals and time is entirely regulated by the innate immune system, which is evident from various

104

P. Dey et al.

Fig. 1 Regulation of microbial homeostasis by innate and adaptive immunity. Direct protection is provided by the microbiota through competition for nutrients, effects on physicochemical conditions of the local microenvironment, and downregulation of virulence factors through the production of bacteriocins. Commensal microorganisms can contribute to indirect, immune-mediated protection by triggering the proper maturation of the mucosa-associated lymphoid tissue and maintaining immunological inflammation through Treg and Th17 cells. Peptidoglycan stimulates AMP and mucin production in the intestinal environment through RIP2 and NF-κβ. Adaptive mechanism of microbial regulation involves the production of sIgA via the T follicular helper (TFH) cells. Treg regulatory T-cells, AMP antimicrobial peptides, RIP2 receptor-interacting protein 2, NFκβ nuclear factor-κβ, sIgA secretory IgA

genetic studies of other models (Levy et al. 2015). A number of studies have been conducted using gnotobiotic mice to investigate the effect of a single or a consortium of bacteria on intestinal homeostasis, as well as affecting local and systemic immunity (Fiebiger et al. 2016). An innate immune response in the gut is first triggered when luminal contents and organisms directly interact with intestinal epithelial cells (IECs). Pattern-recognition receptors (PRRs) of microorganisms strike an equilibrium between the host and microbes. This further leads to the production of cytokines and chemokines necessary to synchronize a protective immune response (Fukata and Arditi 2013). The proper activation of PRRs is so crucial that their inappropriate activation might lead to overexpression of immune responses, inflammatory disease, or even autoimmune conditions. Thus, positive feedback loops and cross-regulation are necessary to tightly regulate PRR expression (Cao 2016). Antimicrobial peptides are essential components of the innate immune system, whose expression is directly related to the type of microbes present in the microbiota, and they work to limit the pathogen interaction with the epithelium (Vandamme et al. 2012). The gut microbiota can also influence the immune response by using dietary supplements, host products, or other microbial metabolites (Chen and

Association of Probiotics and Prebiotics with Human Microbiome and. . .

105

Stappenbeck 2019). Metabolites such as short-chain fatty acids (SCFAs), tryptophan metabolites (Boya et al. 2021; Kumar et al. 2021), and bile acid derivatives are reported to possess immunoprotective abilities. In addition to enhancing the production of antimicrobial peptides and mucus, SCFAs maintain intestinal homeostasis and play a crucial role in the proliferation of innate lymphoid cells which are important to the induction of antimicrobial molecules by epithelial cells (Schnupf et al. 2018). Tryptophan metabolites such as indoles act as ligands for the aryl hydrocarbon receptor, a receptor having a notable role in the maintenance of intestinal homeostasis (Lloyd-Price et al. 2019; Rannug 2020; Kumar et al. 2021). In addition to promoting intestinal homeostasis, bile acid derivatives also activate farnesoid X receptors and G protein-coupled bile acid receptors to affect a wide range of host functions (Baars et al. 2015). Thus, microbial metabolites greatly influence the functioning and maintenance of the host immune system.

4 Role of Gut Microbiota in Immunity The gut microbiota can be defined as the group of organisms inhabiting and interacting within the gastrointestinal tract of the human system (Grice and Segre 2011). Such a population may be comprised of commensal, mutualistic, or pathogenic organisms which form a complex ecosystem with distinct characteristics that eventually adapt to the environmental conditions of a particular niche (Whiteside et al. 2015; Ogunrinola et al. 2020). The interplay of these various interactions influences the immunity of a human being. The establishment of indigenous microbiota initiates during birth. It continues till death evolving through various stages of host-related features like age, diet, inherited genes, way of living, hormonal changes, and underlying disease at any given time (Whiteside et al. 2015). Interaction between the microbes and the immune system occurs in the gastrointestinal tract. The selection of the commensals over the pathogenic microorganisms through competition for nutrients drives the evolution of the immune system (Mezouar et al. 2018). For instance, commensal like Escherichia coli competes with enterohemorrhagic strains over amino acids and other organic acids (Momose et al. 2008a, b). Additionally, the indigenous microflora outcompetes pathogenic organisms by the production of antimicrobials, such as bacteriocins or indirect resistance against pathogens mediated by immune systems (Mezouar et al. 2018). For example, mice can be protected against Listeria monocytogenes by a bacteriocin produced in vivo from Lactobacillus salivarius UCC118 (Corr et al. 2007). Several studies on axenic (germ-free) and specific-pathogen-free mice help to demonstrate the role of the microbiome in shaping the immune system throughout. Conversely, the immune system controls the host microflora through compartmentalization and stratification, thereby separating mucosal immune responses geographically and functionally from systemic immune responses (Mezouar et al. 2018). The mucus and the antimicrobial molecules are responsible for stratification or segregation, whereas the mucosal-associated lymphoid tissue provides immune

106

P. Dey et al.

compartmentalization towards commensal bacteria. Moreover, the adaptive immune response of the mammalian system is greatly influenced by the composition of the microbiota (Rojo et al. 2017). Recent studies report that the absence of the microbiota or simple alteration of commensal bacteria might induce type II immunity or even allergies due to immune response anomaly. Commensal microbiota and dietary antigens contribute to the high concentration of organisms in the gut, affecting the intestinal immune system and its ability to eliminate pathogens. In such a case, homeostasis is achieved by the activation of regulatory T-cells or Tregcells (Thomas et al. 2017). In summary, immune homeostasis is achieved by the finely interwoven interaction between the microbiome and the immune system, which can be further used to justify various multifactorial diseases. However, the cause of such diseases is still unclear whether it occurs due to those alterations or as a consequence of immune system modifications that are directly related to those diseases.

5 The Role of Probiotics and Prebiotics in Immune System Elie Metchnikoff was the first scientist to propose the correlation between the consumption of beneficial lactic acid-producing bacteria with the reduction of toxin-producing bacteria within the colon, which eventually promoted homeostasis within the host. He experimentally established this fact by isolating Bacillus bulgaricus and using it as a therapy to maintain homeostasis (Mackowiak 2013). This finding brought limelight to the regular use of yogurt as a major source of probiotics (Mackowiak 2013). Probiotics are defined by the World Health Organization (WHO) as live microorganisms that confer health benefits in humans when administered in adequate quantities (WHO 2001). Consequently, another term came into existence which was prebiotics or oligosaccharide food components that cannot be directly digested by the host but can stimulate the activity of specific members of the gut microbiota, which eventually proves to be beneficial for the host’s health (Gibson et al. 2004). For example, fibre carbohydrates such as pectin, cellulose, betaglucan, gums, and lignin cannot be digested in the upper gastrointestinal tract due to a lack of these carbohydrate-specific degrading enzymes (Gloux et al. 2011). Alternatively, when these substances are present in the colon, they are selectively fermented by gut bacteria into SCFAs, acetate, propionate, butyrate, and lactate (Ríos-Covián et al. 2016). Probiotics have also been reported to enhance the treatment of GI-tract related dysfunctions (Vieira et al. 2013). The impact of probiotics in preventing diarrhoea in newborns and children has been validated by clinical trials. A diet supplemented with Bifidobacterium lactis and Streptococcus thermophilus was found to reduce antibiotic-associated diarrhoea in infants (Correa et al. 2005). Probiotics and prebiotics when administered in combination are known as symbiotics, which show synergistic actions. In addition to prebiotics, living bacteria (probiotics) could be administered to enhance the host’s health by utilizing the energy source (Vieira et al. 2013; Siddique et al. 2022).

Association of Probiotics and Prebiotics with Human Microbiome and. . .

107

6 Metabolism and Immune System The dietary consumption pattern and their metabolism are known to showcase notable influence on the functioning and sustainability of the immune system. In many ways, nutrient metabolism and the immune system are interconnected, ranging from development, proliferation, and various effector functions to endocrine signalling and even direct sensing of nutrients by immune cells (Kau et al. 2011; Ganeshan and Chawla 2014). Table 1 represents a number of immune-cell-associated sensors which are involved in the coordination of local immune responses based on nutrient or metabolite information (Kau et al. 2011). Elucidating the leptin signalling system could throw some light on the complex signalling interactions within the body. Leptin is a pleiotropic cytokine which is associated with the regulation of appetite. Maintaining thymic output and cell density promotes the dominance of T helper 1 (TH1) cells over T helper 2 (TH2) cells while suppressing Treg cell proliferation. The leptin influences cellular immunity during periods of nutrient deprivation (La Cava and Matarese 2004; Matarese et al. 2005). It also affects innate immune cells. For instance, a mouse model with a mutated leptin receptor showed increased susceptibility to severe disease when exposed to Entamoeba histolytica. A number Table 1 Metabolite sensors associated with immune cells Sensor TLR4, CD14 mTOR PKR AHR RAR–RXR GPR120 GPR43 P2X receptors VDR–RXR SERCA NLRX1 NLRC3

Effector response Bactericidal activity, vascular permeability Inhibits Treg-cell proliferation, differentiation, function, and maintenance, promotes TH1-cell differentiation Promotes insulin resistance through inhibitory phosphorylation of IRS-1 TH17-cell differentiation and IL-22 production by TH17 cells, promotes Treg-cell induction Promotes intestinal T-cell homing, promotes Treg-cell generation, promotes TH2-cell differentiation over TH1 cells Inhibits inflammatory cytokine production and chemotaxis by macrophages Promotes resolution of intestinal inflammation Promotes TH17-cell generation Inhibits lymphocyte proliferation, inhibits interferon-γ, IL-17, and IL-2 expression, promotes emergence of Treg cells, promotes T-cell expression of CCR10 Anti-tumour signalling in T-cells Regulation of the host innate immune response in the context of pathogen sensing, inflammation, ROS production, ER stress, and autophagy Suppressor of T-cell activation

TLR4 toll-like receptor, mTOR mammalian target of rapamycin, PKR protein kinase-R, AHR aryl hydrocarbon receptor, RAR–RXR retinoic acid receptor–retinoid X receptor, GPR G proteincoupled receptors, VDR vitamin D receptor, SERCA sarco/endoplasmic reticulum; NLRX1 nucleotide-binding domain and leucine-rich repeat-containing protein X, NLRC3 NLR family CARD domain containing 3, IRS-1 insulin receptor substrate-1, CCR10 C-C motif chemokine receptor 10, ROS reactive oxygen species; endoplasmic reticulum, IL interleukin

108

P. Dey et al.

of engineered mutations in the leptin receptor were also studied on mice with misfolded liver cells (Tyr1138Ser and Tyr985Leu, both of which disrupt signalling in humans). As a result of these mutations, mice became more susceptible to E. histolytica infection. A leptin-receptor deficiency and E. histolytica pathogenesis provide an opportunity to explore the intersections between the immune and endocrine systems, enteric infection, and gut microbiology (Guo et al. 2011). Utilization of macronutrients is essential for generating and maintaining protective effector immunity. There is a noticeable increase in glucose and amino acid uptake by T-cells as they meet metabolic needs when stimulated and co-stimulated through T-cell receptor and CD28, respectively (Fox et al. 2005; Michalek and Rathmell 2010). SCFAs demonstrate that the microbiota and host diet work together to shape immune responses. SCFAs being the end products of macronutrients via microbial fermentation cannot be digested by humans alone as the human genome does not encode glycoside hydrolases and polysaccharide lyases (Qin et al. 2010). These enzymes are encoded by the microbiome which bears the ability to cleave the glycans made of variety of glycosidic linkages. Research studies clearly reflect the relatedness of nutrient metabolism with the functioning of the immune system.

7 Role of Micronutrients The intestinal microbiota plays a substantial role in the synthesis of micronutrients, i.e., vitamins and minerals, which play a crucial role in microbial and host metabolism. These vitamins include vitamin B12 or cobalamin, vitamin B6 or pyridoxal phosphate, vitamin B5 or pantothenic acid, vitamin B3 or niacin, vitamin K, biotin, and tetrahydrofolate (Kau et al. 2011). Gut microbes are also associated with the production of a wide range of molecules from non-absorbed dietary vitamin B12, known as corrinoids which can be absorbed easily (Allen and Stabler 2008; Goodman et al. 2009). Various metabolites produced by the gut microbiota perform numerous roles, such as folate and cobalamin affect host DNA methylation, whereas microbial fermentation-aided acetate modifies chromatin structure and gene transcription through histone acetylation (Kau et al. 2011). The importance of micronutrients associated with the immune system is evident by the fact that their deficiencies could lead to several immune dysfunctions. Studies have reported that vitamin A deficiency can lead to immune malfunction with increased susceptibility to infection (Hall et al. 2011). Additionally, deficiencies in vitamins A, D, and E and zinc are reported to affect many immune responses, particularly T-cell responses. Furthermore, vitamin A, which is absorbed from fruits and vegetables, is enzymatically converted to retinoic acid, which is assigned to multiple immune processes like the development of lymphoid tissue during embryogenesis (van de Pavert et al. 2009). Retinoic acid is associated with a wide range of functions, starting from activation of mucosal adaptive immune responses, development of CD103+ intestinal dendritic cells from their precursors to differentiation of ILC3s (type 3 innate lymphoid cells), which is a subtype of lymphoid tissue inducer cells and is important

Association of Probiotics and Prebiotics with Human Microbiome and. . .

109

for the production of lymph nodes, etc. (Klebanoff et al. 2013; Beijer et al. 2014; Spencer et al. 2014). Zinc is another dietary essential trace element whose deficiency is sufficient to induce an imbalance between TH1 cell and TH2 cell functions as well as impairment of natural killer cell functioning (Prasad 2008). Zinc deficiency is a common problem in sub-Saharan Africa and South Asia, where it accounts for a considerable number of mortality cases (Wessells and Brown 2012). The most common deficiency of micronutrients is iron deficiency, which affects more than 25% of people globally. Iron is critical for innate immune responses to bacteria as it is essential for the differentiation of monocyte to macrophages and for restricting intracellular bacteria by the NADPH-mediated oxidative burst (Cherayil 2011). Micronutrients are therefore critical for maintaining the immune system’s structural and functional integrity.

8 Role of Environmental Factors on Immune Systems Microbiome composition in the human body is primarily derived from two factors viz. (1) genetic or immunological factors and (2) environmental biodiversity. Human diet and daily hygienic practices are two environmental correlates leading to construct the shape of the gut microbiome (Gupta et al. 2017). Several other lifestyles and environmental factors that can also affect human well-being include changes in diet, physical activity, lifestyle, ageing, exposure to xenobiotics (Kelsen and Wu 2012). A rise in autoimmune, inflammatory, and metabolic diseases may be linked to post-industrial societies adopting new lifestyles and environmental factors, compared with conditions prevalent during human evolution. There are also several environmental pollutants including heavy metals, phthalates, bisphenol A, and particulate matter that may negatively impact our mental and neurological health by altering the intricate microbiota–gut–brain axis (Singh et al. 2022). Evolutionary factors consist of two main categories: phylogeny of hosts plays a crucial role in microbiome composition and differential diets affect different subsets of bacteria at different times (Groussin et al. 2017). The clinical manifestations of undernutrition range from asymptomatic, mild micronutrient deficiencies to life-threatening conditions such as Marasmus and Kwashiorkor. Malnutrition and undernutrition remain momentous public health worries in low and middle-income countries (LMICs), contributing to 45% of mortality in children under 5 years old (Caulfield et al. 2004). Growing children are vitally dependent on their gut microbiota for their health and well-being. As a child grows, a combination of habits, such as lifestyles and diets, may affect its richness and diversity (Di Profio et al. 2022). Undernutrition can be defined as insufficient caloric intake and malnutrition denotes insufficient quantities of specific nutrients and vitamins. In the developing gut, it is unclear how nutrient deficiency affects the microbiota and microbiome, whether in the mother or child. The microbiota of a mother may be impacted by nutrient deficiencies by altering her gut microbiota or milk nutrients and immunity. We still have a lot to learn about the development of infant microbiota during the suckling of breast milk, whether a

110

P. Dey et al.

mother is healthy or malnourished, and how breast milk and the infant microbiota co-evolve. A better understanding of how gut’s microbiome is affected by malnutrition is needed which may indeed lead to improved clinical outcomes. The gut’s microbial metabolic organ could be delayed by malnutrition or shifted towards a permanently altered configuration that increases disease risk by inhibiting the essential functions. Patients suffering from severe forms of malnutrition often exhibit many symptoms of environmental enteropathy. The small intestine is mainly affected by environmental enteropathy, which is also known as tropical sprue or tropical enteropathy. People with this disorder are often exposed to faecalcontaminated water and food, as well as living in areas with poor sanitation (Campbell et al. 2003; Ferreira et al. 2010; Kau et al. 2011). Currently, antibiotic treatment and diet are the most well-studied environmental factors in diversifying human microbiota. It is undeniable that antibiotics are proven as a much needed solution to infectious diseases, and the introduction of the same has revolutionized the healthcare system. Antibiotic use during childhood, however, appears to be associated with a range of immune-mediated disorders, including allergies and inflammatory bowel disease (IBD). Antibiotic intake has profound effects on the gut microbiota and may have long-term negative consequences on the host (Russell et al. 2012; Becattini et al. 2016; Yamamoto-Hanada et al. 2017). The role of dietary microbiota modulation in host immunity has been studied in recent years. In the USA, an average person consumes over 70 kg of sugar/year, which has become a dominant factor in the Western diet. In addition, increasing additives, such as emulsifiers, salt, and sugar, enhances the durability and palatability of food in Western diets which profoundly alters gut microbiome configuration and adversely impacts the immune system of hosts (Johnson et al. 2007; Monteiro et al. 2013; Christ et al. 2019). Chemically induced murine colitis can also be aggravated by a high-fat diet which disrupts intestinal dendritic cells homeostasis by decreasing butyrate and retinoic acid levels (Cheng et al. 2016). Long-chain fatty acids may aggravate autoimmunity in the central nervous system by modulating gut microbiota and metabolome. It has been demonstrated that the consumption of carbohydrates, probiotics, emulsifiers, and artificial sweeteners can regulate immunity and body inflammation through changing the composition of the gut microbiome in mice (Haghikia et al. 2015; He et al. 2017; Rodriguez-Palacios et al. 2018). There is also evidence that timing of dietary intake along with quantity and content influences microbiome composition and immunity. An intermittent fasting regime reduces the severity of disease in an autoimmune murine model with encephalomyelitis and multiple sclerosis by balancing IL-17 production and Treg cells, mediated by the microbiota (Cignarella et al. 2018). Dysbiosis, which affects the composition of microbiomes as well as their metagenomic function, is linked to many multifactorial diseases that continue to increase in incidence. Implementation of practices like breastfeeding, adding zinc and vitamins to diets, improving hygiene measures as hand washing, and optimizing acute severe malnutrition treatment could enrich the body’s immunity and the subsequent health of the gut microbiota. The World Health Organization (WHO)

Association of Probiotics and Prebiotics with Human Microbiome and. . .

111

estimates a 40% reduction in infant mortality by 2025 if one compliance with these practices (WHO 2013).

9 Conclusion A human gut microbiome is a signalling hub that integrates environmental and genetic inputs to influence metabolism, immunity, and infection resistance. It is important to study gut microbiome in order to gain a deeper understanding of how humans interact with their indigenous microbiota. To combat life-threatening diseases, further research studies are needed to optimize these organisms. In addition, the rampant use of wide-spectrum antibiotics is disrupting the human microbiota and leading to a microbial imbalance, facilitating pathogen invasion. It is always difficult to define the diet that humans evolved to eat, and our culture, customs, and technology make observing our natural diet very challenging. Microbiota modulates much of what we eat, and we respond to different diets based on our microbiomes. In order to develop probiotic therapies for the treatment of infectious diseases with preand probiotics, more research is needed. In the future, we will still need to gain a deeper understanding of the interactions between diet, the microbiome, and the immune system to design diets with better disease-resolution potential.

References Allen RH, Stabler SP (2008) Identification and quantitation of cobalamin and cobalamin analogues in human feces. Am J Clin Nutr 87(5):1324–1335 Baars A, Oosting A, Knol J, Garssen J, van Bergenhenegouwen J (2015) The gut microbiota as a therapeutic target in IBD and metabolic disease: a role for the bile acid receptors FXR and TGR5. Microorganisms 3(4):641–666 Becattini S, Taur Y, Pamer EG (2016) Antibiotic-induced changes in the intestinal microbiota and disease. Trends Mol Med 22(6):458–478 Beijer MR, Kraal G, den Haan JM (2014) Vitamin A and dendritic cell differentiation. Immunology 142(1):39–45 Belkaid Y, Hand TW (2014) Role of the microbiota in immunity and inflammation. Cell 157(1): 121–141 Bonilla FA, Oettgen HC (2010) Adaptive immunity. J Allergy Clin Immunol 125(2 Suppl 2):S33– S40 Boya BR, Kumar P, Lee JH, Lee J (2021) Diversity of the tryptophanase gene and its evolutionary implications in living organisms. Microorganisms 9(10):2156 Campbell DI, Murch SH, Elia M, Sullivan PB, Sanyang MS, Jobarteh B, Lunn PG (2003) Chronic T cell-mediated enteropathy in rural west African children: relationship with nutritional status and small bowel function. Pediatr Res 54(3):306–311 Cao X (2016) Self-regulation and cross-regulation of pattern-recognition receptor signalling in health and disease. Nat Rev Immunol 16(1):35–50

112

P. Dey et al.

Caulfield LE, de Onis M, Blössner M, Black RE (2004) Undernutrition as an underlying cause of child deaths associated with diarrhea, pneumonia, malaria, and measles. Am J Clin Nutr 80(1): 193–198 Chen F, Stappenbeck TS (2019) Microbiome control of innate reactivity. Curr Opin Immunol 56: 107–113 Cheng L, Jin H, Qiang Y, Wu S, Yan C, Han M, Xiao T, Yan N, An H, Zhou X, Shao Q, Xia S (2016) High fat diet exacerbates dextran sulfate sodium induced colitis through disturbing mucosal dendritic cell homeostasis. Int Immunopharmacol 40:1–10 Cherayil BJ (2011) The role of iron in the immune response to bacterial infection. Immunol Res 50(1):1–9 Christ A, Lauterbach M, Latz E (2019) Western diet and the immune system: an inflammatory connection. Immunity 51(5):794–811 Chu H, Mazmanian S (2013) Innate immune recognition of the microbiota promotes host-microbial symbiosis. Nat Immunol 14:668–675 Cignarella F, Cantoni C, Ghezzi L, Salter A, Dorsett Y, Chen L, Phillips D, Weinstock GM, Fontana L, Cross AH, Zhou Y, Piccio L (2018) Intermittent fasting confers protection in CNS autoimmunity by altering the gut microbiota. Cell Metab 27(6):1222–35.e6 Corr SC, Li Y, Riedel CU, O'Toole PW, Hill C, Gahan CG (2007) Bacteriocin production as a mechanism for the anti-infective activity of Lactobacillus salivarius UCC118. Proc Natl Acad Sci U S A 104(18):7617–7621 Correa NB, Peret Filho LA, Penna FJ, Lima FM, Nicoli JR (2005) A randomized formula controlled trial of Bifidobacterium lactis and Streptococcus thermophilus for prevention of antibioticassociated diarrhea in infants. J Clin Gastroenterol 39:385–389 Dethlefsen L, McFall-Ngai M, Relman D (2007) An ecological and evolutionary perspective on human–microbe mutualism and disease. Nature 449:811–818 Di Profio E, Magenes VC, Fiore G, Agostinelli M, La Mendola A, Acunzo M, Francavilla R, Indrio F, Bosetti A, D'Auria E, Borghi E, Zuccotti G, Verduci E (2022) Special diets in infants and children and impact on gut microbioma. Nutrients 14(15):3198 Ferreira RB, Antunes LC, Finlay BB (2010) Should the human microbiome be considered when developing vaccines? PLoS Pathog 6(11):e1001190 Fiebiger U, Bereswill S, Heimesaat MM (2016) Dissecting the interplay between intestinal microbiota and host immunity in health and disease: lessons learned from germfree and gnotobiotic animal models. Eur J Microbiol Immunol 6(4):253–271 Food and Agriculture Organization and World Health Organization Expert Consultation (2001) Evaluation of health and nutritional properties of powder milk and live lactic acid bacteria. Food and Agriculture Organization of the United Nations and World Health Organization, Córdoba Fox CJ, Hammerman PS, Thompson CB (2005) Fuel feeds function: energy metabolism and the T-cell response. Nat Rev Immunol 5(11):844–852 Fukata M, Arditi M (2013) The role of pattern recognition receptors in intestinal inflammation. Mucosal Immunol 6(3):451–463 Ganeshan K, Chawla A (2014) Metabolic regulation of immune responses. Annu Rev Immunol 32: 609–634 Gibson GR, Probert HM, Loo JV, Rastall RA, Roberfroid MB (2004) Dietary modulation of the human colonic microbiota: updating the concept of prebiotics. Nutr Res Rev 17:259–275 Gloux K, Berteau O, El Oumami H, Beguet F, Leclerc M, Dore J (2011) A metagenomic betaglucuronidase uncovers a core adaptive function of the human intestinal microbiome. Proc Natl Acad Sci U S A 108(Suppl 1):4539–4546 Goodman AL, McNulty NP, Zhao Y, Leip D, Mitra RD, Lozupone CA, Knight R, Gordon JI (2009) Identifying genetic determinants needed to establish a human gut symbiont in its habitat. Cell Host Microbe 6(3):279–289 Grice EA, Segre JA (2011) The skin microbiome. Nat Rev Microbiol 9(4):244–253. Erratum in: Nature Reviews Microbiology. 2011; 9(8):626.

Association of Probiotics and Prebiotics with Human Microbiome and. . .

113

Groussin M, Mazel F, Sanders JG, Smillie CS, Lavergne S, Thuiller W, Alm EJ (2017) Unraveling the processes shaping mammalian gut microbiomes over evolutionary time. Nat Commun 8: 14319 Guo X, Roberts M, Becker S et al (2011) Leptin signaling in intestinal epithelium mediates resistance to enteric infection by Entamoeba histolytica. Mucosal Immunol 4:294–303 Gupta VK, Paul S, Dutta C (2017) Geography, ethnicity or subsistence-specific variations in human microbiome composition and diversity. Front Microbiol 8:1162 Hacquard S, Garrido-Oter R, González A, Spaepen S, Ackermann G, Lebeis S, McHardy AC, Dangl JL, Knight R, Ley R, Schulze-Lefert P (2015) Microbiota and host nutrition across plant and animal kingdoms. Cell Host Microbe 17(5):603–616 Haghikia A, Jörg S, Duscha A, Berg J, Manzel A, Waschbisch A, Hammer A, Lee DH, May C, Wilck N, Balogh A, Ostermann AI, Schebb NH, Akkad DA, Grohme DA, Kleinewietfeld M, Kempa S, Thöne J, Demir S, Müller DN, Gold R, Linker RA (2015) Dietary fatty acids directly impact central nervous system autoimmunity via the small intestine. Immunity 43(4):817–829. Erratum in: Immunity 2016; 44(4):951–3. Hall JA, Grainger JR, Spencer SP, Belkaid Y (2011) The role of retinoic acid in tolerance and immunity. Immunity 35(1):13–22 He B, Hoang TK, Wang T, Ferris M, Taylor CM, Tian X, Luo M, Tran DQ, Zhou J, Tatevian N, Luo F, Molina JG, Blackburn MR, Gomez TH, Roos S, Rhoads JM, Liu Y (2017) Resetting microbiota by Lactobacillus reuteri inhibits Treg deficiency-induced autoimmunity via adenosine A2A receptors. J Exp Med 214(1):107–123 Hillion S, Arleevskaya MI, Blanco P, Bordron A, Brooks WH, Cesbron JY, Kaveri S, Vivier E, Renaudineau Y (2020) The innate part of the adaptive immune system. Clin Rev Allergy Immunol 58(2):151–154 Integrative HMP (iHMP) Research Network Consortium (2019) The integrative human microbiome project. Nature 569(7758):641–648 Johnson RJ, Segal MS, Sautin Y, Nakagawa T, Feig DI, Kang DH, Gersch MS, Benner S, SánchezLozada LG (2007) Potential role of sugar (fructose) in the epidemic of hypertension, obesity and the metabolic syndrome, diabetes, kidney disease, and cardiovascular disease. Am J Clin Nutr 86(4):899–906 Kau AL, Ahern PP, Griffin NW, Goodman AL, Gordon JI (2011) Human nutrition, the gut microbiome and the immune system. Nature 474(7351):327–336 Kelsen JR, Wu GD (2012) The gut microbiota, environment and diseases of modern society. Gut Microbes 3(4):374–382 Klebanoff CA, Spencer SP, Torabi-Parizi P, Grainger JR, Roychoudhuri R, Ji Y, Sukumar M, Muranski P, Scott CD, Hall JA, Ferreyra GA, Leonardi AJ, Borman ZA, Wang J, Palmer DC, Wilhelm C, Cai R, Sun J, Napoli JL, Danner RL, Gattinoni L, Belkaid Y, Restifo NP (2013) Retinoic acid controls the homeostasis of pre-cDC-derived splenic and intestinal dendritic cells. J Exp Med 210(10):1961–1976 Kumar P, Lee JH, Lee J (2021) Diverse roles of microbial indole compounds in eukaryotic systems. Biol Rev Camb Philos Soc 96(6):2522–2545 La Cava A, Matarese G (2004) The weight of leptin in immunity. Nat Rev Immunol 4(5):371–379 Levy M, Thaiss CA, Elinav E (2015) Metagenomic cross-talk: the regulatory interplay between immunogenomics and the microbiome. Genome Med 7:120 Lloyd-Price J, Arze C, Ananthakrishnan AN et al (2019) Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases. Nature 569:655–662 Lynch JB, Hsiao EY (2019) Microbiomes as sources of emergent host phenotypes. Science 365(6460):1405–1409 Mackowiak PA (2013) Recycling Metchnikoff: probiotics, the intestinal microbiome and the quest for long life. Front Public Health 1:52 Macpherson AJ, Geuking MB, McCoy KD (2005) Immune responses that adapt the intestinal mucosa to commensal intestinal bacteria. Immunology 115(2):153–162

114

P. Dey et al.

Matarese G, Moschos S, Mantzoros CS (2005) Leptin in immunology. J Immunol 174(6): 3137–3142 Mezouar S, Chantran Y, Michel J, Fabre A, Dubus J-C, Leone M, Sereme Y, Mège J-L, Ranque S, Desnues B, Chanez P, Vitte J (2018) Microbiome and the immune system: from a healthy steady-state to allergy associated disruption. Human Microb J 10:11–20 Michalek RD, Rathmell JC (2010) The metabolic life and times of a T-cell. Immunol Rev 236:190– 202 Momose Y, Hirayama K, Itoh K (2008a) Competition for proline between indigenous Escherichia coli and E. coli O157:H7 in gnotobiotic mice associated with infant intestinal microbiota and its contribution to the colonization resistance against E. coli O157:H7. Antonie Van Leeuwenhoek 94(2):165–171 Momose Y, Hirayama K, Itoh K (2008b) Effect of organic acids on inhibition of Escherichia coli O157:H7 colonization in gnotobiotic mice associated with infant intestinal microbiota. Antonie Van Leeuwenhoek 93(1–2):141–149 Monteiro CA, Moubarac JC, Cannon G, Ng SW, Popkin B (2013) Ultra-processed products are becoming dominant in the global food system. Obes Rev 14(Suppl 2):21–28 Ogunrinola GA, Oyewale JO, Oshamika OO, Olasehinde GI (2020) The human microbiome and its impacts on health. Int J Microbiol 2020:8045646 Parkin J, Cohen B (2001) An overview of the immune system. Lancet 357(9270):1777–1789 Petersen C, Round JL (2014) Defining dysbiosis and its influence on host immunity and disease. Cell Microbiol 16(7):1024–1033 Peterson J, Garges S, Giovanni M, McInnes P, Wang L, Schloss JA, Bonazzi V, McEwen JE, Wetterstrand KA, Deal C, Baker CC, Di Francesco V, Howcroft TK, Karp RW, Lunsford RD, Wellington CR, Belachew T, Wright M, Giblin C, David H, Mills M, Salomon R, Mullins C, Akolkar B, Begg L, Davis C, Grandison L, Humble M, Khalsa J, Little AR, Peavy H, Pontzer C, Portnoy M, Sayre MH, Starke-Reed P, Zakhari S, Read J, Watson B, Guyer M (2009) The NIH human microbiome project. Genome Res 19(12):2317–2323 Prasad AS (2008) Zinc in human health: effect of zinc on immune cells. Mol Med 14(5–6):353–357 Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, Mende DR, Li J, Xu J, Li S, Li D, Cao J, Wang B, Liang H, Zheng H, Xie Y, Tap J, Lepage P, Bertalan M, Batto JM, Hansen T, Le Paslier D, Linneberg A, Nielsen HB, Pelletier E, Renault P, Sicheritz-Ponten T, Turner K, Zhu H, Yu C, Li S, Jian M, Zhou Y, Li Y, Zhang X, Li S, Qin N, Yang H, Wang J, Brunak S, Doré J, Guarner F, Kristiansen K, Pedersen O, Parkhill J, Weissenbach J, MetaHIT Consortium, Bork P, Ehrlich SD, Wang J (2010) A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464(7285):59–65 Rannug A (2020) How the AHR became important in intestinal homeostasis—a diurnal FICZ/ AHR/CYP1A1 feedback controls both immunity and immunopathology. Int J Mol Sci 21(16): 5681 Ríos-Covián D, Ruas-Madiedo P, Margolles A, Gueimonde M, de Los Reyes-Gavilán CG, Salazar N (2016) Intestinal short chain fatty acids and their link with diet and human health. Front Microbiol 7:185 Rodriguez-Palacios A, Harding A, Menghini P, Himmelman C, Retuerto M, Nickerson KP, Lam M, Croniger CM, McLean MH, Durum SK, Pizarro TT, Ghannoum MA, Ilic S, McDonald C, Cominelli F (2018) The artificial sweetener Splenda promotes gut proteobacteria, dysbiosis, and myeloperoxidase reactivity in Crohn’s disease-like ileitis. Inflamm Bowel Dis 24(5):1005–1020 Rojo D, Méndez-García C, Raczkowska BA, Bargiela R, Moya A, Ferrer M, Barbas C (2017) Exploring the human microbiome from multiple perspectives: factors altering its composition and function. FEMS Microbiol Rev 41(4):453–478 Russell SL, Gold MJ, Hartmann M, Willing BP, Thorson L, Wlodarska M, Gill N, Blanchet MR, Mohn WW, McNagny KM, Finlay BB (2012) Early life antibiotic-driven changes in microbiota enhance susceptibility to allergic asthma. EMBO Rep 13(5):440–447 Schnupf P, Gaboriau-Routhiau V, Cerf-Bensussan N (2018) Modulation of the gut microbiota to improve innate resistance. Curr Opin Immunol 54:137–144

Association of Probiotics and Prebiotics with Human Microbiome and. . .

115

Siddique F, Akram K, Alghamdi ES, Arshad Q, Siddique A (2022) The immunomodulatory role of probiotics. In: Robles EF (ed) Prebiotics and probiotics—from food to health. IntechOpen, London Singh S, Sharma P, Pal N, Kumawat M, Shubham S, Sarma DK, Tiwari RR, Kumar M, Nagpal R (2022) Impact of environmental pollutants on gut microbiome and mental health via the gut-brain axis. Microorganisms 10(7):1457 Spencer SP, Wilhelm C, Yang Q, Hall JA, Bouladoux N, Boyd A, Nutman TB, Urban JF Jr, Wang J, Ramalingam TR, Bhandoola A, Wynn TA, Belkaid Y (2014) Adaptation of innate lymphoid cells to a micronutrient deficiency promotes type 2 barrier immunity. Science 343(6169):432–437 Thaiss CA, Levy M, Suez J, Elinav E (2014) The interplay between the innate immune system and the microbiota. Curr Opin Immunol 26:41–48 Thaiss CA, Zmora N, Levy M, Elinav E (2016) The microbiome and innate immunity. Nature 535(7610):65–74 Thomas S, Izard J, Walsh E, Batich K, Chongsathidkiet P, Clarke G, Sela DA, Muller AJ, Mullin JM, Albert K, Gilligan JP, DiGuilio K, Dilbarova R, Alexander W, Prendergast GC (2017) The host microbiome regulates and maintains human health: a primer and perspective for non-microbiologists. Cancer Res 77(8):1783–1812 Turnbaugh P, Ley R, Hamady M et al (2007) The human microbiome project. Nature 449:804–810 van de Pavert SA, Olivier BJ, Goverse G, Vondenhoff MF, Greuter M, Beke P, Kusser K, Höpken UE, Lipp M, Niederreither K, Blomhoff R, Sitnik K, Agace WW, Randall TD, de Jonge WJ, Mebius RE (2009) Chemokine CXCL13 is essential for lymph node initiation and is induced by retinoic acid and neuronal stimulation. Nat Immunol 10(11):1193–1199 Vandamme D, Landuyt B, Luyten W, Schoofs L (2012) A comprehensive summary of LL-37, the factotum human cathelicidin peptide. Cell Immunol 280(1):22–35 Vieira AT, Teixeira MM, Martins FS (2013) The role of probiotics and prebiotics in inducing gut immunity. Front Immunol 12(4):445 Wessells KR, Brown KH (2012) Estimating the global prevalence of zinc deficiency: results based on zinc availability in national food supplies and the prevalence of stunting. PLoS One 7(11): e50568 Whiteside SA, Razvi H, Dave S, Reid G, Burton JP (2015) The microbiome of the urinary tract—a role beyond infection. Nat Rev Urol 12(2):81–90 WHO (2013) Guideline: updates on the management of severe acute malnutrition in infants and children. World Health Organization, Geneva Wiertsema SP, van Bergenhenegouwen J, Garssen J, Knippels LMJ (2021) The interplay between the gut microbiome and the immune system in the context of infectious diseases throughout life and the role of nutrition in optimizing treatment strategies. Nutrients 13(3):886 Yamamoto-Hanada K, Yang L, Narita M, Saito H, Ohya Y (2017) Influence of antibiotic use in early childhood on asthma and allergic diseases at age 5. Ann Allergy Asthma Immunol 119(1): 54–58

Human Microbiome and the Susceptibility to Infections V. T. Anju, Siddhardha Busi, Mahima S. Mohan, and Madhu Dyavaiah

Abstract Human body comprises trillions of microbial cells associated with different parts of the body. The composition of microorganisms is different in all the parts of the body. Skin, oral, respiratory, placental, gut, and vaginal microbiome are well explored and studied for their effect on human health and disease. The largest part of humans, skin contains millions of microorganisms. The largest and diverse microbiome is observed in gut region. Microbiome influences human health by modulating the innate and adaptive immune responses. There is a close connection between human microbiome with health and disease. Microbiome maintains an equilibrium state with the human body through the host–microbial symbiotic associations. The role of microbiome shaping the host immune functions and development is well explored. The balance of host system and microbiome may get altered by external or environmental stimuli like exposure to antibiotics. The frequent imbalance of microbiota is called as dysbiosis leading to pathological conditions. Dysbiosis associated with antibiotic treatment reduces the occurrence and number of commensals from body leading to the invasion of pathogens by breaking the colonization resistance. The restoration of microbiome is necessary to reduce the infections. Bacterial chemical signalling or quorum sensing plays important role in shaping the balance of microbiome, thereby reducing the pathogenic interactions. Keywords Microbiota · Host · Symbiosis · Immune system · Dysbiosis · Infections

V. T. Anju · M. Dyavaiah Department of Biochemistry and Molecular Biology, School of Life Sciences, Pondicherry University, Pondicherry, India S. Busi (✉) · M. S. Mohan Department of Microbiology, School of Life Sciences, Pondicherry University, Pondicherry, India e-mail: [email protected] © The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd. 2023 V. Kothari et al. (eds.), Probiotics, Prebiotics, Synbiotics, and Postbiotics, https://doi.org/10.1007/978-981-99-1463-0_7

117

118

V. T. Anju et al.

1 Introduction: Human Microbiome Human body consists of a complex environment where 10–100 trillions of microbial communities are inhabited, together called microbiome (Mohajeri et al. 2018). These inhabitants play vital role in the maintenance of host health, but sometimes it may lead to diseases. They can colonize on various body parts such as skin, gut, respiratory tract, urinary tract, genital tract, mammary glands, mucosal layers, etc. The colonization and establishment of microbiome initiate itself from the time of birth (Senn et al. 2020). Microbiome helps the host via metabolism, gut health, immune system, neural development, energy balance (Barko et al. 2018). Microbiome composition can be varied according to the factors such as diet, stress, antibiotics, infection, age that will affect the health of the host (Fig. 1). It can also be dynamic due to microbial transfer between the organisms. The microbiome keeps the host healthy as well as protects from the pathogens. The human microbiome research started with Human Microbiome Project studied millions of microbial inhabitants but the available studies are limited. Through high throughput sequencing, large number of samples can be sequenced simultaneously. Microbiome can be used as a target for treating various diseases through personalized medicines, which requires further studies. Microbiomes are necessary for maintaining the host metabolism and the health (Thomas et al. 2017). They help in the metabolism of drugs such as cardiac glycoside, digoxin by increasing the bioavailability of the drugs (Li et al. 2016). Recent studies show that Eggerthella lenta contains an operon for the reduction of digoxin (Young 2017). Microbes in the gut mediate the conversion of conjugated Fig. 1 The different factors affecting the microbial communities in host. Some factors regulate the composition of commensal microbes, whereas some factors mediate the dysbiosis of microbiome

Human Microbiome and the Susceptibility to Infections

119

bile salts to unconjugated bile acids, which leads to the formation of secondary bile acids (Kho and Lal 2018). Microbiome can also affect the immune system via modification of systemic and epithelial responses (Young 2017). Microbiome maintains the equilibrium of immune system and also the energy. Microbiota present in the female genital tract secretes cytokines, antimicrobial peptides, and inhibitory substances via innate immunity (Wang et al. 2022). Microorganisms such as Bifidobacterium spp., Bacteroides spp., and Enterobacteria are involved in the metabolism of vitamin K essential for the host development (Ogunrinola et al. 2020). With the help of next generation sequence (NGS) approaches, the characterisation of microbiome became easier and can get better understanding on effect of host health and disease progression. Therapeutic approaches are looking forward to the precision medicines, which are focusing on host variables influencing the health and treatment response (Seyhan and Carini 2019). The niche specific commensal microbiome is important in maintaining the host health and also affects the treatment, so it can be added as a parameter in precision medicines (Young 2017). Microbiome in precision medicines can be considered as potential method to avoid and/or cure the infections.

2 Microbial Interactions Microbiome affects the host health and also protects the host from invading pathogens. They can perform various metabolic activities involving bioconversion of metabolites which have effects on both the host and microbiota. These microbiomes act as commensals, symbionts, and pathogens to the human body. Interspecies interactions are crucial among microbiomes where they interact with other species in the form of mutualism, parasitism, and competition (Belizário and Napolitano 2015). Microbes co-evolve with the host from the birth and continue up to death. The major part of microbiome is acquired during the early life followed by other stages of life. The early life or infant microbiome can undergo huge modification influenced by the course of life and different dietary components. It has been studied that a stable microbiome develops by the age of 2–3 years (York 2019). Studies showed a slow colonization and succession rate in caesarean section-delivered infants in compared to vaginal birth newborns (Wampach et al. 2017). Microbiome actively adjusts with the niches and provides the well-being of the host. These microbes can restrict the invasion of foreign microbes by modifying the nutrient accessibility, inhabiting the available spaces, and also interacting the intruder via predation, competition, facilitation (Kurkjian et al. 2021). In mutualism, both the members are cooperative and benefitted. Recent study reported that the production of 6-N-hydroxyaminopurine (6-HAP) produced by commensal skin bacteria Staphylococcus epidermidis negatively affects the tumour growth via inhibition of DNA polymerase activity (Tshikantwa et al. 2018). In commensalism, one partner in the interaction is benefitted and other remains unaffected.

120

V. T. Anju et al.

3 Quorum Sensing (QS) in Microbiome Bacteria when present at high cell density interact to each other through the production of chemical signals. The process of chemical signalling among bacteria which regulate the bacterial functions is known as quorum sensing (Kalia et al. 2014; Kumar et al. 2015, 2020). The signals produced by bacteria during quorum sensing are known as autoinducers. In general, quorum sensing can regulate expression of several behaviours of bacteria including its virulence, pathogenicity, resistance, and competition (Pena et al. 2019). Quorum sensing mediated properties of bacteria include the synthesis and production of bioluminescence, formation of biofilms by human pathogenic microbes, symbiotic association of bacteria with marine animals, and degradation of plant tissues by the secreted pectinolytic enzymes (Waters and Bassler 2005). Recent studies showed that interspecies interactions in microbiome lead to the restoration of microbiome dysbiosis occurred through long-term antibiotic exposure (Stecher et al. 2010). In a mice model which received long-term exposure to streptomycin treatment caused the disruption of gut microbiota with decrease in the number of Firmicutes. Mice were then incubated with E. coli capable of synthesizing enhanced levels of autoinducer 2 in their gut. Autoinducer 2 mediated signalling is common in bacterial kingdom and especially in Vibrio spp. Surprisingly, the mice with engineered E. coli restored gut microbiota by increasing the phyla Firmicutes. Thus, autoinducer 2 was able to restore the effects of antibiotic treatment mediated gut symbiosis (Thompson et al. 2015). Autoinducer 2 mediated cell-to-cell signalling can restore the gut microbiome symbiosis along with the prevention of colonization of pathogens. Recently, autoinducer 2 signalling by V. cholerae was shown to inhibit the colonization of Ruminococcus obeum in the gut of a mouse model. The QS mediated signals also modulate host apoptosis and secretion of QS mediated immune mediator molecules. They are also involved in the epithelial cell differentiation and improve the function of epithelial cell barrier (Wu and Luo 2021; Hooper et al. 2012). The cross talk of microbiota with host system mediated by microbiota derived N-acyl homoserine signals is also studied. These inter-kingdom or intra-kingdom cell-to-cell communications are also associated with pathogenesis in host (Xue et al. 2021). For instance, autoinducers produced by a lung pathogen Pseudomonas aeruginosa like 3-oxo-C12-HSL and C4-HSL interfere with host immune responses and improve the growth of pathogens. In another study, murine fibroblasts and human lung epithelial cells showed stimulated pro-inflammatory gene expression by the production of 3-oxo-C12-HSL by P. aeruginosa (Kravchenko et al. 2008). Some of the acyl homoserine signals produced by bacteria can mediate cell apoptosis and inhibit contraction of smooth muscle. Studies showed that gut microbiota can produce signalling molecules through quorum sensing and act as microbiota derived metabolites and affect health of host systems (Jahoor et al. 2008).

Human Microbiome and the Susceptibility to Infections

121

4 Human Microbiome Studies related to the human microbiome are expanding, as it was important to know how it is affecting the human health and well-being. It is a dynamic complex system, which is affected by various factors. Change in any of the factors can disrupt the microbiome and leads to various illness. The use of antibiotics will negatively affect the gut microbiome by creating an unevenness in the microbial structure and also increase the antibiotic resistant bacteria (Hayes and Sahu 2020). Alteration in the normal commensal microbiome can cause dysbiosis to the host. Trillions of microbial cells are habituated in human body and each site is occupied with different types of microorganisms with change in distribution patterns. Some of the common microbiome and the dysbiosis microbiome present in various body sites such as skin, oral cavity, respiratory tract, gastrointestinal tract, placenta, vagina are described below (Table 1).

4.1

Skin Microbiome

The main part of human body, skin is composed of millions of microorganisms. Skin acts as a protective shield by creating an interface to the external environment, which is colonized by various bacteria, fungi, virus. Skin surface is having low pH, desiccated, and aerobic in nature, while the sebaceous gland units have anaerobic and lipid containing environment (Chen et al. 2018). Due to the change in the niche condition, glands and hair follicles make the skin more diverse with different kinds of microorganisms. Most of the microorganisms form symbiotic association or commensalism interaction with the host skin. These commensals occupy the niches and nutrients available in the skin and thereby prevent the attachment site to the invaders. The colonization of microbiome begins from the birth and changes at different stages of life. Similar to gut, the microbiome is essential for preventing the invading pathogens, improving immune system and breakdown of metabolites (Byrd et al. 2018). Factors that affect the microbiome composition are age, nutrition, hygiene, environment, immune system, underlying diseases, etc. Cutibacterium species are the predominant members of sebaceous gland sites, whereas Staphylococcus species and Corynebacterium species were predominant in moist areas (Byrd et al. 2018). Metagenomic studies reported that the dry skin sites were occupied with mixed populations such as Actinobacteria, Firmicutes, Proteobacteria, and Bacteriodetes. Genus Malassezia are the most prevalent fungi found at core body parts and arms, whereas microbial communities such as Aspergillus spp., Malassezia spp., Cryptococcus spp., Epicoccum spp., Rhodotorula spp., etc. were inhabited in the foot regions (Byrd et al. 2018). Molecular studies revealed that these sites are rich in phylogenetic diversity than the gut and oral cavity (Grice and Segre 2011).

122

V. T. Anju et al.

Table 1 Normal and dysbiosis microbiome associated with different body parts Site/body part Skin

Oral

Respiratory tract

Placenta

Normal microbiome Propionibacterium acnes, staphylococcus, Corynebacterium, Malassezia spp., aspergillus spp., Cryptococcus spp., Rhodotorula spp., Epicoccum spp. Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, Spirochaetes, Fusobacteria Streptococcus, Porphyromonas, Neisseria, Veillonella, Prevotella, Leptotrichia, Fusobacterium, aspergillus, Cladosporium, Eurotium, Penicillium Members of phyla Firmicutes, Tenericutes, Proteobacteria, Bacteroidetes, and Fusobacteria

Gut

Members of Ruminococcaceae family, Bifidobacterium, lactobacillus plantarum

Vagina

Lactobacillus

Dysbiosis microbiome Propionibacterium acnes, S. aureus, Corynebacterium mastitidis, Corynebacterium bovis, Proteobacteria spp.

References Byrd et al. (2018)

Candida, Firmicutes, Actinobacteria, Porphyromonas gingivalis, Tannerella forsythia, Treponema denticola Streptococcus pneumoniae, S. pyogenes, S. agalactiae, Moraxella, haemophilus, P. aeruginosa, Veillonella, Prevotella, haemophilus, Burkholderia

Verma et al. (2018)

Streptococcus agalactiae, Fusobacterium nucleatum, Ureaplasma parvum, Prevotella bivia, Corynebacterium spp., Escherichia coli, Peptostreptococcus magnus, genital mycoplasmas, Gardnerella spp., Arthrobacter, Klebsiella, Acinetobacter Clostridium difficile, campylobacter, enterococcus, streptococcus, staphylococcus, Escherichia coli Salmonella, Proteus, Klebsiella, Shigella, Bacteroides fragilis Gardnerella vaginalis, mycoplasma hominis, Mobiluncus spp., Bacteroides spp., Prevotella spp., Peptostreptococcus spp., Fusobacterium spp., Porphyromonas spp.

Pelzer et al. (2017)

Santacroce et al. (2020)

Mohajeri et al. (2018), Barko et al. (2018) and Tuddenham and Sears (2015)

Saraf et al. (2021)

Human Microbiome and the Susceptibility to Infections

4.2

123

Oral Microbiome

After gut, oral cavity harbours rich and diverse microorganisms, which is the second largest community in humans. Normal body temperature of the oral cavity and pH of the saliva (6.5–7) contribute a better niche for the growth and survival of microbiomes (Lim et al. 2017). The microbial communities that make up the oral microbiome are bacteria, fungi, archaea, virus, and protozoans. They exist in a highly regulated biofilm forms and are involved in homeostasis maintenance, oral cavity protection and prevents disease progression (Deo and Deshmukh 2019). Microbiome studies explored more than 392 taxa of microorganisms and approximately 700 species of prokaryotes were identified (Deo and Deshmukh 2019). Healthy oral cavity contains almost 96% of microorganisms such as Firmicutes (36.7%), Proteobacteria (17.1%), Bacteroidetes (17.1%), Actinobacteria (11.6%), Spirochaetes (7.9%), and Fusobacteria (5.2%) (Verma et al. 2018). The protozoans usually observed in oral cavity are Entamoeba gingivalis and Trichomonas tenax, whereas Candida species is the predominant fungal species (Deo and Deshmukh 2019). The oral microbiota exists in a highly regulated biofilm form. About 85% species of fungi were reported as an oral microbiome and Candida species was the most prevalent among them. Candida forms biofilm with Streptococcus, when the skin is injured. Viruses such as phage exist in the mouth and other viruses such as mumps virus and HIV are present only during pathogenic condition. Common oral bacteria include Streptococcus mutans, Porphyromonas gingivalis, Staphylococcus, and Lactobacillus which inhabit the oral cavity of humans (Lu et al. 2019).

4.3

Respiratory Microbiome

Human respiratory tract starts from the nostrils and extended up to the alveoli of the lungs. Each site of the respiratory tract is inhabited by site specific microbiome. The respiratory system especially the upper regions is closely in contact with the external environment and also it was connected to the oral cavity. Lung and oral cavity microbiome are almost similar in composition (Dickson et al. 2016). The upper respiratory system filters, heats, and humidifies the air before it reaches the lungs. The upper and lower respiratory tract microbiome starts colonization from the time of delivery and it may change with age, lifestyle, diet, and antibiotics (Santacroce et al. 2020). Indigenous microbiome restricts the attachment of pathogenic microorganisms by occupying the spaces, depleting the available nutrients. The mucosal surface of these sites was inhabited by bacterial genera such as Firmicutes, Actinobacteria, Bacteroidetes, Proteobacteria, and Fusobacteria. The lung microbiome of the healthy individuals constitutes bacteria, fungi, virus, and bacteriophages. The fungal species includes Aspergillus, Cladosporium, Candida, Malassezia, Saccharomyces, Eurotium, Penicillium, etc. (Santacroce et al. 2020).

124

4.4

V. T. Anju et al.

Placental Microbiome

Previous studies reported that placenta is sterile and believed that the amniotic membrane acts as a germ-free barrier which separates maternal urogenital tract and the foetus. This belief was challenged by several studies and reported the existence of bacterial DNA in the placenta (Kuperman et al. 2020). In 2014, the first studies on placental microbiome on healthy subjects reported the placental microbiome is almost same as that of the oral microbiome of non-pregnant women. Fusobacterium nucleatum, an oral anaerobe involved in causing the oral plaques, also reported in placenta. Escherichia coli is another placental bacterium but not present in the oral cavity. In healthy term pregnancies, normal commensal microbiota was reported, which belongs to the phyla Firmicutes, Tenericutes, Proteobacteria, Bacteroidetes, and Fusobacteria (Belizário and Napolitano 2015). The bacterial ligands present in the placenta can trigger immune response and thereby help in the growth of immune cells of foetus (Zakis et al. 2022). Lactobacillus species is the most commonly found bacteria in placenta, vagina, and also in the human breast milk (Fernández et al. 2020; Satokari et al. 2009). Different studies reported the inhabitance of different kinds of microorganisms in placenta and associated parts, suggested the presence of different routes and pathways for the movement of bacteria to placenta and babies (Nuriel-Ohayon et al. 2016).

4.5

Intestinal (Gut) Microbiome

Human intestine is one of the most complex parts inhabited by more than 1000 species of microbiota. Studies showed bifacial association between the microbiome in host health and also in the disease progression (Kastl et al. 2020; Ogunrinola et al. 2020). The colonization of microbiome starts from the beginning of birth and can be changed with age. Infants born through vaginal birth are colonized by Lactobacillus and Prevotella species. Individuals of caesarean birth are primarily occupied by skin microbiome. In addition to age, various aspects that cause differences in the microbiome structure are host immune system, host genetics, antibiotics, diet, etc. (Tuddenham and Sears 2015). Studies on animal models reported that the microbiome is necessary for the development of intestinal epithelial cells, tight junction, and nervous system. Short chain fatty acids produced by commensal bacteria by the fermentation of dietary fibre stimulates the production of mucin, they serve as an energy source for the epithelial cells of the colon and induces the development of tight junctions (Dupont et al. 2020). Short chain fatty acid such as butyrate acts as an intestinal protective barrier for the microbial invasion into the host intestine. The enzyme, bile salt hydrolases produced by the gut microbiome especially, Clostridium perfringens and Clostridium scindens converts the primary bile acids into secondary bile acids, leads to the reabsorption of bile acids by the colon (Kho and Lal 2018). Metagenomic sequencing of human faecal samples shown that

Human Microbiome and the Susceptibility to Infections

125

the metabolism of biomolecules, xenobiotics by the gut microbiome, helps in the harvest of metabolic energy for the host (Kho and Lal 2018). Transcriptome analysis reported that the ingestion of three probiotic bacteria such as Lactobacillus acidophilus, L. casei, and L. rhamnosus caused stimulated gene expression in the major pathways in small intestine mucosa, which is similar to those stimulated by the specific drug or biomolecules (Mohajeri et al. 2018).

4.6

Vaginal Microbiome

About 9% of the total human microbiome is occupied with the vaginal microbiota. These symbiotic bacteria associate and protect the host from invading pathogens, which causes diseases such as bacterial vaginosis, candida infections, urinary tract infections, and sexually transmitted diseases (Saraf et al. 2021). These microbiomes undergo fluctuations at different stages of women’s life. Microbiome fluctuations are more common on reproductive age, but there was a sharp decline observed in case of pregnant women. The presence of Lactobacillus spp., Actinomycetales, Clostridiales, and Bacteroidales are abundant in pregnant women, whereas Lactobacillus spp., Actinobacteria, Prevotella, Veillonellaceae, Streptococcus, Proteobacteria, Bifidobacteriaceae, Bacteroides, and Burkholderiales are reported to be abundant in non-pregnant women (Chen et al. 2021). About 50% of Lactobacillus species abundancy was reported as vaginal microbiome, which maintains acidic pH of the vagina (Greenbaum et al. 2019). Certain bacterial genera such as Prevotella, Atopobium, Gardnerella, Megasphaera, and Mobiluncus are reported to be associated with the abnormal vaginal microbiota in reproductive age women (Saraf et al. 2021).

5 Human Microbiome and the Immune System The interaction of human microbiome and immune system maintains the human health and disease. As microbiome has many roles in the induction, functioning, and training of immune system, host system evolved to maintain symbiotic relationship with each microbial counterparts of microbiome (Qin et al. 2010). Host immune system does not eradicate microbiota as they co-exist with them and provide host with nutrients which otherwise they may not receive it. At the same time, host still remains the capacity to fight with pathogenic microorganisms and eradicate them from their system (Malys et al. 2015). Microbiome trains and functionally tunes the immune system and works as an adjuvant to the system. In turn, microbiome ecology is preserved and shaped with the help of immune system (Puel et al. 2010; Smeekens et al. 2014). It is evident that the commensals of skin, lung, gut, or other barrier sites are involved in the regulation of local and systemic tissues and cells. Failure of improper functioning of immune system as a consequence of altered microbiome

126

V. T. Anju et al.

composition and function may result in the transformation of commensals into pathogens. For instance, long lasting side effects may arise as a result of altered microbiota that leads to the failure to generate proper immune response and cause inflammatory diseases. Variation in the composition and roles of microbiome in neonates showed profound inflammatory diseases (Arrieta et al. 2014). Microbiome plays significant part in the regulation of immune system of humans. Newborns and infants are initially susceptible to infections as their immunity is evolving with the help of maternal antibodies and microbiota shared and acquired through the process of growth. The initial colonization of microbes occurs after the birth that continues to grow to educate host immunity. Maternal antibodies acquired through delivery mode and breast milk impact the initial microbial colonization as well as the establishment of immune system. Microbiota helps in the prevention of excessive inflammation and occurrence of devastating conditions by potential pathogens (Zheng et al. 2020; Dominguez-Bello et al. 2010; Caballero-Flores et al. 2019). The host tries to keep the microbial cells aways from the epithelial cell surface to maintain a homeostatic association between microbiota and immune system. Thus, it reduces the microbial translocation and inflammation. Cumulative action of epithelial cells, antimicrobial peptides, immune cells, and immunoglobulin A acts as a shield to avoid the translocation of microbiota to the tissues. The mucus produced by the intestinal epithelial cells keeps the microbiota away from the surface (McGuckin et al. 2011). A demilitarized zone is created by the host, where a separation between host and microbiota will develop. The secretion of antimicrobial peptides and other proteins by intestinal epithelial lineages helps to maintain a segregation between host and microbiota (Vaishnava et al. 2011). Still, the microbial metabolites are commonly found in the blood even though anatomical separation developed. The proper tuning of microbial related metabolites can regulate the haematopoiesis and haematopoietic cell education. Microbially conditioned metabolites directly act on the local intestinal cells as well as cross mucosa to the blood stream and peripheral tissues where they tune immune cells (Belkaid and Harrison 2017). According to WHO and Global Burden of Diseases, Injuries, and Risk Factors Study of 2015, enteric disease including diarrhoea is one of the major underlying reasons for the high mortality rate under the age group of 5 (Kirk et al. 2015). The microbiota and epithelial barrier of gastrointestinal tract and the mucosa layer immune system reduces the incidence of infectious enteric diseases (Iacob et al. 2019). The intestinal homeostasis is maintained by the constant and continuous interaction of gut microbiome and epithelial lining which leads to stable immune signalling (Harris et al. 2017). Local and systemic immunity contributed by the gut microbiome regulated the intestinal homeostasis. The initial recognition of microbes by the pattern-recognition receptors (PRRs) followed by the release of chemokines and cytokines elicit protective immune responses. It is very important to activate PRRs and downstream PRR signalling for the appropriate activity of immune cells. It may cause compromised immunity and increased susceptibility to infections if there is an inefficient regulation of PRRs (Fukata and Arditi 2013; Kubinak et al. 2015). Antimicrobial peptides produced by intestinal epithelial cells can limit the

Human Microbiome and the Susceptibility to Infections

127

pathogen entry to epithelial barrier. Also, the composition of microbiota as well as specific microbes regulates the expression of these peptides, thus shaping the whole innate immune system response (Iacob et al. 2019; Vandamme et al. 2012). Metabolites produced by microbiota aid in the propagation and differentiation of different immune cells, thereby regulating the homeostasis of intestine. The metabolites such as bile acid derivatives, short chain fatty acids and tryptophan metabolites, etc. stimulate the production of antimicrobial peptides and mucus by epithelial cells. The gut microbiota derived short chain fatty acids are important for the proliferation and maturation of innate lymphoid cells and colon regulatory T cells (Chen and Stappenbeck 2019; Schnupf et al. 2018; Chun et al. 2019). Both the tryptophan metabolites and bile acid derivatives play vital role in regulating and maintaining the intestinal homeostasis. Lack of metabolite production may lead to the incidence of inflammatory bowel disease (Wiertsema et al. 2021).

6 Human Microbiome: Susceptibility to Infections Immune system of humans is evolved to contain both innate and adaptive system that protect and provide defence against potential pathogens. The microbiota associated with different parts of host is co-evolved to function as commensal to maintain homeostasis of immune system. Host immune systems act appropriately for the timely removal of pathogens and to avoid damage to the host resources by the commensals. Still, environmental factors involving diet, antibiotic therapy, and variations in geography, host–microbiota distractions, and immune system alterations may cause complete removal of commensals from the tissues and result in the invasion of pathogens and abnormal immune responses (Zheng et al. 2020). Microbiota develops several anti-infective barriers in the host system through the evolution of different specific and non-specific immune system components. The anti-infective barrier is efficient in the prevention of pathogen entry, colonization, and subsequent production of toxins and bacteriocins (Gérard 2014). Anti-infective barrier is intact and efficient only if the microbiota is complex and stable. This barrier may lose its efficacy once microbiome dysbiosis occurs due to different reasons such as antibiotic therapy, disturbed diet, secondary immunodeficient conditions contributed by pathologies and deprived colonization and establishment of microbiome. Host became more susceptible to infections once the barrier loses its effectiveness. Also, some members of microbiota are capable of producing pathogenic behaviour during dysbiosis (Lazar et al. 2018). Recent reports indicate that microbiome changes may lead to numerous diseases and infections. The interactions of host–microbiota are complex and dynamic. Thus, alterations in microbiome may disrupt the host homeostasis and increase the host susceptibility to infections (Wang et al. 2017). The major factors such as antibiotic therapy, diet, invasion by pathogenic microorganisms and lifestyle changes cause the dysbiosis of microbiota and leads to the increased susceptibility to infections. Several immune associated diseases like type I diabetes, rheumatoid arthritis, and

V. T. Anju et al.

128

inflammatory diseases can occur due to the change in composition of microbiota (Verwoerd et al. 2016). An altered gut microbiome can cause several immune diseases, metabolic diseases, inflammation, modified innate, and adaptive immunity to infections (Libertucci and Young 2019). Several studies suggest that differences in human microbiome based on geography may be a predisposing factor for enhanced enteric infections. The study conducted with germ-free mice exposed to microbiome from different geographical regions exhibited varied susceptibility towards C. rodentium (Porras et al. 2021).

6.1

Dysbiosis of Microbiota

Alteration in the host microbiota contributes to several difficulties such as skin disorders, bacterial vaginosis, obesity, and diabetes. The disease phenotypes can be spread to normal persons during the transplantation of microbiota. Dysbiosis of microbiota can either lead to diseases or in some cases may even turn to cure diseases. Altered microbiota may improve host health by including modifications in the diet. Thus, modified microbiota through transplantation, introduction of probiotic strains, or removal of harmful members by antibiotic treatment can serve as potential therapeutic treatments (Parfrey and Knight 2012; Pflughoeft and Versalovic 2012) (Fig. 2).

Fig. 2 Understating the role of microbiota in symbiosis and dysbiosis. Microbiome interacts with host in a symbiotic relationship to benefit, whereas the dysbiosis occurred in the microbiota leads to harmful consequences

Human Microbiome and the Susceptibility to Infections

129

Antibiotic Therapy Antibiotics are the best drugs to treat several deadliest infections. Antibiotics usage is also associated with side effects along with the beneficial roles on host health. The effects of antibiotic usage have been associated with alterations in host microbiota leading to increased vulnerability to diseases like diarrhoea, pathogenic microbial infections, and other dysbiosis-related immune diseases. There are several reports of altered gut microbiome due to terramycin usage during intestinal surgery that leads to more colonization by pathogens (Di Caprio and Rantz 1950). Clostridium difficile is a toxin producing bacterium that causes infections such as colitis and death in animals. Acute antibiotic-associated diarrhoea and pseudomembranous colitis are observed in humans due to C. difficile infections and can damage gut epithelial barrier (Keeney et al. 2014). One of the factors determining the colonization of C. difficile and development of diarrhoea in humans is the gut dysbiosis by antibiotic treatment. It is evident in several animal-based studies where complex antibiotic treatment exhibited gut symbiosis (Chen et al. 2008; Corthier et al. 1989). Continuous use of antibiotics can break the microbiome mediated colonization resistance leading to infections. It was evidenced in animal models, where antibiotic use has caused severe gastrointestinal infections to death due to the bacterium, Clostridium difficile (Douce and Goulding 2010). The use of amoxicillin for diarrhoea treatment caused complete removal of butyrate producing Clostridial cluster from the gut microbiota. The removal of these bacterial cluster led to the growth of harmful microbial flora which is related to the occurrence of antibiotic-associated diarrhoea (Young and Schmidt 2004). Salmonellosis is characterized by abdominal pain, fever, diarrhoea, and hospital stay for severe infections in patients. Generally, immune deficient persons including older and younger individuals and antibiotic treated patients are more prone to Salmonella infections. Studies showed people who had received antibiotic treatment such as tetracycline, oxacillin, tetracycline, sulfonamide, chloramphenicol, and ampicillin for salmonellosis can develop systemic disease (Adler et al. 1970; Keeney et al. 2014). In a study, a mice model system of streptomycin treatment has resulted in Salmonella enterica serovar Typhimurium infection (Wlodarska et al. 2011). In another mice model study, a single dose treatment with streptomycin caused increased susceptibility towards Salmonella infection by 10,000-fold (Bohnhoff et al. 1964). C. rodentium is a model bacterium for the pathogens, enteropathogenic and enterohemorrhagic Escherichia coli to study the effect of antibiotic treatment on intestinal colonization. C. rodentium infections reduced the mucus layer of epithelium which interfered with the colonization resistance. The bacterial infections altered the microbiota which decreased the occurrence of Bacteroidetes and Porphyromonadaceae. The altered microbiota reduced the production of epithelial mucus layer. In a study, metronidazole treatment caused more severe colitis associated with C. rodentium (Wlodarska et al. 2011). The colonization of Citrobacter

130

V. T. Anju et al.

enhanced more by 10- to 50- fold when a mouse is treated with 20 mg of streptomycin (Bergstrom et al. 2010). Dysbiosis caused by antibiotic treatment leads to other diseases states like rheumatoid arthritis, inflammatory bowel disease, type 1 diabetes, atopy, and obesity. The decrease in the number of several bacterial phyla such as Firmicutes to Bacteroides in gut leads to the dysbiosis-related diseases (Lepage et al. 2011; Manichanh et al. 2006). One of the driving factors for juvenile idiopathic arthritis (JIA) common in childhood is the dysbiosis of microbiota along with genetic factors. It has been reported that antibiotic consumption in the initial life stages may contribute to JIA in later stages of life (Arvonen et al. 2015; Horton et al. 2015). Gut microbiota not only benefit intestine but also regulate liver functions. There is a close connection between gut and liver where gut microbiota related metabolites reach liver through blood supply. Dysbiosis of gut microbiome and altered production of gut metabolites may increase the susceptibility to many liver diseases like chronic hepatitis B, steatosis, oxidative liver injury, and cirrhosis (Pan and Zhang 2022). Studies found that increased dietary content of cholesterol, fat, fibre, and sugar can change the structure and variety of gut microbiome. These alterations cause the removal of Bifidobacterium and Bacteroides and increase the number of Anaerotruncus, Desulfovibrio, Mucispirillum, and Desulfovibrionaceae leading to the chronic liver inflammation (Zhang et al. 2021; Makki et al. 2018). There has been always a link observed between microbiota and autism spectrum disorder. The altered gut microbiota is assumed to be a factor to influence brain function and social behaviour in autism patients. It is reported that gut dysbiosis may affect permeability of gut, immune system functions, and microbial mediated metabolite production in autism individuals (Alharthi et al. 2022).

Emergence of Antibiotic Resistance It is believed that the effect on human microbiota by the antibiotic exposure can be restored. Recent culture and molecular based studies reported long-term exposure of antibiotics resulted in the advent and rapid spread of antibiotic resistant strains along with the dysbiosis leading to the failure of therapy in next time (De La Cochetière et al. 2005; Sjölund et al. 2005). Short term exposure to clindamycin restored the gut microbiome after weeks, whereas long-term exposure exhibited adverse effects (Sullivan 2001). An increased antibiotic resistance and disparity of gut Bacteroides were observed for up to years (Jernberg et al. 2007). The long-term use of clindamycin not only increased intrinsic resistance on the family Enterobacteriaceae but also showed resistance towards ampicillin. The high resistance was observed up to 9 months after the exposure (Nyberg et al. 2007). Treatment with amoxicillin alone or with clavulanic acid exhibited side effects on gut microbiome. Studies showed a rise in the number of resistant enterobacteria and decreased number of aerobic Gram-positive cocci shaped bacteria in the gut (Yang et al. 2021).

Human Microbiome and the Susceptibility to Infections

131

The treatment of Helicobacter infections using clarithromycin, metronidazole, and omeprazole disturbed the gut microbiota. In addition, the faecal microbiome was also drastically affected and detected in sequencing-based method even after 4 years post the antibiotic treatment. They also analysed the effect of treatment on throat microbiota and found to be less affected than faecal microbiota (Jakobsson et al. 2010). Studies linked the persistent infections of Clostridium difficile with long-term use of antibiotics. The use of clindamycin contributed the emergence of antibiotic resistant genes in the host against penicillins, cephalosporins, lincomycin, aminoglycosides, erythromycin, and tetracyclins (Johanesen et al. 2015). In a mice model, exposure to ciprofloxacin or fosfomycin causes notable reduction in the gut microbiota. In addition, an amplified expression of several antibiotic resistant genes and mobile genetic elements is observed, as indicative of emergence of antibiotic resistance (Xu et al. 2020).

7 Human Microbiome in Health and Disease Human microbiome containing trillions of microbes plays pivotal role in the regulation of human health and disease. The genome of microbiome especially the gut microbiome carries a greater number of genes than the entire human genome. Hence, gut microbiome is known as an essential organ. Recent literature shows a strong association between human health and disease with human microbiome (Wang et al. 2017; Kumar et al. 2021). The interactions of microbiome regulate the general health and well-being of humans by enhancing or impairing the metabolic and immune properties. The change or dysbiosis of microbiome owing to different factors may lead to illness ranging from acute to chronic and life-threatening conditions. These factors are hormonal changes, age, lifestyle changes, nutritional factors, inherited genes, and diseases. The illnesses like cancer, cardiovascular diseases, inflammatory bowel diseases, and untreatable bacterial infections and alterations in immune system conditions may lead to the dysbiosis of microbiota and lead to different health severities (Whiteside et al. 2015; Morgan and Huttenhower 2012; Pascal et al. 2018). There are several techniques identified and used so far for the enumeration of microbiome. It states that the abundance of microbial communities is different in all parts of the body and in between health and diseased individuals. The difference in the number and frequency of microbiome may either the result of disease or dysbiosis (Bresalier and Chapkin 2020). In normal conditions, microbiome of body co-ordinates among themselves so that both healthy and pathogenic microorganisms co-exist in the system. Microbial communities may work as symbiotic to human host and pathogenic organisms reside in system without creating any health issues. The microbiome can lead to infections only if the equilibrium of microbiome is disturbed by different factors (Li et al. 2008).

132

V. T. Anju et al.

Microbiome which is in symbiotic relationship with humans improves host health and individual modifications may lead to diseases and affect drug metabolism, toxicity, and efficacy (Li et al. 2008). Microbiome of human helps in the regulation of immune system in newborn and young children, balances inflammatory homeostasis, and host nutrition (Thomas et al. 2017). Microbiota can shape the innate as well as adaptive immunity. To provide immune homeostasis, several immune cells like antigen presenting cells were co-evolved with microbiome and serve to defend body from getting infection. Microbiome helps in the balance and regulation of T cells and B-cells. Some of the members of microbiome can alter the consequences of autoimmune diseases (Wu and Wu 2012). Few examples of microbiota of gut containing anaerobes avoid the translocation of aerobic or facultative anaerobes and subsequently prevent infections in immunodeficient persons. In addition, Bacteroides fragilis is involved in the production of various vitamins like biotin, B1, B2, B5, B6, B12 and folic acid. Fusobacterium spp. and B. fragilis of gut microbiota have the capacity to breakdown xenobiotics and sterols, participate in the deconjugation of biliary acids (Gérard 2014; Yoshii et al. 2019). Microbiota involve in the normal differentiation and maturation of immune cells, thereby reducing the incidence of infections in the host. Some microbiome members can reduce the pathogenic invasion through colonization resistance. Intestinal commensals act as a barrier to avoid the colonization of enteric pathogens. Intestinal bacteria may compete for nutrients with pathogen, thereby excluding pathogen from the gut. Bacteroidetes thetaiotaomicron, an intestinal commensal competes for carbohydrates for the elimination of pathogen, Citrobacter rodentium (Gordon et al. 2012; Rolhion and Chassaing 2016). Bacteroides fragilis of intestinal microbiome is involved in the development of CD4 T lymphocytes and helps to eliminate the pathogen, C. rodentium (Mazmanian et al. 2005; Rolhion and Chassaing 2016).

8 Conclusions Human microbiome is used as a collective word representing the whole community of commensal, symbiotic, and pathogenic microbes in the body. The new culture independent techniques including sequencing allowed to discover the structure and dynamics of microbial communities and their association with the host. The microbiota induced substances and metabolites and its effect on host enabled us to focus on the relationship of microbiome on health and disease. Human microbiome has vital role in the maturation and differentiation of immune system and modulate its responses influencing the host heath. There are several culture and molecular based techniques developed to explore the broad range of human microbiome and its functions. The understanding of microbiome composition and functions can help to improve human health and to control several infections. Among human microbiota, gut microbiota holds effective role in maintaining human health and emerged as a potential therapeutic target. Human microbiota participates in various roles such as

Human Microbiome and the Susceptibility to Infections

133

digestion, modulate metabolism, and maintains host immune homeostasis. The microbiota can be altered by dietary changes, disease conditions, and antibiotic exposure. Available studies provided the information of microbiome dysbiosis and its role in enhancing the host susceptibility to get infections. The altered microbiome can produce pathogenic factors which favours the entry of pathogens or reduces the number of commensals from the host. The altered microbiome is associated with the dysregulated immune responses which may leads to the infections by pathogens as well as immune related diseases.

References Adler JL, Anderson RL, Boring JR, Nahmias AJ (1970) A protracted hospital-associated outbreak of salmonellosis due to a multiple-antibiotic-resistant strain of Salmonella indiana. J Pediatr 77: 970–975. https://doi.org/10.1016/S0022-3476(70)80079-8 Alharthi A, Alhazmi S, Alburae N, Bahieldin A (2022) The human gut microbiome as a potential factor in autism spectrum disorder. Int J Mol Sci 23:1363. https://doi.org/10.3390/ ijms23031363 Arrieta M-C, Stiemsma LT, Amenyogbe N et al (2014) The intestinal microbiome in early life: health and disease. Front Immunol 5:427. https://doi.org/10.3389/fimmu.2014.00427 Arvonen M, Virta LJ, Pokka T et al (2015) Repeated exposure to antibiotics in infancy: a predisposing factor for juvenile idiopathic arthritis or a sign of this group’s greater susceptibility to infections? J Rheumatol 42:521–526. https://doi.org/10.3899/jrheum.140348 Barko PC, McMichael MA, Swanson KS, Williams DA (2018) The gastrointestinal microbiome: a review. J Vet Intern Med 32:9–25. https://doi.org/10.1111/jvim.14875 Belizário JE, Napolitano M (2015) Human microbiomes and their roles in dysbiosis, common diseases, and novel therapeutic approaches. Front Microbiol 6:1050. https://doi.org/10.3389/ fmicb.2015.01050 Belkaid Y, Harrison OJ (2017) Homeostatic immunity and the microbiota. Immunity 46:562–576. https://doi.org/10.1016/j.immuni.2017.04.008 Bergstrom KSB, Kissoon-Singh V, Gibson DL et al (2010) Muc2 protects against lethal infectious colitis by disassociating pathogenic and commensal bacteria from the colonic mucosa. PLoS Pathog 6(5):e1000902. https://doi.org/10.1371/journal.ppat.1000902 Bohnhoff M, Miller CP, Martin WR (1964) Resistance of the mouse’s intestinal tract to experimental salmonella infection. I. Factors which interfere with the initiation of infection by oral inoculation. J Exp Med 120:805–816. https://doi.org/10.1084/Jem.120.5.805 Bresalier RS, Chapkin RS (2020) Human microbiome in health and disease: the good, the bad, and the bugly. Dig Dis Sci 65:671–673. https://doi.org/10.1007/s10620-020-06059-y Byrd AL, Belkaid Y, Segre JA (2018) The human skin microbiome. Nat Rev Microbiol 16:143– 155. https://doi.org/10.1038/nrmicro.2017.157 Caballero-Flores G, Sakamoto K, Zeng MY et al (2019) Maternal immunization confers protection to the offspring against an attaching and effacing pathogen through delivery of IgG in breast milk. Cell Host Microbe 25:313–323.e4. https://doi.org/10.1016/j.chom.2018.12.015 Chen F, Stappenbeck TS (2019) Microbiome control of innate reactivity. Curr Opin Immunol 56: 107–113. https://doi.org/10.1016/j.coi.2018.12.003 Chen X, Katchar K, Goldsmith JD et al (2008) A mouse model of Clostridium difficile-associated disease. Gastroenterology 135:1984–1992. https://doi.org/10.1053/j.gastro.2008.09.002 Chen YE, Fischbach MA, Belkaid Y (2018) Skin microbiota-host interactions. Nature 553:427– 436. https://doi.org/10.1038/nature25177

134

V. T. Anju et al.

Chen X, Lu Y, Chen T, Li R (2021) The female vaginal microbiome in health and bacterial vaginosis. Front Cell Infect Microbiol 11:1–15. https://doi.org/10.3389/fcimb.2021.631972 Chun E, Lavoie S, Fonseca-Pereira D et al (2019) Metabolite-sensing receptor Ffar2 regulates colonic group 3 innate lymphoid cells and gut immunity. Immunity 51:871–884.e6. https://doi. org/10.1016/j.immuni.2019.09.014 Corthier G, Muller MC, Elmer GW et al (1989) Interrelationships between digestive proteolytic activities and production and quantitation of toxins in pseudomembranous colitis induced by Clostridium difficile in gnotobiotic mice. Infect Immun 57:3922–3927. https://doi.org/10.1128/ iai.57.12.3922-3927.1989 De La Cochetière MF, Durand T, Lepage P et al (2005) Resilience of the dominant human fecal microbiota upon short-course antibiotic challenge. J Clin Microbiol 43:5588–5592. https://doi. org/10.1128/JCM.43.11.5588-5592.2005 Deo PN, Deshmukh R (2019) Oral microbiome: unveiling the fundamentals. J Oral Maxillofac Pathol 23:122–128. https://doi.org/10.4103/jomfp.JOMFP_304_18 Di Caprio JM, Rantz LA (1950) Effects of terramycin on the bacterial flora of the bowel in man. Arch Intern Med 86:649–657. https://doi.org/10.1001/archinte.1950.00230170002001 Dickson RP, Erb-Downward JR, Martinez FJ, Huffnagle GB (2016) The microbiome and the respiratory tract. Annu Rev Physiol 78:481–504. https://doi.org/10.1146/annurev-physiol021115-105238 Dominguez-Bello MG, Costello EK, Contreras M et al (2010) Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proc Natl Acad Sci 107:11971–11975. https://doi.org/10.1073/pnas.1002601107 Douce G, Goulding D (2010) Refinement of the hamster model of Clostridium difficile disease. Methods Mol Biol 646:215–227. https://doi.org/10.1007/978-1-60327-365-7_14 Dupont HL, Jiang ZD, Dupont AW, Utay NS (2020) The intestinal microbiome in human health and disease. Trans Am Clin Climatol Assoc 131:178–197 Fernández L, Pannaraj PS, Rautava S, Rodríguez JM (2020) The microbiota of the human mammary ecosystem. Front Cell Infect Microbiol 10:586667. https://doi.org/10.3389/fcimb. 2020.586667 Fukata M, Arditi M (2013) The role of pattern recognition receptors in intestinal inflammation. Mucosal Immunol 6:451–463. https://doi.org/10.1038/mi.2013.13 Gérard P (2014) Metabolism of cholesterol and bile acids by the gut microbiota. Pathogens 3:14– 24. https://doi.org/10.3390/pathogens3010014 Gordon JI, Dewey KG, Mills DA, Medzhitov RM (2012) The human gut microbiota and undernutrition. Sci Transl Med 4:137ps12. https://doi.org/10.1126/scitranslmed.3004347 Greenbaum S, Greenbaum G, Moran-Gilad J, Weintraub AY (2019) Ecological dynamics of the vaginal microbiome in relation to health and disease. Am J Obstet Gynecol 220:324–335. https://doi.org/10.1016/j.ajog.2018.11.1089 Grice EA, Segre JA (2011) The skin microbiome. Nat Rev Microbiol 9:244–253. https://doi.org/10. 1038/nrmicro2537 Harris VC, Haak BW, Boele van Hensbroek M, Wiersinga WJ (2017) The intestinal microbiome in infectious diseases: the clinical relevance of a rapidly emerging field. Open Forum Infect Dis 4: ofx144. https://doi.org/10.1093/ofid/ofx144 Hayes W, Sahu S (2020) The human microbiome: history and future. J Pharm Pharm Sci 23:404– 411. https://doi.org/10.18433/jpps31525 Hooper LV, Littman DR, Macpherson AJ (2012) Interactions between the microbiota and the immune system. Science 336:1268–1273. https://doi.org/10.1126/science.1223490 Horton DB, Scott FI, Haynes K et al (2015) Antibiotic exposure and juvenile idiopathic arthritis: a case–control study. Pediatrics 136:e333–e343. https://doi.org/10.1542/peds.2015-0036 Iacob S, Iacob DG, Luminos LM (2019) Intestinal microbiota as a host defense mechanism to infectious threats. Front Microbiol 9:3328. https://doi.org/10.3389/fmicb.2018.03328

Human Microbiome and the Susceptibility to Infections

135

Jahoor A, Patel R, Bryan A et al (2008) Peroxisome proliferator-activated receptors mediate host cell proinflammatory responses to Pseudomonas aeruginosa autoinducer. J Bacteriol 190:4408– 4415. https://doi.org/10.1128/JB.01444-07 Jakobsson HE, Jernberg C, Andersson AF et al (2010) Short-term antibiotic treatment has differing long-term impacts on the human throat and gut microbiome. PloS One 5:e9836. https://doi.org/ 10.1371/journal.pone.0009836 Jernberg C, Löfmark S, Edlund C, Jansson JK (2007) Long-term ecological impacts of antibiotic administration on the human intestinal microbiota. ISME J 1:56–66. https://doi.org/10.1038/ ismej.2007.3 Johanesen P, Mackin K, Hutton M et al (2015) Disruption of the gut microbiome: Clostridium difficile infection and the threat of antibiotic resistance. Genes (Basel) 6:1347–1360. https://doi. org/10.3390/genes6041347 Kalia VC, Wood TK, Kumar P (2014) Evolution of resistance to quorum-sensing inhibitors. Microb Ecol 68:13–23. https://doi.org/10.1007/s00248-013-0316-y Kastl AJ, Terry NA, Wu GD, Albenberg LG (2020) The structure and function of the human small intestinal microbiota: current understanding and future directions. Cell Mol Gastroenterol Hepatol 9:33–45. https://doi.org/10.1016/j.jcmgh.2019.07.006 Keeney KM, Yurist-Doutsch S, Arrieta MC, Finlay BB (2014) Effects of antibiotics on human microbiota and subsequent disease. Annu Rev Microbiol 68:217–235. https://doi.org/10.1146/ annurev-micro-091313-103456 Kho ZY, Lal SK (2018) The human gut microbiome—a potential controller of wellness and disease. Front Microbiol 9:1–23. https://doi.org/10.3389/fmicb.2018.01835 Kirk MD, Pires SM, Black RE et al (2015) World Health Organization estimates of the global and regional disease burden of 22 foodborne bacterial, protozoal, and viral diseases, 2010: a data synthesis. PLoS Med 12:e1001940. https://doi.org/10.1371/journal.pmed.1001921 Kravchenko VV, Kaufmann GF, Mathison JC et al (2008) Modulation of gene expression via disruption of NF-κB signaling by a bacterial small molecule. Science 321:259–263. https://doi. org/10.1126/science.1156499 Kubinak JL, Petersen C, Stephens WZ et al (2015) MyD88 signaling in T cells directs IgA-mediated control of the microbiota to promote health. Cell Host Microbe 17:153–163. https://doi.org/10. 1016/j.chom.2014.12.009 Kumar P, Koul S, Patel SKS et al (2015) Heterologous expression of quorum sensing inhibitory genes in diverse organisms. In: Kalia VC (ed) Quorum sensing vs quorum quenching: a battle with no end in sight. Springer, New Delhi, pp 343–356 Kumar P, Lee JH, Beyenal H et al (2020) Fatty acids as antibiofilm and antivirulence agents. Trends Microbiol 28:753–768. https://doi.org/10.1016/j.tim.2020.03.014 Kumar P, Lee J, Lee J (2021) Diverse roles of microbial indole compounds in eukaryotic systems. Biol Rev 96:2522–2545. https://doi.org/10.1111/brv.12765 Kuperman AA, Zimmerman A, Hamadia S et al (2020) Deep microbial analysis of multiple placentas shows no evidence for a placental microbiome. BJOG 127:159–169. https://doi.org/ 10.1111/1471-0528.15896 Kurkjian HM, Akbari MJ, Momeni B (2021) The impact of interactions on invasion and colonization resistance in microbial communities. PLoS Comput Biol 17:e1008643. https://doi.org/10. 1371/journal.pcbi.1008643 Lazar V, Ditu LM, Pircalabioru GG et al (2018) Aspects of gut microbiota and immune system interactions in infectious diseases, immunopathology, and cancer. Front Immunol 9:1830. https://doi.org/10.3389/fimmu.2018.01830 Lepage P, Hösler R, Spehlmann ME et al (2011) Twin study indicates loss of interaction between microbiota and mucosa of patients with ulcerative colitis. Gastroenterology 141:227–236. https://doi.org/10.1053/j.gastro.2011.04.011 Li M, Wang B, Zhang M et al (2008) Symbiotic gut microbes modulate human metabolic phenotypes. Proc Natl Acad Sci U S A 105:2117–2122. https://doi.org/10.1073/pnas. 0712038105

136

V. T. Anju et al.

Li H, He J, Jia W (2016) The influence of gut microbiota on drug metabolism and toxicity. Expert Opin Drug Metab Toxicol 12:31–40. https://doi.org/10.1517/17425255.2016.1121234 Libertucci J, Young VB (2019) The role of the microbiota in infectious diseases. Nat Microbiol 16(3):107–114. https://doi.org/10.1016/j.tim.2007.12.008 Lim Y, Totsika M, Morrison M, Punyadeera C (2017) Oral microbiome: a new biomarker reservoir for oral and oropharyngeal cancers. Theranostics 7:4313–4321. https://doi.org/10.7150/thno. 21804 Lu M, Xuan S, Wang Z (2019) Oral microbiota: a new view of body health. Food Sci Human Wellness 8:8–15. https://doi.org/10.1016/j.fshw.2018.12.001 Makki K, Deehan EC, Walter J, Bäckhed F (2018) The impact of dietary fiber on gut microbiota in host health and disease. Cell Host Microbe 23:705–715. https://doi.org/10.1016/j.chom.2018. 05.012 Malys MK, Campbell L, Malys N (2015) Symbiotic and antibiotic interactions between gut commensal microbiota and host immune system. Medicina (Kaunas) 51:69–75. https://doi. org/10.1016/j.medici.2015.03.001 Manichanh C, Rigottier-Gois L, Bonnaud E et al (2006) Reduced diversity of faecal microbiota in Crohn’s disease revealed by a metagenomic approach. Gut 55:205–211. https://doi.org/10.1136/ gut.2005.073817 Mazmanian SK, Cui HL, Tzianabos AO, Kasper DL (2005) An immunomodulatory molecule of symbiotic bacteria directs maturation of the host immune system. Cell 122:107–118. https://doi. org/10.1016/j.cell.2005.05.007 McGuckin MA, Lindén SK, Sutton P, Florin TH (2011) Mucin dynamics and enteric pathogens. Nat Rev Microbiol 9:265–278. https://doi.org/10.1038/nrmicro2538 Mohajeri MH, Brummer RJM, Rastall RA et al (2018) The role of the microbiome for human health: from basic science to clinical applications. Eur J Nutr 57:1–14. https://doi.org/10.1007/ s00394-018-1703-4 Morgan XC, Huttenhower C (2012) Chapter 12: human microbiome analysis. PLoS Comput Biol 8: e1002808. https://doi.org/10.1371/journal.pcbi.1002808 Nuriel-Ohayon M, Neuman H, Koren O (2016) Microbial changes during pregnancy, birth, and infancy. Front Microbiol 7:1031. https://doi.org/10.3389/fmicb.2016.01031 Nyberg SD, Österblad M, Hakanen AJ et al (2007) Long-term antimicrobial resistance in Escherichia coli from human intestinal microbiota after administration of clindamycin. Scand J Infect Dis 39:514–520. https://doi.org/10.1080/00365540701199790 Ogunrinola GA, Oyewale JO, Oshamika OO, Olasehinde GI (2020) The human microbiome and its impacts on health. Int J Microbiol 2020:8045646. https://doi.org/10.1155/2020/8045646 Pan Y, Zhang X (2022) Diet and gut microbiome in fatty liver and its associated liver cancer. J Gastroenterol Hepatol 37:7–14. https://doi.org/10.1111/jgh.15713 Parfrey LW, Knight R (2012) Spatial and temporal variability of the human microbiota. Clin Microbiol Infect 18:5–7. https://doi.org/10.1111/j.1469-0691.2012.03861.x Pascal M, Perez-Gordo M, Caballero T et al (2018) Microbiome and allergic diseases. Front Immunol 9:1584. https://doi.org/10.3389/fimmu.2018.01584 Pelzer E, Gomez-Arango LF, Barrett HL, Nitert MD (2017) Review: maternal health and the placental microbiome. Placenta 54:30–37. https://doi.org/10.1016/j.placenta.2016.12.003 Pena RT, Blasco L, Ambroa A et al (2019) Relationship between quorum sensing and secretion systems. Front Microbiol 10:1100. https://doi.org/10.3389/fmicb.2019.01100 Pflughoeft KJ, Versalovic J (2012) Human microbiome in health and disease. Annu Rev Pathol 7: 99–122. https://doi.org/10.1146/annurev-pathol-011811-132421 Porras AM, Shi Q, Zhou H et al (2021) Geographic differences in gut microbiota composition impact susceptibility to enteric infection. Cell Rep 36:109457. https://doi.org/10.1016/j.celrep. 2021.109457 Puel A, Döffinger R, Natividad A et al (2010) Autoantibodies against IL-17A, IL-17F, and IL-22 in patients with chronic mucocutaneous candidiasis and autoimmune polyendocrine syndrome type I. J Exp Med 207:291–297. https://doi.org/10.1084/jem.20091983

Human Microbiome and the Susceptibility to Infections

137

Qin J, Li R, Raes J et al (2010) A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464:59–65. https://doi.org/10.1038/nature08821 Rolhion N, Chassaing B (2016) When pathogenic bacteria meet the intestinal microbiota. Philos Trans R Soc Lond Ser B Biol Sci 371:20150504. https://doi.org/10.1098/rstb.2015.0504 Santacroce L, Charitos IA, Ballini A et al (2020) The human respiratory system and its microbiome at a glimpse. Biology (Basel) 9:318. https://doi.org/10.3390/biology9100318 Saraf VS, Sheikh SA, Ahmad A et al (2021) Vaginal microbiome: normalcy vs dysbiosis. Arch Microbiol 203:3793–3802. https://doi.org/10.1007/s00203-021-02414-3 Satokari R, Grönroos T, Laitinen K et al (2009) Bifidobacterium and lactobacillus DNA in the human placenta. Lett Appl Microbiol 48:8–12. https://doi.org/10.1111/j.1472-765X.2008. 02475.x Schnupf P, Gaboriau-Routhiau V, Cerf-Bensussan N (2018) Modulation of the gut microbiota to improve innate resistance. Curr Opin Immunol 54:137–144. https://doi.org/10.1016/j.coi.2018. 08.003 Senn V, Bassler D, Choudhury R et al (2020) Microbial colonization from the fetus to early childhood–a comprehensive review. Front Cell Infect Microbiol 10:573735. https://doi.org/ 10.3389/fcimb.2020.573735 Seyhan AA, Carini C (2019) Are innovation and new technologies in precision medicine paving a new era in patients centric care? J Transl Med 17:114. https://doi.org/10.1186/s12967-0191864-9 Sjölund M, Tano E, Blaser MJ et al (2005) Persistence of resistant Staphylococcus epidermidis after single course of clarithromycin. Emerg Infect Dis 11:1389–1393. https://doi.org/10.3201/ eid1109.050124 Smeekens SP, Huttenhower C, Riza A et al (2014) Skin microbiome imbalance in patients with STAT1/STAT3 defects impairs innate host defense responses. J Innate Immun 6:253–262. https://doi.org/10.1159/000351912 Stecher B, Chaffron S, Käppeli R et al (2010) Like will to like: abundances of closely related species can predict susceptibility to intestinal colonization by pathogenic and commensal bacteria. PLoS Pathog 6:e1000711. https://doi.org/10.1371/journal.ppat.1000711 Sullivan A (2001) Effect of antimicrobial agents on the ecological balance of human microflora. Lancet Infect Dis 1:101–114. https://doi.org/10.1016/S1473-3099(01)00066-4 Thomas S, Izard J, Walsh E et al (2017) The host microbiome regulates and maintains human health: a primer and perspective for non-microbiologists. Cancer Res 77:1783–1812. https://doi. org/10.1158/0008-5472.CAN-16-2929 Thompson JA, Oliveira RA, Djukovic A et al (2015) Manipulation of the quorum sensing signal AI-2 affects the antibiotic-treated gut microbiota. Cell Rep 10:1861–1871. https://doi.org/10. 1016/j.celrep.2015.02.049 Tshikantwa TS, Ullah MW, He F, Yang G (2018) Current trends and potential applications of microbial interactions for human welfare. Front Microbiol 9:1156. https://doi.org/10.3389/ fmicb.2018.01156 Tuddenham S, Sears CL (2015) The intestinal microbiome and health. Curr Opin Infect Dis 28: 464–470. https://doi.org/10.1097/QCO.0000000000000196 Vaishnava S, Yamamoto M, Severson KM, Ruhn KA, Yu X, Koren O, Ley R, Wakeland EK, Hooper LV (2011) The antibacterial lectin RegIIIgamma promotes the spatial segregation of microbiota and host in the intestine. Science 334:255–258. https://doi.org/10.1126/science. 1209791 Vandamme D, Landuyt B, Luyten W, Schoofs L (2012) A comprehensive summary of LL-37, the factotum human cathelicidin peptide. Cell Immunol 280:22–35. https://doi.org/10.1016/j. cellimm.2012.11.009 Verma D, Garg PK, Dubey AK (2018) Insights into the human oral microbiome. Arch Microbiol 200:525–540. https://doi.org/10.1007/s00203-018-1505-3 Verwoerd A, Ter Haar NM, de Roock S et al (2016) The human microbiome and juvenile idiopathic arthritis. Pediatr Rheumatol 14:55. https://doi.org/10.1186/s12969-016-0114-4

138

V. T. Anju et al.

Wampach L, Heintz-Buschart A, Hogan A et al (2017) Colonization and succession within the human gut microbiome by archaea, bacteria, and microeukaryotes during the first year of life. Front Microbiol 8:738. https://doi.org/10.3389/fmicb.2017.00738 Wang B, Yao M, Lv L et al (2017) The human microbiota in health and disease. Engineering 3:71– 82. https://doi.org/10.1016/J.ENG.2017.01.008 Wang Y, Wang X, Zhu M et al (2022) The interplay between cervicovaginal microbial dysbiosis and cervicovaginal immunity. Front Immunol 13:1–11. https://doi.org/10.3389/fimmu.2022. 857299 Waters CM, Bassler BL (2005) Quorum sensing: cell-to-cell communication in bacteria. Annu Rev Cell Dev Biol 21:319–346. https://doi.org/10.1146/annurev.cellbio.21.012704.131001 Whiteside SA, Razvi H, Dave S et al (2015) The microbiome of the urinary tract—a role beyond infection. Nat Rev Urol 12:81–90. https://doi.org/10.1038/nrurol.2014.361 Wiertsema SP, van Bergenhenegouwen J, Garssen J, Knippels LMJ (2021) The interplay between the gut microbiome and the immune system in the context of infectious diseases throughout life and the role of nutrition in optimizing treatment strategies. Nutrients 13:886. https://doi.org/10. 3390/nu13030886 Wlodarska M, Willing B, Keeney KM et al (2011) Antibiotic treatment alters the colonic mucus layer and predisposes the host to exacerbated Citrobacter rodentium-induced colitis. Infect Immun 79:1536–1545. https://doi.org/10.1128/IAI.01104-10 Wu L, Luo Y (2021) Bacterial quorum-sensing systems and their role in intestinal bacteria-host crosstalk. Front Microbiol 12:611413. https://doi.org/10.3389/fmicb.2021.611413 Wu H-J, Wu E (2012) The role of gut microbiota in immune homeostasis and autoimmunity. Gut Microbes 3:4–14. https://doi.org/10.4161/gmic.19320 Xu L, Surathu A, Raplee I et al (2020) The effect of antibiotics on the gut microbiome: a metagenomics analysis of microbial shift and gut antibiotic resistance in antibiotic treated mice. BMC Genomics 21:263. https://doi.org/10.1186/s12864-020-6665-2 Xue J, Chi L, Tu P et al (2021) Detection of gut microbiota and pathogen produced N-acyl homoserine in host circulation and tissues. NPJ Biofilms Microbiomes 7:53. https://doi.org/ 10.1038/s41522-021-00224-5 Yang L, Bajinka O, Jarju PO et al (2021) The varying effects of antibiotics on gut microbiota. AMB Express 11:116. https://doi.org/10.1186/s13568-021-01274-w York A (2019) Microbiota succession in early life. Nat Rev Microbiol:s8–s9. https://www.nature. com/articles/d42859-019-00010-6. Yoshii K, Hosomi K, Sawane K, Kunisawa J (2019) Metabolism of dietary and microbial Vitamin B family in the regulation of host immunity. Front Nutr 6:48. https://doi.org/10.3389/fnut.2019. 00048 Young VB (2017) The role of the microbiome in human health and disease: an introduction for clinicians. BMJ 356:j831. https://doi.org/10.1136/bmj.j831 Young VB, Schmidt TM (2004) Antibiotic-associated diarrhea accompanied by large-scale alterations in the composition of the fecal microbiota. J Clin Microbiol 42:1203–1206. https://doi. org/10.1128/JCM.42.3.1203-1206.2004 Zakis DR, Paulissen E, Kornete L et al (2022) The evidence for placental microbiome and its composition in healthy pregnancies: a systematic review. J Reprod Immunol 149:103455. https://doi.org/10.1016/j.jri.2021.103455 Zhang X, Coker OO, Chu ESH et al (2021) Dietary cholesterol drives fatty liver-associated liver cancer by modulating gut microbiota and metabolites. Gut 70:761–774. https://doi.org/10.1136/ gutjnl-2019-319664 Zheng D, Liwinski T, Elinav E (2020) Interaction between microbiota and immunity in health and disease. Cell Res 30:492–506. https://doi.org/10.1038/s41422-020-0332-7

Human Microbiome and the Neurological Disorders Rajesh Pamanji and Joseph Selvin

Abstract A disease is a multifactorial dysfunction of system that affects the structure and function in an organism. In the same way, neurological disorders are associated with multiple factors like gene overexpression, repression, complete knockout, protein misfolding, metabolic dysfunction, microbial infection, or dysbiosis of microbiome. It is an established fact that several neurodegenerative, neurobehavioural, mental, and metabolic disorders including Alzheimer’s, Parkinson’s, Huntington’s, schizophrenia, multiple sclerosis, depression, and obesity have been allied to microbiota. Microbiome solely might not be the cause of any disease, but its contribution is significant. The molecular interactions between gut microbiome and nervous system are complex and bidirectional; any alterations in the gut–brain axis might leads to gastrointestinal and neurological disorders. It is easy to manipulate gut microbiome rather than the brain for better therapies, so this chapter deals with microbiome association in development of neurological disorders. Keywords Gut · Microbiome · Neurodegeneration · Disorders · Multiple sclerosis · Alzheimer’s

1 Introduction Human body is the hub of diversified microbial colonization, as the complete ecosystem lies in human body like skin as earth element, fluids as water element, digestion as fiery element, and respiration as an air element. Microbes colonize the human body through these elements as food, water, and air. Their cohabitation is bidirectional, which can help and harm. It was well known fact that, from genesis to the extirpation of human body, the role of microbes is invaluable. The gut microbiome is integral and an essential part in gastrointestinal system assisting digestion, absorption, and other key essential functions (Kumar et al. 2021). A

R. Pamanji (✉) · J. Selvin Department of Microbiology, Pondicherry University, Puducherry, India e-mail: [email protected] © The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd. 2023 V. Kothari et al. (eds.), Probiotics, Prebiotics, Synbiotics, and Postbiotics, https://doi.org/10.1007/978-981-99-1463-0_8

139

140

R. Pamanji and J. Selvin

healthy gut with a diversified microbiome contributes to a healthy brain (Suganya and Koo 2020). Gut is called as second brain, as its lining with enteric nervous system composing of more than 100 million nerve cells from oesophagus to rectum. Development of pre- and post-natal healthy, functional brain depends on molecular signals received from the gut microbiome. Early clinical data suggested that gut microbiome can influence the processes like dendrite formation, myelination (Duncan and Watters 2019), neurotransmission, neurogenesis (Cerdó et al. 2020), and blood–brain barrier formation (Parker et al. 2020), which further influence cognitive and behavioural patterns (Kelly et al. 2021). Neurological disorders are a group of diseases that affect central and peripheral nervous system (Borsook 2012). The origin of neurological diseases might vary, but mostly include genetic, congenital, infections, lifestyle, malnutrition, environmental issues, and accidental. Depending upon the extent of damage, multiple functions like communication, hearing, locomotory, vision, and cognition are impacted. As per the U.S. National Library of Medicine, more than 600 neurological disorders were identified; some are relatively common, and many are rare (Siuly and Zhang 2016). Neurological disorders include a wide range of diseases, including neurodegenerative, neuromuscular, brain tumours, autism, attention deficit disorder, epilepsy, learning disabilities, cerebral palsy, and more (Macleod and Appleton 2007). The emerging role of psychobiotics in treating neurodegenerative diseases and neurodevelopmental disorders is invaluable (Mohankumar et al. 2022). Psychobiotics might be pre- or probiotic bacteria which supports the gut–brain relationship in ameliorating mental health issues (Sarkar et al. 2016). Psychobiotics usage can improve gastrointestinal function, autism spectrum disorder (ASD) symptoms, cognition in AD patients, and motor function in PD patients (Cheng et al. 2019). The present chapter describes neurological disorders, which are high incident and highly studied, and their common causes and microbiome association in their onset.

2 Neurological Disorders Associated with Microbiome From headache to dementia, epilepsy to brain stroke, all are neurological in origin. Based on the available research data a very few neurological disorders are linked to gut microbiome (Fig. 1), which includes Alzheimer’s disease (AD), Parkinson’s disease (PD), amyotrophic lateral sclerosis (ALS), Huntington’s disease (HD), multiple sclerosis (MS), and schizophrenia (Checkoway et al. 2011).

Human Microbiome and the Neurological Disorders

141

Fig. 1 Neurological disorders associated with human microbiome

3 Alzheimer’s Disease Alzheimer’s disease (AD) is a progressive neurodegenerative disorder (Haque and Levey 2019) that causes the atrophy in brain. AD is the most typical type of dementia and contributes to 60–70% (Chin-Chan et al. 2015) of cases with symptoms of altered cognitive, behavioural, and locomotor patterns, which makes individuals dependent (Abuelezz et al. 2021). The hallmark of AD is extracellular plaque deposits of the β-amyloid peptide and neurofibrillary tangles of the microtubule binding protein tau (Murphy and LeVine 2010). It is noticed that people with AD have lower levels of neurotransmitter, acetylcholine esterase in their brains (DeTure and Dickson 2019). In a recent study, it was confirmed that AD is directly linked to Porphyromonas gingivalis infection, which is the cause of chronic periodontitis. A key metabolite of this microbe called gingipains was found in the brains of AD patients confirming its role in AD disease progression (Dominy et al. 2019). The gut microbiome can change the brain’s functioning and the living being’s behaviour (Carabotti et al. 2015). Stress, antibiotics, diet, and probiotic interventions can induce alterations in gut microbiome by enhancing or lowering the risk of AD. The metabolites produced by gut microbiome could influence neurochemical system of host which may enhance or lower the risk of AD, which includes

142

R. Pamanji and J. Selvin

5-hydroxytryptamine (5-HT), gamma-aminobutyric acid (GABA), betamethylamino-L-alanine (BMAA), the expression of N-methyl-D-aspartate glutamate (NMDA) receptor and BDNF, and more. AD progression can be linked to infections like herpes simplex virus (HSV), human cytomegalovirus (HCMV), human immune deficiency virus (HIV), Chlamydia pneumoniae, Helicobacter pylori (Hu et al. 2016). Minter et al. (2016) reported that in a murine AD model, decreased β-amyloid plaque deposition and neuroinflammation were observed because of antibiotic disturbance in gut microbiota. Elderly patients with dementia have shown less abundance of Eubacterium rectale, and Bacteroides fragilis which display an anti-inflammatory activity, compared to Escherichia/Shigella, which has pro-inflammatory activity. Supplementation with Bifidobacteria and Lactobacilli-based probiotics has improved sensory and cognitive functions in AD patients (Mancuso and Santangelo 2018; He et al. 2020; Wu et al. 2021). People with AD were characterized by less abundance of Eubacterium rectale, Eubacterium hallii, Eubacterium eligens, Butyrivibrio proteoclasticus, Butyrivibrio hungatei, Clostridium sp. strain SY8519, Faecalibacterium prausnitzii, Roseburia hominis, which are known to produce butyrate. Similarly, there is an increased abundance of Klebsiella pneumoniae, Eggerthella lenta, and Odoribacter splanchnicus (Haran et al. 2019). A study conducted by Akbari et al. (2016) confirmed an improvement of cognitive and metabolic functions in AD patients supplemented with probiotic milk consisting of bacterial species Lactobacillus fermentum, Lactobacillus casei, Lactobacillus acidophilus, and Bifidobacterium bifidum for 12 weeks. In AD mice, the bacterial species Lactobacillus plantarum PS128 prevents cognitive dysfunction by modulating propionic acid levels, glycogen synthase kinase 3 beta activity, and gliosis (Huang et al. 2021). Similarly, Bacillus Subtilis is delaying neurodegeneration in Caenorhabditis Elegans AD model (Cogliati et al. 2020) and Bifidobacterium breve in improving brain function AD mice model (Zhu et al. 2021).

4 Parkinson’s Disease Parkinson’s disease (PD) is the second most highly incident progressive, multifactorial neurodegenerative disorder next to Alzheimer’s disease (Beitz 2014; Lotankar et al. 2017). The pathological hallmark of PD is the intracellular deposition of α-synuclein aggregation, which leads to neuroinflammation and neuronal cell death. Dopaminergic neurons are the most affected in PD, leading to decreased dopamine production, which causes tremors, rigidity, motor impairments, and balance difficulties (Gómez-Benito et al. 2020). PD equally affects the central and peripheral nervous system, resulting in non-motor symptoms like constipation or gastroparesis (Cersosimo and Benarroch 2012). Multiple studies support the role of gut microbiota in PD progression and associated symptoms (Sampson et al. 2016).

Human Microbiome and the Neurological Disorders

143

Parkinson’s disease often preceded by alterations of the gastrointestinal symptoms and enteric nervous system. The major alteration in the gut microbiome of PD patients is an enrichment of some bacterial genera like Bifidobacterium, Lactobacillus, and Akkermansia. Similarly, short-chain fatty acids producing bacterial genera Faecalibacterium and Lachnospiraceae are less abundant in PD patients. Dysbiosis of these strains is consistent in PD patients which lead to pro-inflammation and gastrointestinal symptoms (Romano et al. 2021). Lactobacillus plantarum PS128, a psychobiotic found to be inhibit neurodegeneration in mice Parkinson’s disease model (Lu et al. 2021; Liao et al. 2020).

5 Huntington’s Disease Huntington’s disease (HD) is a an autosomal-dominant, monogenic, progressive neurodegenerative disorder with distinct features like chorea, dystonia, progressive motor, behavioural, and cognitive decline (Walker 2007; Ghosh and Tabrizi 2018). HD is caused due to abnormal expansion of a trinucleotide—CAG repeats in the first exon of huntingtin gene which is expressed ubiquitously throughout brain and peripheral tissues (Kong et al. 2020). The mutation of huntingtin (HTT) gene leads to abnormal functioning of protein and death of specific neurons (Pandey and Rajamma 2018). Peripheral organ dysfunctions like severe metabolic phenotype, cardiomyopathy, muscle atrophy, and weight loss are common features of HD patients (Zielonka et al. 2014). The presence of mutant HTT protein in the gut leads to abnormalities in gut function (Lakra et al. 2019). The microbiome has significantly diverged in HD patients from that of healthy individuals. From phylum to genus level, there is a higher abundance of Actinobacteria, Deltaproteobacteria, Actinobacteria, Desulfovibrionales, Oxalobacteraceae, Lactobacillaceae, Desulfovibrionaceae, Intestinimonas, Bilophila, Lactobacillus, Oscillibacter, Gemmiger, Dialister (Du et al. 2021), and Bacteroidetes (Kong et al. 2020) and reduction of Firmicutes, Lachnospiraceae, and Akkermansiaceae (Wasser et al. 2020) in HD group. A study by Alonso et al. (2019) reported the brain microbiota of HD patients, including bacterial genera Pseudomonas, Acinetobacter, Burkholderia, and genera Ramularia are unique to HD patients.

6 Amyotrophic Lateral Sclerosis Amyotrophic lateral sclerosis (ALS) is an idiopathic, fatal neurodegenerative disorder with progressive deterioration and loss of motor neuron function leads to muscle weakness and eventual paralysis (Hulisz 2018; Hardiman et al. 2017). ALS is associated with mutations in more than 25 genes, which include TARDBP/TDP43, FUS, C9orf72, and SOD1 (Nguyen et al. 2018). Clinical symptoms include amyotrophy, lateral sclerosis, progressive muscular atrophy, progressive bulbar

144

R. Pamanji and J. Selvin

atrophy, muscle weakness, spastic limbs, and hyperreflexia (Verma 2021). The chemical toxicants can contribute ALS like β-Methylamino-L-alanine (Proctor et al. 2019; Delcourt et al. 2017) and formaldehyde (Seals et al. 2017; Roberts et al. 2016). There are multiple reports stating the connection between ALS pathogenesis and gut microbiome. In ALS patients the relative abundance of butyrate-producing bacteria Eubacterium rectale and Roseburia intestinalis is significantly low (Nicholson et al. 2021). In ALS patients, Bacteroidetes were enhanced at phylum level and Firmicutes were decreased (Zeng et al. 2020). Similarly, there is a decrease in Oscillibacter, Anaerostipes, Lachnospiraceae population and overgrowth of Dorea was found in ALS patients (Obrenovich et al. 2020). In ALS conditions, it was identified that there is a shift of microbiome profile, reduction in beneficial bacteria and intestinal inflammation (Zhang et al. 2022; Burberry et al. 2020; Blacher et al. 2019). A study by Sun et al. (2019) reported that prolonged antibiotic usage is associated with risk of ALS. Apart from genetic factors in causing ALS, gut microbiota has shed some light on how its onset is linked.

7 Multiple Sclerosis Multiple sclerosis (MS) is a chronic autoimmune, inflammatory, demyelinating, neurodegenerative disease, which is found to be multifactorial, heterogenous, and immune-mediated (Filippi et al. 2018). MS progression is linked to more than 100 different genetic variants which promote susceptibility to disease (Dendrou et al. 2015); the major susceptibility allele is HLA (human leukocyte antigen Class II gene) (Waubant et al. 2019). Multiple factors associated with MS progression are vitamin D deficiency, migraine, family history of MS and smoking (Taan et al. 2021). The blood metabolome of MS patients like fatty acid biosynthesis, linoleate metabolic pathway, methionine, chalcone, 4-nitrocatechol and dihydrochalcone was significantly altered in MS patients (Cantoni et al. 2022). A compromised immune system due to changes in gut microbiome can trigger MS development and associated affects (Fan and Zhang 2019). Gut microbiomes in MS patients were significantly different from those in healthy individuals, which include increased abundance of Dorea, Mycoplana, Pseudomonas, Blautia, and Haemophilus (Chen et al. 2016). In a different study, Streptococcus, Acinetobacter, Eggerthella, Flavobacterium, Pedobacteria, and Akkermansia populations are elevated in MS patients (Amini et al. 2020). Probiotic intake in MS patients for a period of 12 weeks has positive effect on mental health parameters, EDSS, insulin resistance markers, and inflammatory factors (Kouchaki et al. 2017).

Human Microbiome and the Neurological Disorders

145

8 Schizophrenia Schizophrenia is a chronic psychological disorder which disrupts various cognitive functions, includes perception, thought, memory, and volition (Morera-Fumero and Abreu-Gonzalez 2013). The exact cause of schizophrenia is unclear, but researchers are linking genetic and molecular basis. Schizophrenia patients have different gut biomes compared to healthy individuals (Akhondzadeh 2019). There are many facultative anaerobes in the gut of schizophrenic patients, including Alkaliphilus oremlandii, Lactobacillus fermentum, Cronobacter sakazakii/turicensis, and Enterococcus faecium. In schizophrenia patients there are metabolic alterations in synthesis/degradation of neurotransmitters, tryptophan metabolism, and short-chain fatty acids synthesis (Zhu et al. 2020). Consumption of Lactobacillus group bacteria (Schwarz et al. 2018) and probiotic Bifidobacterium breve A-1 (Okubo et al. 2019) reduced anxiety and depressive symptoms in schizophrenia patients.

9 Dysbiosis and Neurological Disorders It is evident from the literature that one of the common causes of neurological and intestinal disorders is dysbiosis of gut microbiome (Carding et al. 2015). Gut dysbiosis might led to malfunctioning of gut–brain axis signalling system, thereby leads to enhanced oxidative stress, imbalanced metabolism, and disturbances in immune functions (Peterson 2020).

10

Cause of Dysbiosis

Dysbiosis is the result of multiple factors like dietary change, accidental chemical and pesticide exposure, alcohol consumption, general medication, antibiotics use, poor dental hygiene, stress or anxiety, and unprotected sex (Martinez et al. 2021). Oxidative stress, bacterial toxins, bacteriophages induction might trigger rapid shift of gut microbiome and lead to dysbiosis (Weiss and Hennet 2017).

11

Stress

The most common issue that the today’s world is facing is stress, it might be physical, mental, and drug related. Every disease has its roots in stress. Stress is bidirectional, it can make an organism stronger or weaker depending upon the adaptability. Stress can reshape gut microbiome by means of stress hormones, which in turn makes gut microbiome to produce metabolites, toxins, and

146

R. Pamanji and J. Selvin

neurotransmitters that can alter behaviour (Madison and Kiecolt-Glaser 2019; Geng et al. 2020). A study with frontline health workers confirmed that stressful work environment induced gut dysbiosis might persist for 6 months. The bacterial species associated with mental health were Eubacterium spp. and Faecalibacterium spp. (Gao et al. 2022). Antibiotics being broad spectrum in nature kills non-targeted organism, which leads to dysbiosis of gut (Wang et al. 2021; Karakan et al. 2021).

12

Future Direction

It is concluded from all these published studies that the dysbiosis of microbiome is common path to neurological disorders. So, future therapy for neurological disorders would be manipulation of the gut microbiome and usage of psychobiotics. Need to address how different psychobiotics are effective on different neurological disorders and on different stages of severity. Further research is warranted to decipher the association of other neurological disorders with gut microbiome and psychobiotics usage, safety and effectiveness in treatment should be studied. Similarly, is dysbiosis the real cause of neurological disorders has to be explored. Acknowledgement The author is thankful to Vice Chancellor and Registrar, Pondicherry University, Pondicherry, India for providing the facilities for ongoing research work and to UGC, Govt. of India for providing financial assistance in the form of DSK postdoctoral fellowship BL/19-20/0302.

References Abuelezz NZ, Nasr FE, AbdulKader MA, Bassiouny AR, Zaky A (2021) MicroRNAs as potential orchestrators of Alzheimer’s disease-related pathologies: insights on current status and future possibilities. Front Aging Neurosci 13:743573. https://doi.org/10.3389/fnagi.2021.743573 Akbari E, Asemi Z, Daneshvar Kakhaki R, Bahmani F, Kouchaki E, Tamtaji OR, Hamidi GA, Salami M (2016) Effect of probiotic supplementation on cognitive function and metabolic status in Alzheimer’s disease: a randomized, double-blind and controlled trial. Front Aging Neurosci 10(8):256. https://doi.org/10.3389/fnagi.2016.00256 Akhondzadeh S (2019) Microbiome and schizophrenia. Avicenna J Med Biotechnol 11(4): 269. PMID: 31908733; PMCID: PMC6925402 Alonso R, Pisa D, Carrasco L (2019) Brain microbiota in Huntington’s disease patients. Front Microbiol 10:2622. https://doi.org/10.3389/fmicb.2019.02622 Amini ME, Shomali N, Bakhshi A, Rezaei S, Hemmatzadeh M, Hosseinzadeh R, Eslami S, Babaie F, Aslani S, Torkamandi S, Mohammadi H (2020) Gut microbiome and multiple sclerosis: new insights and perspective. Int Immunopharmacol 88:107024. https://doi.org/10. 1016/j.intimp.2020.107024 Beitz JM (2014) Parkinson’s disease: a review. Front Biosci (Schol Ed) 6(1):65–74. https://doi.org/ 10.2741/s415 Blacher E, Bashiardes S, Shapiro H, Rothschild D, Mor U, Dori-Bachash M et al (2019) Potential roles of gut microbiome and metabolites in modulating ALS in mice. Nature 572:474–480. https://doi.org/10.1038/s41586-019-1443-5

Human Microbiome and the Neurological Disorders

147

Borsook D (2012) Neurological diseases and pain. Brain 135(pt 2):320–344. https://doi.org/10. 1093/brain/awr271 Burberry A, Wells MF, Limone F, Couto A, Smith KS, Keaney J et al (2020) C9orf72 suppresses systemic and neural inflammation induced by gut bacteria. Nature 582:89–94. https://doi.org/10. 1038/s41586-020-2288-7 Cantoni C, Qingqi L, Dorsett Y, Ghezzi L, Liu Z, Pan Y, Chen K, Han Y, Li Z, Xiao H, Gormley M, Liu Y, Bokoliya S, Panier H, Suther C, Evans E, Deng L, Locca A, Mikesell R, Zhou Y (2022) Alterations of host-gut microbiome interactions in multiple sclerosis. EBioMedicine 76:103798. https://doi.org/10.1016/j.ebiom.2021.103798 Carabotti M, Scirocco A, Maselli MA, Severi C (2015) The gut-brain axis: interactions between enteric microbiota, central and enteric nervous systems. Ann Gastroenterol 28(2): 203–209. PMID: 25830558; PMCID: PMC4367209 Carding S, Verbeke K, Vipond DT, Corfe BM, Owen LJ (2015) Dysbiosis of the gut microbiota in disease. Microb Ecol Health Dis 26:26191. https://doi.org/10.3402/mehd.v26.26191 Cerdó T, Diéguez E, Campoy C (2020) Impact of gut microbiota on neurogenesis and neurological diseases during infancy. Curr Opin Pharmacol 50:33. https://doi.org/10.1016/j.coph.2019. 11.006 Cersosimo MG, Benarroch EE (2012) Pathological correlates of gastrointestinal dysfunction in Parkinson’s disease. Neurobiol Dis 46:559–564. https://doi.org/10.1016/j.nbd.2011.10.014 Checkoway H, Lundin JI, Kelada SN (2011) Neurodegenerative diseases. IARC Sci Publ 163:407– 419. PMID: 22997874 Chen J, Chia N, Kalari KR, Yao JZ, Novotna M, Paz Soldan MM, Luckey DH, Marietta EV, Jeraldo PR, Chen X, Weinshenker BG, Rodriguez M, Kantarci OH, Nelson H, Murray JA, Mangalam AK (2016) Multiple sclerosis patients have a distinct gut microbiota compared to healthy controls. Sci Rep 6:28484. https://doi.org/10.1038/srep28484 Cheng LH, Liu YW, Wu CC, Wang S, Tsai YC (2019) Psychobiotics in mental health, neurodegenerative and neurodevelopmental disorders. J Food Drug Anal 27(3):632–648. https://doi. org/10.1016/j.jfda.2019.01.002 Chin-Chan M, Navarro-Yepes J, Quintanilla-Vega B (2015) Environmental pollutants as risk factors for neurodegenerative disorders: Alzheimer and Parkinson diseases. Front Cell Neurosci 9:124. https://doi.org/10.3389/fncel.2015.00124 Cogliati S, Clementi V, Francisco M, Crespo C, Argañaraz F, Grau R (2020) Bacillus subtilis delays neurodegeneration and behavioral impairment in the Alzheimer’s disease model Caenorhabditis elegans. J Alzheimers Dis 73(3):1035–1052. https://doi.org/10.3233/JAD-190837 Delcourt N, Claudepierre T, Maignien T, Arnich N, Mattei C (2017) Cellular and molecular aspects of the β-N-methylamino-l-alanine (BMAA) mode of action within the neurodegenerative pathway: facts and controversy. Toxins (Basel) 10(1):6. https://doi.org/10.3390/ toxins10010006 Dendrou CA, Fugger L, Friese MA (2015) Immunopathology of multiple sclerosis. Nat Rev Immunol 15(9):545–558. https://doi.org/10.1038/nri3871 DeTure MA, Dickson DW (2019) The neuropathological diagnosis of Alzheimer’s disease. Mol Neurodegener 14:32. https://doi.org/10.1186/s13024-019-0333-5 Dominy SS, Casey L, Florian E, Malgorzata B, Agata M, Andrei K, Mai N, Ursula H, Debasish R, Griffin C, Leslie HJ, Shirin A-K, Samer K, Alexander L, Mark RI, Barbara P, Piotr M, Annelie H, Karina A, Hatice H, Glenn WD, Eri RC, Faull RLM, Curtis Maurice A, Mike D, Jan P (2019) Porphyromonas gingivalis in Alzheimer’s disease brains: evidence for disease causation and treatment with small-molecule inhibitors. Sci Adv 5:eaau3333. https://doi.org/10. 1126/sciadv.aau3333 Du G, Dong W, Yang Q, Yu X, Ma J, Gu W, Huang Y (2021) Altered gut microbiota related to inflammatory responses in patients with Huntington’s disease. Front Immunol 11:603594. https://doi.org/10.3389/fimmu.2020.603594 Duncan ID, Watters JJ (2019) Remyelination and the gut-brain axis. Proc Natl Acad Sci U S A 116:24922. https://doi.org/10.1073/pnas.1918897116

148

R. Pamanji and J. Selvin

Fan Y, Zhang J (2019) Dietary modulation of intestinal microbiota: future opportunities in experimental autoimmune encephalomyelitis and multiple sclerosis. Front Microbiol 10:740. https://doi.org/10.3389/fmicb.2019.00740 Filippi M, Bar-Or A, Piehl F et al (2018) Multiple sclerosis. Nat Rev Dis Primers 4:43. https://doi. org/10.1038/s41572-018-0041-4 Gao F, Guod R, Ma Q, Li Y, Wang W, Fan Y, Ju Y, Zhao B, Gao Y, Qian L, Yang Z, He X, Jin X, Liu Y, Peng Y, Chen C, Chen Y, Gao C et al (2022) Stressful events induce long-term gut microbiota dysbiosis and associated post-traumatic stress symptoms in healthcare workers fighting against COVID-19. J Affect Disord 303(15):187–195. https://doi.org/10.1016/j.jad. 2022.02.024 Geng S, Yang L, Cheng F, Zhang Z, Li J, Liu W, Li Y, Chen Y, Bao Y, Chen L, Fei Z, Li X, Hou J, Lin Y, Liu Z, Zhang S, Wang H, Zhang Q, Wang H, Wang X, Zhang J (2020) Gut microbiota are associated with psychological stress-induced defections in intestinal and blood–brain barriers. Front Microbiol 10:3067. https://doi.org/10.3389/fmicb.2019.03067 Ghosh R, Tabrizi SJ (2018) Clinical features of Huntington’s disease. Adv Exp Med Biol 1049:1– 28. https://doi.org/10.1007/978-3-319-71779-1_1 Gómez-Benito M, Granado N, García-Sanz P, Michel A, Dumoulin M, Moratalla R (2020) Modeling Parkinson’s disease with the alpha-synuclein protein. Front Pharmacol 11:356. https://doi.org/10.3389/fphar.2020.00356 Haque RU, Levey AI (2019) Alzheimer’s disease: a clinical perspective and future nonhuman primate research opportunities. Proc Natl Acad Sci U S A 116(52):26224–26229. https://doi. org/10.1073/pnas.1912954116 Haran JP, Bhattarai SK, Foley SE, Dutta P, Ward DV, Bucci V, McCormick BA (2019) Alzheimer’s disease microbiome is associated with dysregulation of the anti-inflammatory P-glycoprotein pathway. MBio 10(3):e00632–e00619. https://doi.org/10.1128/mBio.00632-19 Hardiman O, Al-Chalabi A, Chio A, Corr EM, Logroscino G, Robberecht W, Shaw PJ, Simmons Z, van den Berg LH (2017) Amyotrophic lateral sclerosis. Nat Rev Dis Primers 3:17071. https:// doi.org/10.1038/nrdp.2017.71 He Y, Li B, Sun D, Chen S (2020) Gut microbiota: implications in Alzheimer’s disease. J Clin Med 9(7):2042. https://doi.org/10.3390/jcm9072042 Hu X, Wang T, Jin F (2016) Alzheimer’s disease and gut microbiota. Sci China Life Sci 59(10): 1006–1023. https://doi.org/10.1007/s11427-016-5083-9 Huang HJ, Chen JL, Liao JF, Chen YH, Chieu MW, Ke YY, Hsu CC, Tsai YC, Hsieh-Li HM (2021) Lactobacillus plantarum PS128 prevents cognitive dysfunction in Alzheimer’s disease mice by modulating propionic acid levels, glycogen synthase kinase 3 beta activity, and gliosis. BMC Complement Med Ther 21(1):259. https://doi.org/10.1186/s12906-021-03426-8 Hulisz D (2018) Amyotrophic lateral sclerosis: disease state overview. Am J Manag Care 24:S320– S326. PMID: 30207670 Karakan T, Ozkul C, Küpeli Akkol E, Bilici S, Sobarzo-Sánchez E, Capasso R (2021) Gut-brainmicrobiota axis: antibiotics and functional gastrointestinal disorders. Nutrients 13(2):389. https://doi.org/10.3390/nu13020389 Kelly JR, Minuto C, Cryan JF, Clarke G, Dinan TG (2021) The role of the gut microbiome in the development of schizophrenia. Schizophr Res 234:4–23. https://doi.org/10.1016/j.schres.2020. 02.010 Kong G, Cao KL, Judd LM, Li S, Renoir T, Hannan AJ (2020) Microbiome profiling reveals gut dysbiosis in a transgenic mouse model of Huntington’s disease. Neurobiol Dis 135:104268. https://doi.org/10.1016/j.nbd.2018.09.001 Kouchaki E, Tamtaji OR, Salami M, Bahmani F, Daneshvar Kakhaki R, Akbari E, TajabadiEbrahimi M, Jafari P, Asemi Z (2017) Clinical and metabolic response to probiotic supplementation in patients with multiple sclerosis: a randomized, double-blind, placebo-controlled trial. Clin Nutr 36(5):1245–1249. https://doi.org/10.1016/j.clnu.2016.08.015 Kumar P, Lee JH, Lee J (2021) Diverse roles of microbial indole compounds in eukaryotic systems. Biol Rev Camb Philos Soc 96(6):2522–2545. https://doi.org/10.1111/brv.12765

Human Microbiome and the Neurological Disorders

149

Lakra P, Aditi K, Agrawal N (2019) Peripheral expression of mutant huntingtin is a critical determinant of weight loss and metabolic disturbances in Huntington’s disease. Sci Rep 9: 10127. https://doi.org/10.1038/s41598-019-46470-8 Liao JF, Cheng YF, You ST, Kuo WC, Huang CW, Chiou JJ, Hsu CC, Hsieh-Li HM, Wang S, Tsai YC (2020) Lactobacillus plantarum PS128 alleviates neurodegenerative progression in 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine-induced mouse models of Parkinson’s disease. Brain Behav Immun 90:26–46. https://doi.org/10.1016/j.bbi.2020.07.036 Lotankar S, Prabhavalkar KS, Bhatt LK (2017) Biomarkers for Parkinson’s disease: recent advancement. Neurosci Bull 33(5):585–597. https://doi.org/10.1007/s12264-017-0183-5 Lu CS, Chang HC, Weng YH, Chen CC, Kuo YS, Tsai YC (2021) The add-on effect of Lactobacillus plantarum PS128 in patients with Parkinson’s disease: a pilot study. Front Nutr 8:650053. https://doi.org/10.3389/fnut.2021.650053 Macleod S, Appleton RE (2007) Neurological disorders presenting mainly in adolescence. Arch Dis Child 92(2):170–175. https://doi.org/10.1136/adc.2005.088070 Madison A, Kiecolt-Glaser JK (2019) Stress, depression, diet, and the gut microbiota: humanbacteria interactions at the core of psychoneuroimmunology and nutrition. Curr Opin Behav Sci 28:105–110. https://doi.org/10.1016/j.cobeha.2019.01.011 Mancuso C, Santangelo R (2018) Alzheimer’s disease and gut microbiota modifications: the long way between preclinical studies and clinical evidence. Pharmacol Res 129:329–336. https://doi. org/10.1016/j.phrs.2017.12.009 Martinez JE, Kahana DD, Ghuman S, Wilson HP, Wilson J, Kim SCJ, Lagishetty V, Jacobs JP, Sinha-Hikim AP, Friedman TC (2021) Unhealthy lifestyle and gut dysbiosis: a better understanding of the effects of poor diet and nicotine on the intestinal microbiome. Front Endocrinol (Lausanne) 12:667066. https://doi.org/10.3389/fendo.2021.667066 Minter M, Zhang C, Leone V et al (2016) Antibiotic-induced perturbations in gut microbial diversity influences neuro-inflammation and amyloidosis in a murine model of Alzheimer’s disease. Sci Rep 6:30028. https://doi.org/10.1038/srep30028 Mohankumar A, Kalaiselvi D, Thiruppathi G, Patteswari D, Tawata S, Sundararaj P (2022) Psychobiotics in health, longevity, and neurological disorders. In: Rajagopal S, Ramachandran S, Sundararaman G, Gadde Venkata S (eds) Role of nutrients in neurological disorders. Nutritional neurosciences. Springer, Singapore. https://doi.org/10.1007/978-981-168158-5_2 Morera-Fumero AL, Abreu-Gonzalez P (2013) Role of melatonin in schizophrenia. Int J Mol Sci 14(5):9037–9050. https://doi.org/10.3390/ijms14059037 Murphy MP, LeVine H III (2010) Alzheimer’s disease and the amyloid-beta peptide. J Alzheimers Dis 19(1):311–323. https://doi.org/10.3233/JAD-2010-1221 Nguyen HP, Van Broeckhoven C, van der Zee J (2018) ALS genes in the genomic era and their implications for FTD. Trends Genet 34(6):404–423. https://doi.org/10.1016/j.tig.2018.03.001 Nicholson K, Bjornevik K, Abu-Ali G, Chan J, Cortese M, Dedi B, Jeon M, Xavier R, Huttenhower C, Ascherio A, Berry JD (2021) The human gut microbiota in people with amyotrophic lateral sclerosis. Amyotroph Lateral Scler Frontotemporal Degener 22(3-4): 186–194. https://doi.org/10.1080/21678421.2020.1828475 Obrenovich M, Jaworski H, Tadimalla T, Mistry A, Sykes L, Perry G, Bonomo RA (2020) The role of the microbiota-gut-brain axis and antibiotics in ALS and neurodegenerative diseases. Microorganisms 8(5):784. https://doi.org/10.3390/microorganisms8050784 Okubo R, Koga M, Katsumata N et al (2019) Effect of Bifidobacterium breve A-1 on anxiety and depressive symptoms in schizophrenia: a proof-of-concept study. J Affect Disord 245:377–385. https://doi.org/10.1016/j.jad.2018.11.011 Pandey M, Rajamma U (2018) Huntington’s disease: the coming of age. J Genet 97(3):649–664. https://doi.org/10.1007/s12041-018-0957-1

150

R. Pamanji and J. Selvin

Parker A, Fonseca S, Carding SR (2020) Gut microbes and metabolites as modulators of bloodbrain barrier integrity and brain health. Gut Microbes 11(2):135–157. https://doi.org/10.1080/ 19490976.2019.1638722 Peterson CT (2020) Dysfunction of the microbiota-gut-brain axis in neurodegenerative disease: the promise of therapeutic modulation with prebiotics, medicinal herbs, probiotics, and synbiotics. J Evid-Based Integr Med 25:2515690X20957225. https://doi.org/10.1177/2515690X20957225 Proctor EA, Mowrey DD, Dokholyan NV (2019) β-Methylamino-L-alanine substitution of serine in SOD1 suggests a direct role in ALS etiology. PLoS Comput Biol 15(7):e1007225. https://doi. org/10.1371/journal.pcbi.1007225 Roberts AL, Johnson NJ, Cudkowicz ME et al (2016) Job-related formaldehyde exposure and ALS mortality in the USA. J Neurol Neurosurg Psychiatry 87:786–788. https://doi.org/10.1136/jnnp2015-310750 Romano S, Savva GM, Bedarf JR et al (2021) Meta-analysis of the Parkinson’s disease gut microbiome suggests alterations linked to intestinal inflammation. NPJ Parkinsons Dis 7:27. https://doi.org/10.1038/s41531-021-00156-z Sampson TR, Debelius JW, Thron T, Janssen S, Shastri GG, Ilhan ZE, Challis C, Schretter CE, Rocha S, Gradinaru V, Chesselet MF, Keshavarzian A, Shannon KM, Krajmalnik-Brown R, Wittung-Stafshede P, Knight R, Mazmanian SK (2016) Gut microbiota regulate motor deficits and neuroinflammation in a model of Parkinson’s disease. Cell 167(6):1469–1480.e12. https:// doi.org/10.1016/j.cell.2016.11.018 Sarkar A, Lehto SM, Harty S, Dinan TG, Cryan JF, Burnet P (2016) Psychobiotics and the manipulation of bacteria-gut-brain signals. Trends Neurosci 39(11):763–781. https://doi.org/ 10.1016/j.tins.2016.09.002 Schwarz E, Maukonen J, Hyytiäinen T et al (2018) Analysis of microbiota in first episode psychosis identifies preliminary associations with symptom severity and treatment response. Schizophr Res 192:398–403. https://doi.org/10.1016/j.schres.2017.04.017 Seals RM, Kioumourtzoglou MA, Gredal O, Hansen J, Weisskopf MG (2017) Occupational formaldehyde and amyotrophic lateral sclerosis. Eur J Epidemiol 32(10):893–899. https://doi. org/10.1007/s10654-017-0249-8 Siuly S, Zhang Y (2016) Medical big data: neurological diseases diagnosis through medical data analysis. Data Sci Eng 1:54–64. https://doi.org/10.1007/s41019-016-0011-3 Suganya K, Koo BS (2020) Gut–brain axis: role of gut microbiota on neurological disorders and how probiotics/prebiotics beneficially modulate microbial and immune pathways to improve brain functions. Int J Mol Sci 21(20):7551. https://doi.org/10.3390/ijms21207551 Sun J, Zhan Y, Mariosa LH, Almqvist C, Ingre C et al (2019) Antibiotics use and risk of amyotrophic lateral sclerosis in Sweden. Eur J Neurol 26:1355–1361. https://doi.org/10.1111/ ene.13986 Taan M, Al Ahmad F, Ercksousi MK, Hamza G (2021) Risk factors associated with multiple sclerosis: a case-control study in Damascus, Syria. Mult Scler Int 2021:8147451. https://doi.org/ 10.1155/2021/8147451 Verma A (2021) Clinical manifestation and management of amyotrophic lateral sclerosis. In: Araki T (ed) Chapter 1. Amyotrophic Lateral Sclerosis. Exon Publications, Brisbane. https://doi.org/ 10.36255/exonpublications.amyotrophiclateralsclerosis.management.2021 Walker FO (2007) Huntington’s disease. Lancet 369(9557):218–228. https://doi.org/10.1016/ S0140-6736(07)60111-1 Wang P, Tu K, Cao P, Yang Y, Zhang H, Qiu XT, Zhang MM, Wu XJ, Yang H, Chen T (2021) Antibiotics-induced intestinal dysbacteriosis caused behavioral alternations and neuronal activation in different brain regions in mice. Mol Brain 14(1):49. https://doi.org/10.1186/s13041021-00759-w Wasser CI, Mercieca EC, KongG HAJ, McKeown SJ, Glikmann-Johnston Y, Stout JC (2020) Gut dysbiosis in Huntington’s disease: associations among gut microbiota, cognitive performance,

Human Microbiome and the Neurological Disorders

151

and clinical outcomes. Brain Commun 2(2):fcaa110. https://doi.org/10.1093/braincomms/ fcaa110 Waubant E, Lucas R, Mowry E, Graves J, Olsson T, Alfredsson L, Langer-Gould A (2019) Environmental and genetic risk factors for MS: an integrated review. Ann Clin Transl Neurol 6(9):1905–1922. https://doi.org/10.1002/acn3.50862 Weiss GA, Hennet T (2017) Mechanisms and consequences of intestinal dysbiosis. Cell Mol Life Sci 74(16):2959–2977. https://doi.org/10.1007/s00018-017-2509-x Wu S, Liu X, Jiang R, Yan X, Ling Z (2021) Roles and mechanisms of gut microbiota in patients with Alzheimer’s disease. Front Aging Neurosci 13:650047. https://doi.org/10.3389/fnagi. 2021.650047 Zeng Q, Shen J, Chen K et al (2020) The alteration of gut microbiome and metabolism in amyotrophic lateral sclerosis patients. Sci Rep 10:12998. https://doi.org/10.1038/s41598-02069845-8 Zhang S, Cooper-Knock J, Weimer AK, Shi M, Moll T, JNG M, Harvey C, Nezhad HG, Franklin J, CDS S, Ning K, Wang C, Li J, Dilliott AA, Farhan S, Elhaik E, Pasniceanu I, Livesey MR, Eitan C, Hornstein E, Kenna KP, Project MinE ALS Sequencing Consortium, Veldink JH, Ferraiuolo L, Shaw PJ, Snyder MP (2022) Genome-wide identification of the genetic basis of amyotrophic lateral sclerosis. Neuron 110(6):992–1008.e11. https://doi.org/10.1016/j.neuron. 2021.12.019 Zhu F, Ju Y, Wang W et al (2020) Metagenome-wide association of gut microbiome features for schizophrenia. Nat Commun 11:1612. https://doi.org/10.1038/s41467-020-15457-9 Zhu G, Zhao J, Zhang H, Chen W, Wang G (2021) Administration of Bifidobacterium breve improves the brain function of Aβ1-42-treated mice via the modulation of the gut microbiome. Nutrients 13(5):1602. https://doi.org/10.3390/nu13051602 Zielonka D, Piotrowska I, Marcinkowski JT, Mielcarek M (2014) Skeletal muscle pathology in Huntington’s disease. Front Physiol 5:380. https://doi.org/10.3389/fphys.2014.00380

Exploring the Unexplored Arena: Butyrate as a Dual Communicator in Gut–Brain Axis Zeel Bhatia, Sunny Kumar, and Sriram Seshadri

Abstract It has been thought lately that gut microbiota plays a predominant role in the neuronal behavior via the gut–brain alliance. The plausible mechanisms of involvement of gut microbiota in neuropsychological disorders might lie within the metabolites produced by them. One such chief metabolite is butyrate. It is a short chain fatty acid produced by the gut microbiota via fermentation of indigestible fibers in the gut. Butyrate works as a dual communicator between gut–brain axis by triggering the anti-inflammatory responses in the central nervous system (CNS), thereby helps to combat neurological diseases such as Parkinson’s disease Alzheimer’s disease, stress, anxiety, and depression. The main focus of this chapter revolves around roles of gut microbiota, production of butyrate, the role of butyrate in maintaining gut as well as the blood–brain barrier permeability and its signaling pathways. Moreover, understanding the balanced gut microbiota composition in the gut–brain axis and the potential therapeutic interventions of butyrate may help in relieving various neurological disorders. Keywords Gut–brain axis · Butyrate · Gut microbiota · Neurological disorders · Blood–brain barrier (BBB) · SCFA

1 Introduction Have you ever had any gut feeling or butterflies in your stomach? If yes, then it emanates from your belly suggesting that your gut and brain are connected. This crosstalk between gut and brain is known as gut–brain axis. Substantial body of evidences suggests that there is a bidirectional interaction between gut and brain (Rao and Gershon 2016). There is a “brain in your gut” known as enteric nervous system (ENS). It is a large, complex component of peripheral nervous system which enables monitoring Z. Bhatia · S. Kumar · S. Seshadri (✉) Institute of Science, Nirma University, Ahmedabad, Gujarat, India e-mail: [email protected]; [email protected]; [email protected] © The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd. 2023 V. Kothari et al. (eds.), Probiotics, Prebiotics, Synbiotics, and Postbiotics, https://doi.org/10.1007/978-981-99-1463-0_9

153

154

Z. Bhatia et al.

and control of the gastrointestinal behavior independently of the central nervous system (CNS). The ENS is two thin layers comprising more than 100 million nerve cells which line the gastrointestinal tract (GIT) from esophagus to rectum. ENS has become an evident part in playing pivotal role in neurological disorders. It regulates majority of enteric processes such as detecting nutrients, ions, bioactive peptides, epithelial secretion fluids, maintaining intestinal barrier function, and regulating immune response (Nezami and Srinivasan 2010). ENS acts as the key modulator of the gut barrier function and as a regulator of enteric system homeostasis. ENS makes use of more than 30 neurotransmitters, most of which resembles that of CNS such as dopamine, serotonin, and acetylcholine. Of which, 95% of body’s serotonin and 50% of dopamine are produced in the gut (Yaghoubfar et al. 2020). These neurotransmitters monitor and regulate the blood circulation, gut motility, gastrointestinal innate immune system, nutrient absorption, and the gut microbiome (Mittal et al. 2017).

2 Serotonin: A Critical Signaling Regulator The gut–brain axis is a network of bidirectional communication between gut and brain, where serotonin (5-HT) is critical signaling regulator. It modulates complex physiological functions including body temperature control, gastric secretions, etc. The synthesis cascade of 5-HT is similar in both ENS and CNS. In ENS, 5-HT is synthesized from tryptophan in enterochromaffin cells of the GIT. Tryptophan is a precursor molecule of 5-HT that is an essential amino acid which must be supplemented in the diet. Once, tryptophan is absorbed from the gut, it is transported in the blood circulation. The large amino acid transporters facilitate its transport via crossing the blood–brain barrier (BBB), reaches to CNS participates in serotonin synthesis (Höglund et al. 2019). 5-HT appears to play supreme role in mood, emotions, digestion, and appetite. Serotonin is also able to modulate the immune response and therefore it eventually influences the intestinal inflammation. Its receptors are closely linked with immune cells like monocytes, lymphocytes, dendritic cells, and macrophage which implicate that 5-HT plays an important role in immune response. Serotonin is also involved in development of the vagal innervations (vagus nerve) which connects the two way neural network between gut and brain providing both motor and sensory interventions for various functions (Ratcliffe et al. 2011).

3 Appetite Related Hormones Feeling of hunger and satiety are principle voluntary stimulus for feeding behavior. CNS, hormones, and vagal afferents have a convoluted appetite system which initiates or stops feeding. Appetite related hormones are ghrelin, leptin, and insulin

Exploring the Unexplored Arena: Butyrate as a Dual Communicator. . .

155

which are produced by peripheral organs like, gut, pancreas, and adipose. Here, we outline the roles of these hormones that play a predominant part in modulating the brain behavior via humoral or neuronal pathways. Ghrelin is gut derived hunger hormone that transmits signals of starvation to brain by binding to various receptors on the vagal afferent (Han et al. 2021a, b). It can also cross the BBB and activate neuropeptide tyrosine (NPY) that leads to an increased food intake and decreased energy expenditure. In contrary to ghrelin, leptin is responsible for inhibiting the host appetite. Leptin is produced chiefly in white adipose tissue and intestine, where its receptors are present. It can cross the BBB via vagus nerve and inhibit the NPY cascade which eventually leads to obstructed host appetite. Insulin is another hormone which regulates glucose and energy homeostasis. It also acts as a satiety signal. It has been reported that insulin related satiety signaling pathways are related to decreased intake of food in humans and rodents (Loh et al. 2017). Same as leptin and ghrelin, insulin can also cross the BBB and control the feeding behavior.

4 Gut Microorganisms: The Autocrats Why so much emphasis has been given to ENS, CNS, and hormones? This is owing to their direct or indirect regulation via the gut residing microorganisms. Gastrointestinal tract (GIT) harbors a dynamic and complex community of approximately 100 trillion microorganisms (Valdes et al. 2018). Gut microbiota possesses dynamic hallmark features throughout the different stages of life, starting from a very simple microbial composition just after birth to highly complex community as one matures. Gut microbiota comprises more than 100 bacterial species belonging to majorly six phyla: Firmicutes, Bacteriodetes, Actinobacteria Proteobacteria, Fusobacteria, and Verrucomicrobia (Verduci et al. 2020). Ninety percent of gut microbiota is represented by two prime phyla Firmicutes and Bacteroidetes. The Gram positive bacteria belong to phyla Firmicutes, major genera are Bacillus, Enterococcus, Clostridium, Lactobacillus, etc. While Bacteroidetes includes Gram negative bacteria that are from genera Bacteroides, Prevotella, Parabacteroids, E. coli etc. Overall host homeostasis is associated with the ratio between these two phyla Firmicutes/ Bacteroidetes (F/B ratio) (Stojanov et al. 2020). A change in this ratio is often known as gut dysbiosis and it is associated with various pathophysiologies like type 2 diabetes, irritable bowel syndrome. In more recent times, it has been associated with brain disorders like Alzheimer’s diseases, Parkinson’s disease, stress, anxiety, depression etc. (Martinez et al. 2021). This complexity is associated with genetic, physiological, and environmental aspects such as lifestyle, hormonal changes, nutrition, immunity, and the microbiome–gut–brain alliance. Gut microbiota is intricately associated with the host to modulate psychological functions as well as physiological functions like strengthening the gut integrity, maintaining its permeability, energy harvesting, protecting against pathogens, and maintaining the overall host homeostasis (Thursby

156

Z. Bhatia et al.

and Juge 2017). It also aids in nutrient, energy, and drug metabolism. There are growing evidences that gut microbes produce neurotransmitters such as gammaaminobutyric acid (GABA) and serotonin, helps in modulating the immune system, alters epigenetic markers. Gut microbiota also produces the energy metabolites and certain bioactive food components (Stilling et al. 2014). Researchers have shown that gut microbes are highly involved in the regulation of appetite through the modulation of ghrelin linked signaling pathways. For instance, administration of prebiotics like oligofructose and inulin would inhibit feed intake by enhancing the GLP-1 and peptide YY (PYY) synthesis, as well as inhibiting the production of ghrelin in healthy and obese individual (Han et al. 2021a, b).

5 Microbial Metabolites as Communicator Between Gut– Brain Axis The interaction between host and gut microbiota is via the production of metabolites, which are small molecules depicting intermediates or end products of microbial metabolism (Agus et al. 2021). Gut microbiota also produces a wide reservoir of microbial metabolites from the dietary components ingested by the host. Such microbial metabolites are key molecules that are involved in host–microbiota crosstalk. Gut microbiota can immensely affect the immune system by activating the vagus nerve; which in turn triggers the bidirectional interaction with the CNS. Alteration of gut microbiota and its derived metabolites may lead to changes in circulating pro-inflammatory and anti-inflammatory cytokines which directly affect different functions of brain (Rogers et al. 2016). The variety of metabolites that are produced by gut bacteria includes bile acids, short chain fatty acids (SCFA), branched-chain fatty acids (BCFA), gamma-aminobutyric acid (GABA), tryptophan and indole derivatives, etc. These are implicated in the pathogenesis of metabolic as well as neurological disorders. Here we will be mainly focusing on SCFAs and its role in nervous system disorders.

5.1

Short Chain Fatty Acids (SCFA)

Gut microbiota produces SCFAs via fermentation of indigestible dietary fibers and resistant starch which cannot be hydrolyzed in host digestive system because of lack of enzymes (Silva et al. 2020). Sources of SCFAs are dietary fibers like oats, wheat bran, butter, fruits, vegetables, some fermented foods, etc. The three most abundant SCFAs derived are acetate, propionate, and butyrate in an approximate proportion of 3:1:1, respectively (Mandaliya and Seshadri 2019). Little amounts

Exploring the Unexplored Arena: Butyrate as a Dual Communicator. . .

157

of other SCFAs are also produced within the gut, namely caproate, formate, and valerate. SCFA impacts the overall host health at several levels of cellular, tissue, and organs by maintaining the gut barrier function, its integrity, glucose homeostasis, and immune-modulation (Portincasa et al. 2022). The relative proportion of SCFA depends mainly upon the type of substrate, gut microbiota composition, and the gut transit time. Moreover, approximately 95% of SCFAs are produced in the gut, and soon after its production, they are absorbed by the colonocytes via an active transport system by monocarboxylate transport (MCTs). MCTs are localized within the GI tract on different organs and are also present in brain (Dalile et al. 2019). Fermentation of dietary fibers to SCFAs in the colon results in decreased levels of pH, increased acidification of fecal matter, and increased growth and diversity of the gut microbiota. Considering the production of SCFAs, Bacteroidetes chiefly produce acetate and propionate, whereas Firmicutes produce more butyrate. Some common SCFA producers are members of genus—Faecalibacterium, Bifidobacterium, Lactobacillus, Ruminococcus, Bacteroides, etc. (Dalile et al. 2019). It is speculated that SCFAs play an important role in microbiota–gut–brain axis (Vijay and Morris 2014). SCFAs are highly related to brain disorders like Parkinson’s disease, Alzheimer’s disease, stress, anxiety, depression, etc.

5.2

SCFA Signaling Through Receptors

SCFA signaling through its receptors on enteroendocrine cells, pancreatic cells, adipocytes, and on neuronal cells plays important role in regulation of host homeostasis. SCFAs bind to G protein-coupled receptors (GPCRs). Most widely studied GPCRs are GPR42 and GPR43 which were later named as free fatty acid receptor (FFAR2) and (FFAR3), respectively, as well as GPR109a/HCAR2 (hydrocarboxylic acid receptor) and GPR164 (Silva et al. 2020). The biological pathway upon activation depends primarily on their localization on specific cells, for instance, presence and activation of receptors on enteroendocrine cells lead to secretion of peptide YY (PYY) and glucagon like peptide (GLP-1). Receptor activation on pancreatic beta cells leads to increased secretion of insulin (Silva et al. 2020) (Fig. 1). Another regulation of systemic functions by SCFA involves the inhibition of inflammatory effects through histone deacetylase (HDAC) inhibition and GPR109A activation (Mirzaei et al. 2021). Lifestyle adaptations such as high sugar and fat rich diet, stress, antibiotic abuse can lead to gut dysbiosis, due to which there is an increase in gut permeability as well as of blood–brain barrier. The toxic metabolites as well as pathogens can enter into the brain and could lead to several neurological disorders.

158

Z. Bhatia et al.

Fig. 1 Figurative depiction of effects of gut dysbiosis on the brain

6 Butyrate Butyrate has been considered as a novel therapeutic molecule because of its various functions such as an inhibitory molecule of HDAC, a GPCR activator and it also serves as an energy metabolite which then produces ATP (Bourassa et al. 2016). Butyrate has a profound beneficial effect on neurological disorders like anxiety, mood disorders, Parkinson’s disease, Alzheimer’s disease, etc. The key butyrate producing bacteria in gut belongs to the phylum Firmicutes, such as Clostridium leptum and Faecalibacterium prausnitzii of the family Ruminococcaceae, Roseburia spp. and Eubacterium of the family Lachnospiraceae. It has been demonstrated that butyrate is the chief energy source for the colonocytes which consumes around 70% of oxygen via butyrate oxidation (Roediger 1980). Butyrate acts an anti-inflammatory molecule by suppressing lipopolysaccharide (LPS) induced NFκ-B activation via GPR109A in vitro in colonic cell lines and ex vivo in mouse colon (Parada Venegas et al. 2019). Butyrate can cross the BBB and helps in maintaining the BBB integrity (Mirzaei et al. 2021). Butyrate plays an important role in cell repair; it improves brain plasticity by increasing key neurotrophic factors like nerve growth factor (NGF), glial cell-derived neurotrophic factor (GDNF), brain-derived neurotrophic factor (BDNF), etc. (Dalile et al. 2019). It has been also demonstrated that butyrate decreases the pro-inflammatory cytokines

Exploring the Unexplored Arena: Butyrate as a Dual Communicator. . .

159

and improves learning and memory in mouse models of neurodegenerative disease (Govindarajan et al. 2011). Postbiotics have been identified as metabolic by-products which are produced by probiotic strains to confer overall health benefits to the host. Profound example of postbiotics includes SCFAs, of which butyrate is one of a kind. Administration of oral butyrate has multiple beneficial effects such as reducing the inflammation and oxidative stress. It improves the colonic barrier function and promotes satiety (Huang and Huang 2021).

6.1

Biosynthesis of Butyrate

Fermentation of indigestible fibers by gut microbiota in the colon results in butyrate production. Two molecules of acetyl CoA are condensed to form acetoacetyl CoA that is converted into butyryl CoA through L (+)-beta-hydroxybutyryl CoA and crotonyl CoA intermediates. Butyryl CoA is then converted to butyrate as shown in Fig. 2 (Bourassa et al. 2016). Carbohydrate

Formate H2+CO2 Methane

PEP

Fumarate

Pyruvate

Propionate

Acetyl CoA

Acetate

β-hydroxybutyryl CoA

Crotonyl CoA

Butyryl CoA

Butyrate Fig. 2 Schematic representation of butyrate biosynthesis pathway by gut microbes through the fermentation of carbohydrate in colon. The dotted lines represent the intermediate steps; the arrows depict direct production of the following metabolite (Bourassa et al. 2016)

160

6.2

Z. Bhatia et al.

Butyrate in Influencing the Blood–Brain Barrier

A very important part of neurovascular unit is the blood–brain barrier (BBB) which comprises extracellular matrix, microglia, pericytes, and endothelial cells. BBB plays a pivotal role in protecting the brain from brain injuries and diseases via preventing the entry of drugs and other substances in it. BBB segregates the brain from circulating blood via tight junctions. SCFAs like butyrate are a key component in maintaining the integrity of BBB. It can cross BBB via sodium dependent monocarboxylate transporters (SMCT) or transporter H+ dependent or which are expressed abundantly in endothelial cells (Vijay and Morris 2014). MCT and SMCT are known to be high affinity butyrate transporters in gut and brain. These transporters are necessary for mediating direct effect of butyrate in brain uptake into neurons and glial cells from the circulation (Stilling et al. 2014). Moreover, BBB integrity can be regulated by butyrate itself. In a study it has been shown that there is an increased BBB permeability in germ free mice that lacked detectable amounts of butyrate. Those mice were administered with oral butyrate in association with Clostridium tyrobutyricum, it could restore integrity of BBB by upregulating the expression of tight junction protein. This was not achieved on administration of Bacteroides thetaiotaomicron, which mainly produces acetate and propionate, it suggested that BBB integrity is supported by fermentation derived butyrate (Braniste et al. 2014). Butyrate can directly regulate GPR41 mediated sympathetic nervous system activity which maintains metabolic homeostasis and controls the energy expenditure. One more major GPCR activated by butyrate is GPR109A. This GPR109A signaling pathway activates the inflammasome pathway in dendritic cells and colonic macrophages, which results in regulatory T cell differentiation and IL-10 producing T cells. In intestinal epithelial cells, IL-18 secretion is also mediated by GPR109A signaling. Butyrate also acts an anti-inflammatory molecule by inhibiting pro-inflammatory enzymes and cytokines like IFN-ɣ, TNF-α, IL-6, IL-8 (Fu et al. 2015). With an ability of butyrate to cross BBB, butyrate activates the vagus nerve and hypothalamus and affects the host appetite and behavior (Castanys-Muñoz et al. 2016). It can promote the secretion of GLP-1, PYY, cholecystokinin, neurotransmitters like serotonin and peripheral hormones like ghrelin, leptin, and insulin as shown in Fig. 3 (Han et al. 2021a, b).

Exploring the Unexplored Arena: Butyrate as a Dual Communicator. . .

161

Fig. 3 Bidirectional communication between gut–brain axis via vagus nerve

7 Role of Butyrate in Neurological and Neuropsychological Disorders By now, critical emphasis has been given to gut–brain alliance. In more recent times, it has been established that alteration of gut microbial metabolites like SCFA and particularly butyrate is associated with several neurological and neuropsychological disorders, such as Alzheimer’s disease (AD), Parkinson’s disease (PD), autism, stress, depression, dementia, stroke, anxiety, etc. (Zhu et al. 2020). The circulating rates of pro-inflammatory and anti-inflammatory cytokines which act on identical receptors in the brain are governed by gut microbiota and result in behavioral changes like depression and mood swings (Sampson and Mazmanian 2015). Butyrate directly affects serotonin and release of gut hormones in the ENS which stimulates the vagus nerve and induces endocrine signaling, with high impact on brain function (Stilling et al. 2014). Microbial metabolites like SCFAs (butyrate) can be considered as therapeutic agents to improve various neurological conditions. Some of the common bacterial species producing butyrate are Faecalibacterium prausnitzii, Lactobacillus acidophilus, Lactobacillus salivarius, Bifidobacteria spp., Eubacterium rectal, Clostridium butyricum Roseburia intestinalis etc. (Mirzaei et al.

162

Z. Bhatia et al.

Table 1 Roles of butyrate and butyrate producing bacteria in several neurological disorders Neurological disorders Alzheimer’s disease (AD)

Parkinson’s disease (PD)

Depression

Stress and anxiety

Functions of butyrate Butyrate acts as an anti-inflammatory molecule and it decreases the levels of TNF α, IL-6, and IL-1β in the brain of cerebral ischemia/reperfusion injury mice and it modulates the microglia maturation. It suppresses neuroinflammation by inhibition of NF-κB signaling (Mirzaei et al. 2021; Sun et al. 2020) Gut barrier is affected by butyrate in Parkinson’s disease and it induces numerous physiological responses through GPCR activation in enterocytes. It controls the inflammatory pathways. It increases the production of GLP-1 and PYY and GLP-1 receptors in brain which are upregulated to improve the neurobehavioral changes (Wang et al. 2014; Mirzaei et al. 2021) Butyrate boosts the expression of receptors Toll-like receptors (TLRs) that sense microbial compounds, which, in turn, enhance the PYY expression (Lach et al. 2018) Butyrate acts as an anti-inflammatory molecule which interrupts in inflammatory signaling pathway, help in producing serotonin which acts as mood stabilizer (Müller et al. 2021)

2021). We here summarize potential roles of butyrate in various brain related disorders (Table 1).

8 Conclusion In nutshell, substantial body of evidences suggests that gut microbiota plays a crucial role in regulating endocrine, metabolic, and immune functions. Modulation in various neurochemical pathways involves gut microbiota through highly interconnected gut–brain axis. The metabolites produced by gut microbiota are remarkably important to maintain host homeostasis. The short chain fatty acids (SCFAs), highlighting butyrate is a core player in modulating the host physiology. Butyrate is a functionally versatile molecule that is produced by fermentation of dietary fibers in the gut. It can perform bidirectionally to improve immunity and tolerance to combat brain disorders. Furthermore, butyrate can be evaluated to be considered as biomarkers for neurological diseases like Alzheimer’s disease and Parkinson’s disease. Butyrate can be targeted as a therapeutic agent for the treatment of various neurological disorders. High concentration of butyrate can be supplemented artificially; it could act as a potent drug with dynamic systemic functions. Therefore, it is a valuable neuropharmacological agent exploiting its HDAC inhibitory potential. Nevertheless, modulation of gut microbiota by using prebiotics, probiotics, and fecal microbiota transplantation can be administered to ameliorate certain psychological disorders like depression, anxiety, and autism. Yet,

Exploring the Unexplored Arena: Butyrate as a Dual Communicator. . .

163

further evolution of these treatments should define another arena of modern therapies to treat such neurological disorders.

References Agus A, Clément K, Sokol H (2021) Gut microbiota-derived metabolites as central regulators in metabolic disorders. Gut 70(6):1174–1182 Bourassa MW, Alim I, Bultman SJ, Ratan RR (2016) Butyrate, neuroepigenetics and the gut microbiome: can a high fiber diet improve brain health? Neurosci Lett 625:56–63 Braniste V, Al-Asmakh M, Kowal C, Anuar F, Abbaspour A, Tóth M, Korecka A, Bakocevic N, Ng LG, Kundu P, Gulyás B (2014) The gut microbiota influences blood-brain barrier permeability in mice. Sci Transl Med 6(263):263ra158 Castanys-Muñoz E, Martin MJ, Vazquez E (2016) Building a beneficial microbiome from birth. Adv Nutr 7(2):323–330 Dalile B, Van Oudenhove L, Vervliet B, Verbeke K (2019) The role of short-chain fatty acids in microbiota–gut–brain communication. Nat Rev Gastroenterol Hepatol 16(8):461–478 Fu SP, Wang JF, Xue WJ, Liu HM, Liu BR, Zeng YL, Li SN, Huang BX, Lv QK, Wang W, Liu JX (2015) Anti-inflammatory effects of BHBA in both in vivo and in vitro Parkinson’s disease models are mediated by GPR109A-dependent mechanisms. J Neuroinflammation 12(1):1–14 Govindarajan N, Agis-Balboa RC, Walter J, Sananbenesi F, Fischer A (2011) Sodium butyrate improves memory function in an Alzheimer’s disease mouse model when administered at an advanced stage of disease progression. J Alzheimers Dis 26(1):187–197 Han H, Yi B, Zhong RQ, Wang MY, Zhang SF, Ma J et al (2021a) From gut microbiota to host appetite: gut microbiota-derived metabolites as key regulators. Microbiome 9:1–6 Han H, Yi B, Zhong R, Wang M, Zhang S, Ma J, Yin Y, Yin J, Chen L, Zhang H (2021b) From gut microbiota to host appetite: gut microbiota-derived metabolites as key regulators. Microbiome 9(1):1–16 Höglund E, Øverli Ø, Winberg S (2019) Tryptophan metabolic pathways and brain serotonergic activity: a comparative review. Front Endocrinol 10:158 Huang FC, Huang SC (2021) The combined beneficial effects of postbiotic butyrate on active vitamin D3-orchestrated innate immunity to Salmonella Colitis. Biomedicines 9(10):1296. https://doi.org/10.3390/biomedicines9101296 Lach G, Schellekens H, Dinan TG, Cryan JF (2018) Anxiety, depression, and the microbiome: a role for gut peptides. Neurotherapeutics 15(1):36–59 Loh K, Zhang L, Brandon A, Wang Q, Begg D, Qi Y, Fu M, Kulkarni R, Teo J, Baldock P, Brüning JC (2017) Insulin controls food intake and energy balance via NPY neurons. Mol Metab 6(6): 574–584 Mandaliya DK, Seshadri S (2019) Short chain fatty acids, pancreatic dysfunction and type 2 diabetes. Pancreatology 19(4):617–622 Martinez JE, Kahana DD, Ghuman S, Wilson HP, Wilson J, Kim SC, Lagishetty V, Jacobs JP, Sinha-Hikim AP, Friedman TC (2021) Unhealthy lifestyle and gut dysbiosis: a better understanding of the effects of poor diet and nicotine on the intestinal microbiome. Front Endocrinol 12:649 Mirzaei R, Bouzari B, Hosseini-Fard SR, Mazaheri M, Ahmadyousefi Y, Abdi M, Jalalifar S, Karimitabar Z, Teimoori A, Keyvani H, Zamani F (2021) Role of microbiota-derived shortchain fatty acids in nervous system disorders. Biomed Pharmacother 139:111661 Mittal R, Debs LH, Patel AP, Nguyen D, Patel K, O’Connor G, Grati MH, Mittal J, Yan D, Eshraghi AA, Deo SK (2017) Neurotransmitters: the critical modulators regulating gut–brain axis. J Cell Physiol 232(9):2359–2372

164

Z. Bhatia et al.

Müller B, Rasmusson AJ, Just D, Jayarathna S, Moazzami A, Novicic ZK, Cunningham JL (2021) Fecal short-chain fatty acid ratios as related to gastrointestinal and depressive symptoms in young adults. Psychosom Med 83(7):693 Nezami BG, Srinivasan S (2010) Enteric nervous system in the small intestine: pathophysiology and clinical implications. Curr Gastroenterol Rep 12(5):358–365 Parada Venegas D, De la Fuente MK, Landskron G, González MJ, Quera R, Dijkstra G, Harmsen HJ, Faber KN, Hermoso MA (2019) Short chain fatty acids (SCFAs)-mediated gut epithelial and immune regulation and its relevance for inflammatory bowel diseases. Front Immunol 10:277 Portincasa P, Bonfrate L, Vacca M, De Angelis M, Farella I, Lanza E, Khalil M, Wang DQH, Sperandio M, Di Ciaula A (2022) Gut microbiota and short chain fatty acids: implications in glucose homeostasis. Int J Mol Sci 23(3):1105 Rao M, Gershon MD (2016) The bowel and beyond: the enteric nervous system in neurological disorders. Nat Rev Gastroenterol Hepatol 13(9):517–528 Ratcliffe EM, Farrar NR, Fox EA (2011) Development of the vagal innervation of the gut: steering the wandering nerve. Neurogastroenterol Motil 23(10):898–911 Roediger WE (1980) Role of anaerobic bacteria in the metabolic welfare of the colonic mucosa in man. Gut 21(9):793–798 Rogers GB, Keating DJ, Young RL, Wong ML, Licinio J, Wesselingh S (2016) From gut dysbiosis to altered brain function and mental illness: mechanisms and pathways. Mol Psychiatry 21(6): 738–748 Sampson TR, Mazmanian SK (2015) Control of brain development, function, and behavior by the microbiome. Cell Host Microbe 17(5):565–576 Silva YP, Bernardi A, Frozza RL (2020) The role of short-chain fatty acids from gut microbiota in gut-brain communication. Front Endocrinol 11:25 Stilling RM, Dinan TG, Cryan JF (2014) Microbial genes, brain & behaviour–epigenetic regulation of the gut–brain axis. Genes Brain Behav 13(1):69–86 Stojanov S, Berlec A, Štrukelj B (2020) The influence of probiotics on the firmicutes/bacteroidetes ratio in the treatment of obesity and inflammatory bowel disease. Microorganisms 8(11):1715 Sun J, Xu J, Yang B, Chen K, Kong Y, Fang N, Gong T, Wang F, Ling Z, Liu J (2020) Effect of Clostridium butyricum against microglia-mediated neuroinflammation in Alzheimer’s disease via regulating gut microbiota and metabolites butyrate. Mol Nutr Food Res 64(2):1900636 Thursby E, Juge N (2017) Introduction to the human gut microbiota. Biochem J 474(11): 1823–1836 Valdes AM, Walter J, Segal E, Spector TD (2018) Role of the gut microbiota in nutrition and health. BMJ 361:k2179 Verduci E, Carbone MT, Borghi E, Ottaviano E, Burlina A, Biasucci G (2020) Nutrition, microbiota and role of gut-brain axis in subjects with phenylketonuria (PKU): a review. Nutrients 12(11):3319 Vijay N, Morris ME (2014) Role of monocarboxylate transporters in drug delivery to the brain. Curr Pharm Des 20(10):1487–1498 Wang S, Yang H, Yu L, Jin J, Qian L, Zhao H, Xu Y, Zhu X (2014) Oridonin attenuates Aβ1–42induced neuroinflammation and inhibits NF-κB pathway. PloS One 9(8):e104745 Yaghoubfar R, Behrouzi A, Ashrafian F, Shahryari A, Moradi HR, Choopani S, Hadifar S, Vaziri F, Nojoumi SA, Fateh A, Khatami S (2020) Modulation of serotonin signaling/metabolism by Akkermansia muciniphila and its extracellular vesicles through the gut-brain axis in mice. Sci Rep 10(1):1–12 Zhu S, Jiang Y, Xu K, Cui M, Ye W, Zhao G, Jin L, Chen X (2020) The progress of gut microbiome research related to brain disorders. J Neuroinflammation 17(1):1–20

Human Microbiome and Lifestyle Disorders Ankit Gupta and Abhilasha Jha

Abstract The human microbiome builds a multifaceted and dynamic ecosystem with the body that shapes the metabolic as well as immunological behavior of human beings. Over the past decades, our knowledge of the human microbiome suggests that various genetic as well as environmental factors affect the human microbiota and their interaction with the host dictates overall human health. Recent studies have associated nutrition, lifestyle, and physiological variables with human health and affirmed that establishing favorable interactions between the host and its concomitant microbiota is crucial for human health. In this chapter, we discuss the various factors that affect the overall human microbiota and debate the effect of lifestyle, diet, and physiological factors on the gut microbiome. Here, we explain how microbiome health affects human physiology and metabolism and debate the impact of microbiota on lifestyle disorders, mainly diabetes, obesity, and cardiovascular diseases. Next, we talk about the current and future emergence of obesity and diabetes and probable solutions to avoid these anomalies. Here, we highlight the crosstalk between the oral and gut microbiome and discuss the probable treatment of obesity and diabetes by healing the microbiome. In the last section of the review, we also discuss the effect of the microbiome on stress-related disorders and birth-related problems such as premature deliveries and low birth weight. Overall, this chapter outlines a detailed explanation of lifestyle-related disorders, their impact, and possible solutions to these lifestyle-related problems, which in turn is vital for a planned and successful treatment of these disorders. Keywords Lifestyle disorders · Diabetes · Obesity · Cardiovascular diseases · Probiotics

A. Gupta (✉) Center for Alzheimer’s and Neurodegenerative Diseases, Peter O’Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA A. Jha Himalaya Cancer Hospital and Research Institute, Vadodara, Gujarat, India © The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd. 2023 V. Kothari et al. (eds.), Probiotics, Prebiotics, Synbiotics, and Postbiotics, https://doi.org/10.1007/978-981-99-1463-0_10

165

166

A. Gupta and A. Jha

Abbreviations 5-HT AhR ChAT DC GLP-1 GPCRs HDAC ILC3 SAA SCFAs Th Treg TRP PTB

Serotonin Aryl hydrocarbon receptor Choline acetyltransferase Dendritic cell Glucagon-like peptide-1 G protein-coupled receptors Histone deacetylase Innate lymphoid cell-3 Serum amyloid-A Short-chain fatty acids T-helper cell Regulatory T cell Tryptophan Preterm birth

1 Introduction The symbiotic and pathogenic microorganisms present in vertebrates also called microbiota build a complex and dynamic ecosystem that shapes the metabolic as well as immunological behavior of the human being (Turnbaugh et al. 2007; Dong and Gupta 2019; NIH-Wide Microbiome Workshop Writing Team 2019; Rackaityte and Lynch 2020; Fan and Pedersen 2021; Leeuwendaal et al. 2022). This microbial community present in the human body comprehends ~10 times more cells and ~100 times more genes, compared to the cells and genes of the human origin (Turnbaugh et al. 2007; Ursell et al. 2012; Dong and Gupta 2019). These microbes inhabit and colonize various parts of the body including the gut, oro-nasopharyngeal cavity, vagina, skin, etc. Microbes present in the human body comprise thousands of bacterial species heterogeneously distributed throughout the gut intestinal tract, where these microbes secrete various metabolites, modulate the immune system, and are responsible for various phenotypes of medical importance (Dong and Gupta 2019; Almeida et al. 2019). The gut and oral microbiome not only assist in digestion and fermentation of indigestible dietary fiber but also collectively modulate the local and systemic environments through direct or indirect metabolic pathways and help in maintaining the energy homeostasis (Turnbaugh et al. 2007; Riedl et al. 2017; La Flamme and Milling 2020; Dixit et al. 2021; Fan and Pedersen 2021; Kumar et al. 2021; Gao et al. 2022; Lyu et al. 2022). Various metabolites secreted by microbes modulate the mucosal and systemic immune system, as well as the enteric nervous system. Here, the commensal microbes are involved in direct or indirect pathways and they modulate local and systemic environments in the body. These microbes help in the metabolism of indigestible but fermentable polysaccharides in the large

Human Microbiome and Lifestyle Disorders

167

intestine and produce short-chain fatty acids (SCFAs) such as acetate, butyrate, and propionate (Boulange et al. 2016; Marchix et al. 2018; Federici 2019; Fan and Pedersen 2021). These SCFAs bind to G protein-coupled receptors (GPCRs) and induce the secretion of glucagon-like peptide-2 (GLP-2), which contributes to enhancing glucose metabolism and insulin secretion. Furthermore, they also modulate the immune responses and alter gut motility through the GPCR activation or HDAC inhibition. The introduction of food rich in high fiber content, also known as prebiotics, acts as the source for stimulating the growth of pre-existing good bacteria (Holscher 2017; Sanders et al. 2019). These dietary products modulate the microbial diversity in the gut, oral, and intestinal microbiota and help in improving metabolic function and overall human health (Holscher 2017; Kim et al. 2019; Sanders et al. 2019; Zolkiewicz et al. 2020). In addition, the gram-positive segmented filamentous bacteria (SFBs) trigger the immune response by producing antimicrobial peptides and serum amyloid-A in the terminal ileum. Decreased gut and intestinal microbiota diversity is a measure of dysbiosis and is associated with the deterioration of health and various diseases in the human body (Marchix et al. 2018; Valdes et al. 2018). Probiotics play an important role in restoring this balance and maintaining the microbiota diversity (Zolkiewicz et al. 2020; Kim et al. 2019; Wieers et al. 2019). Gut microbiota also modulates various immune cells including lymphoid tissue inducer cells, natural killer cells, T-helper cells, regulatory T cells, B cells, etc. (Sommer and Backhed 2013; Teng et al. 2017; Fan and Pedersen 2021; Owens et al. 2021). The role of microbiota in the metabolism of complex dietary substances and their effect on the immune system and overall human physiology has been summarized in Fig. 1. Using high-throughput human multi-omics data, we learned that various genetic and environmental factors can affect the overall diversity, composition, and function of the microbiota in the human body and overall human health ((NCD-RisC) NRFC 2016; Riedl et al. 2017; Ogurtsova et al. 2017; Dong and Gupta 2019; Ng et al. 2021; Fan and Pedersen 2021; Asadi et al. 2022). These factors include the mode of delivery at birth, the method of infant feeding, diet, exposure to pathogens, age, physiological stress, anxiety, medication, drug usage, alcohol and tobacco usage, physical activity, etc. (Schulfer et al. 2018; Dong and Gupta 2019; Almeida et al. 2019; La Flamme and Milling 2020; Fan and Pedersen 2021). Furthermore, disruption of composition, diversity, and function of microbiota in the human body due to early and late-life events result in inflammatory bowel disease, diabetes, obesity, cardiovascular diseases, arterial stiffness, stress-related disorders, atopic eczema, psoriatic arthritis, birth-related problems such as premature deliveries and low birth weight, cancer, neurological and stress-related disorders, etc. ((NCD-RisC) NRFC 2016; Riedl et al. 2017; Ogurtsova et al. 2017; Farzi et al. 2019; Sharma and Tripathi 2019; Fan and Pedersen 2021; Ng et al. 2021; Asadi et al. 2022; Zhu et al. 2022; Kumar et al. 2021). Various factors that affect the overall microbiome health are summarized in Fig. 2. Among these diseases, obesity and stress-related disorders are one of the most common lifestyle disorders in the modern world. These lifestyle disorders are an outcome of disruption of microbial diversity or microbiome dysbiosis due to

168

A. Gupta and A. Jha

Fig. 1 Interaction of microbiota with intestinal layer and immune system and human physiology. (a) Various metabolites secreted by microbes modulate the mucosal and systemic immune system, along with the enteric nervous system (ENS). Here, the commensal microbes are involved in direct or indirect pathways and they modulate local and systemic environments in the body. Here, the filamentous bacteria produce short-chain fatty acids (SCFAs) such as acetate, butyrate, and

Human Microbiome and Lifestyle Disorders

169

modification in food habits, lack of exercise, excessive smoking and alcohol consumption, increased consumption of certain medication and stressful lifestyles, etc. ((NCD-RisC) NRFC 2016; Riedl et al. 2017; Ogurtsova et al. 2017; Farzi et al. 2019; Sharma and Tripathi 2019; Ng et al. 2021; Fan and Pedersen 2021; Zhu et al. 2022; Asadi et al. 2022). In the past decade, the co-morbidity of diabetes and obesity called “diabesity” and the co-occurrence of nutrition-related metabolic diseases with neuropsychiatric disorders such as depression have become increasingly prevalently worldwide (Valdes et al. 2018; Farzi et al. 2019; Ng et al. 2021; Fan and Pedersen 2021; Zaky et al. 2021; Honarpisheh et al. 2022). As the increasing emergence of lifestyle disorders has important social, financial, and development implications and thus demands a better understanding of the reason for these anomalies. Hence, in this chapter, we discuss the role of the human microbiome on lifestyle disorders, mainly diabetes, obesity, cardiovascular diseases, and stress-related disorders (Kumar et al. 2021). In the first section, we detail our current knowledge of how lifestyle and diet affect the microbiome and microbiota and how derived microbial compounds affect human metabolism. Next, we highlight how changes in diet and stressful lifestyle influence the oral and gut microbiota and result in various metabolic and stressrelated disorders. Further, we also explain how the change in targeted and untargeted interventions including diet, exercise, use of probiotic foods or drugs can help in shifting the microbiota toward a healthy side. Overall, we discuss the importance of microbiota in human life and its role in various lifestyle disorders and syndromes.

2 Factors Affecting Lifestyle Disorders Microbes such as bacteria, archaea, and eukarya as well as some viruses, have been observed to inhabit and colonize various parts of the body including the oral cavity, gut, oro-nasopharyngeal cavity, vagina, skin, etc. (Sommer and Backhed 2013; Barlow et al. 2015; Boulange et al. 2016; Riedl et al. 2017; Zaky et al. 2021). These microbes not only contribute to disease but to human health as well. The focus  ⁄ Fig. 1 (continued) propionate and induce the immune response by binding to G protein-coupled receptors (GPCRs). Furthermore, the gram-positive segmented filamentous bacteria (SFBs) trigger the immune response. (b) Various indoles derived from the human microbiota and its effect on human physiology. Here, we highlight how different indoles influence various immune cells and affects various metabolic and immunologic function in the cells including the release of antimicrobial peptides, secretion of anti-inflammatory cytokines, reduce gut permeability, etc. Here, AhR Aryl hydrocarbon receptor, AMPs antimicrobial peptides and proteins, AroP aromatic amino acid transport protein, ChAT choline acetyltransferase, CYP cytochrome, DC dendritic cell, 5-HT serotonin, GLP-1 glucagon-like peptide-1, HDAC histone deacetylase, IaaH indole-3-acetamide hydrolase, ILC3 innate lymphoid cell-3, IPA indole-3-propionic acid, SAA MAPK mitogenactivated protein kinase, NFκB nuclear factor-kappa B, serum amyloid-A, Th T-helper cell, Treg regulatory T cell, TRP tryptophan. (The figure was adapted from Marchix et al. (2018) and Kumar et al. (2021))

170

A. Gupta and A. Jha

Fig. 2 Lifestyle disorders. This figure lists various lifestyle diseases or disorders (red text) and the reasons responsible for various lifestyle disorders (black text). Changes in lifestyle result in disruption of human microbiota that ultimately leads to various lifestyle diseases/disorders

has thus shifted to understanding the host–microbe symbiotic relationship. The inception of microbial colonization is thought to have begun in utero (Castelao et al. 1989; Kliman 2014), and the microbial flora reaches the adult profile by 2–5 years of age (Schloissnig et al. 2013). The route of entry for the microbes in the systemic complexity of the human body is through the oro-nasopharyngeal cavity. While the first exposure begins with the first feed of maternal milk, the colonization is increasingly observed after the eruption of the first tooth in the oral cavity. In childhood, the microbiota is strongly influenced by many factors such as mode of birth (vaginal>cesarean), feeding choice (breast fed>bottle fed), transition to solid food like cereals as well as the administration and initial exposure to antibiotic drugs (Arrieta et al. 2014). Further, the host–microbiome relationship is affected by various factors such as our diet, genetics, environmental changes, use of antibiotics, and other drugs (Russell et al. 2012; Hillman et al. 2017; Blaser and Falkow 2009) and leads to changes in overall microbiota. These changes are sometimes beneficial or neutral to the body but are mostly deleterious to the overall human health and result in the occurrence of various diseases also called “lifestyle disorders.” Lifestyle diseases or disorders can be described by the deterioration of human health due to sedentary routine, unhealthy diet, physical inactivity, and stressful life in daily routine. These activities in long term can lead to chronic non-communicable diseases such as results in inflammatory bowel disease, diabetes, obesity, cardiovascular diseases, stress-related disorders, birth-related problems such as premature deliveries and low birth weight, cancer, neurological and stress-related disorders, etc. and can have life-threatening consequences (Ogurtsova et al. 2017; Riedl et al. 2017; Farzi et al. 2019; Sharma and Tripathi 2019; Ng et al. 2021; Fan and Pedersen 2021; Asadi et al. 2022; Tan 2022; Zhu et al. 2022). Despite increasing health awareness, a considerable part of the human population across the world is being

Human Microbiome and Lifestyle Disorders

171

Fig. 3 Factors affecting the microbiome health. (a) Maternal factors, postnatal factors, environmental factors across the lifespan, perturbations to the microbiome due to medication, and diseases influence the overall microbiome health in the human body. These changes in the overall microbiota health may lead to various diseases such as obesity, irritable bowel syndrome (IBS), diabetes, etc. (The figure was adapted from Dong and Gupta (2019))

affected by behavioral and lifestyle problems, high cholesterol, obesity, stress, anxiety, etc. The main reason behind these lifestyle disorders is the disruption of human microbiota due to unhealthy eating habits, consumption of tobacco and alcohol, poor sleeping habits, stress, less physical activity, etc. (Fig. 3). In this section, we detail a few major and most common early and late-life events that result in various lifestyle diseases:

2.1

Maternal Reasons and Postnatal Factors

The foundation of microbial colonization begins from the time of birth. Here, the microbes present in the placenta, umbilical cord, amniotic fluid, and uterus are transferred to the baby through the bloodstream. Further, during the delivery also the newborn is exposed to the commensal vaginal and fecal microbiome of the mother (Dunn et al. 2017; Dong and Gupta 2019). A few of the common microorganisms during vaginal delivery vs. cesarean section delivery are Lactobacillus, Prevotella, Sneathia, Bifidobacterium, Bacteroides, Staphylococcus, Propionibacterium, Corynebacterium, etc. (Neu and Rushing 2011; Dunn et al. 2017; Dong and Gupta 2019). Further, during the early life, the breastfeeding as well as consumption of solid food by the newborn are crucial in the overall development of the human microbiome and introduces novel microbiota in the infant such as Bifidobacterium spp., Corynebacterium, Rothia, Staphylococcus, Streptococcus, Serratia, Pseudomonas, Propionibacterium, Sphingomonas, etc. (Riedl et al. 2017; Dong and Gupta 2019). The microbiota present in the breastmilk provides a protective role against asthma, type 1 diabetes, autoimmune disease, obesity, and autism spectrum disorder (Dong and Gupta 2019; Cortes-Macias et al. 2021; Lyu et al. 2022). In modern life, the introduction of cesarean section delivery

172

A. Gupta and A. Jha

as well as bottled milk and food for newborn babies significantly affects the microbiota community that negatively influences the overall body metabolism and immune system. Loss in microbial diversity in infants affects the digestion, eyesight, and overall bone strength, as well as their body becomes more susceptible to allergies, autoimmune disease, diabetes, obesity, malnutrition, etc. (Dong and Gupta 2019).

2.2

Diet

Diet defines the human microbiota and overall human microbiome in early and latelife (Zeevi et al. 2015; Dong and Gupta 2019). In early life, breastfeeding as well as consumption of solid food helps in the development of the human microbiome and protects the newborn from various diseases (Dore and Blottiere 2015; Dong and Gupta 2019). Similarly, in the late-life also the diet is imperative in regulating the colonization of beneficial and harmful microorganisms in the body and has a great impact on the overall human microbiome (Swiatecka et al. 2011; David et al. 2014; De Filippis et al. 2016; Velasquez et al. 2016; Miyoshi et al. 2017). In the modern world, overconsumption of the western diet and minimized use of the Mediterranean diet is the most common diet habit. The western diet contains low dietary fibers and plant proteins but is a source of high sugar and high fats, which leads to reduced short-chain fatty acids but high levels of lipopolysaccharides levels (Fig. 4) (Swiatecka et al. 2011; Valdes et al. 2018; Dong and Gupta 2019; Farzi et al. 2019). Continuous use of such a diet will lead to a loss in the healthy microbiota such as Bifidobacteria, Lactobacilli, Eubacteria, Bacteroides, Prevotella, Roseburia, etc., but an increase in the harmful microbiome including Bacteroides, Enterobacteria and increase in harmful microorganisms (Turnbaugh et al. 2009b; Swiatecka et al. 2011; Miyoshi et al. 2017; Schulfer et al. 2018). Some harmful microorganisms and their relation to diet are listed in Table 1. Unhealthy food habits that contain animal protein, saturated fats, and red processed meat affect metabolism and will increase harmful compounds such as trimethylamine N-oxide, amines, and sulfides in the human body (Fig. 4). Such a diet pattern also activates the toll-like receptor, promotes pro-inflammatory TH1, increases adipose tissue inflammation, and also affects the variety of immune cells and endocrine cells (Turnbaugh et al. 2009b; David et al. 2014). Furthermore, these dietary changes increase the endotoxemia, and overall inflammation, and decrease the gut barrier (Turnbaugh et al. 2009b; Miyoshi et al. 2017; Schulfer et al. 2018; Dong and Gupta 2019; Farzi et al. 2019). Long-term use of such a diet will permanently change the human microbiome and may lead to various life-threatening diseases including obesity, type 2 diabetes, colon cancer, cardiovascular disease, inflammatory bowel disease, etc. (Turnbaugh et al. 2009b; Miyoshi et al. 2017; Schulfer et al. 2018; Dong and Gupta 2019; Farzi et al. 2019).

Human Microbiome and Lifestyle Disorders

173

Fig. 4 Dietary factors affecting the microbiome health. Role of diet in maintaining the gut microbiota in human nutrition, health, and disease. Research shows that gut microbiota affects innate immunity, energy metabolism, etc. Loss of microbial diversity or microbiome dysbiosis leads to metabolic complications, induced obesity, and immune dysregulation. Here, CVD cardiovascular disease, IPA indolepropionic acid, LPS lipopolysaccharide, SCFA short-chain fatty acids, TMAO trimethylamine N-oxide. (The figure was adapted from Valdes et al. (2018))

2.3

Tobacco and Alcohol Consumption

Along with an unhealthy diet, consumption of alcohol and tobacco, as well as the use of energy drinks, is also contributing significantly to deteriorating human health (Seifert et al. 2011; Capurso and Lahner 2017; Huang and Shi 2019). Research shows that smoking not only leads to cancer but regular smoking can also alter the oral and gut microbiome and can change the microbiota permanently (Hall et al.

174

A. Gupta and A. Jha

Table 1 Effect of various dietary elements on microbial diversity and overall human health

Diet Western diet

Animal protein consumption Saturated fats

Increased microbial population count Bacteroides, Enterobacteria

Disease Obesity, colon cancer, type 2 diabetes

Alistipes, Bilophila, Clostridia Bacteroides, Bilophila, Faecalibacterium prausnitzii

Cardiovascular disease, inflammatory bowel disease Cardiovascular disease, inflammatory bowel disease, diabetes, and obesity

References Turnbaugh et al. (2009b), Miyoshi et al. (2017), Schulfer et al. (2018), Dong and Gupta (2019) De Filippis et al. (2016), Velasquez et al. (2016), Miyoshi et al. (2017) Swiatecka et al. (2011), Miyoshi et al. (2017), Dong and Gupta (2019)

This table was adapted from Dong and Gupta (2019)

2017; Huang and Shi 2019; Farzi et al. 2019; Singhvi et al. 2020). An increase in Proteobacteria and Bacteroidetes has been observed in the people who consume tobacco regularly (Capurso and Lahner 2017; Sirisinha 2016; Huang and Shi 2019). Smoking induces the colonization of anaerobic bacteria and also leads to intestinal inflammation as well as change in the tight junction proteins and mucin production (Capurso and Lahner 2017; Antinozzi et al. 2022). Other than tobacco, alcohol consumption and use of energy drinks are also one of the major reasons for the change in the gut intestinal microbiota and a variety of lifestyle disorders including premature death and tissue injury and organ dysfunction in youth (Alsunni 2015; Bajaj 2019; Cui et al. 2020). Alcohol consumption results in an increase in Proteobacteria, Gammaproteobacteria, Bacilli, etc. and a reduction in Bacteroidetes, Verrucomicrobiae, etc. that is associated with mucosa-associated colonic bacterial composition and is considered a key reason for including alcoholic liver disease, oxidative stress, systemic inflammation, and tissue damage/organ pathologies, etc. (Alsunni 2015; Acharya and Bajaj 2017; Bajaj 2019).

2.4

Medications

Excessive use of broad-spectrum antibiotics in modern lifestyle not only affects the pathogenic bacteria but also affects the commensal microbial population existing in the gut and intestinal tract and significantly disrupts the microbial diversity and the gut ecology (Peterson et al. 2015; Kho and Lal 2018; Singhvi et al. 2020). As an example, Ampicillin, Amoxicillin, and Ciprofloxacin affect Enterobacter spp., Enterobacter spp., and Enterobacteria, respectively (Gipponi et al. 1985; Greenwood et al. 2014; Singhvi et al. 2020; Qin et al. 2022). Research suggests that consumption of antibiotics early in life has a considerable effect on the gut microbiome, which can modify the SCFAs levels and fat mass in the body and is

Human Microbiome and Lifestyle Disorders

175

associated with a variety of the disease including obesity, diabetes, asthma, inflammatory bowel disease, etc. (Peterson et al. 2015; Kho and Lal 2018).

3 Various Lifestyle Diseases or Disorders Lifestyle diseases or disorders such as inflammatory bowel disease, diabetes, obesity, cardiovascular diseases, stress-related disorders, atopic eczema, psoriatic arthritis, birth-related problems such as premature deliveries and low birth weight, cancer, neurological and stress-related disorders, etc. are one of the major challenges in the modern world (Ogurtsova et al. 2017; Dong and Gupta 2019; Tan 2022). These lifestyle disorders are non-communicable and degenerative diseases that sometimes result in disability or even death. In a recent survey, the total number of deaths across the world due to chronic lifestyle diseases is expected to increase substantially. Hence, these diseases have greater important social, financial, and development implications. In this section, we discuss a few of the most common but important lifestyle disorders.

3.1

Obesity

The microbiota present in the human gut offers a significant metabolic capability to the human body that helps in the digestion of indigestible dietary polysaccharides and controls the energy balance in the body by regulating the calorie harvesting from the food and how this energy is used and stored (Backhed et al. 2004; Turnbaugh et al. 2006, 2008, 2009a,b; Dong and Gupta 2019). The gut microbiota also affects the mitochondrial biogenesis and metabolism by (1) regulating the expression of various transcription factors, enzymes, and coactivators and (2) production of inflammatory cytokines and activation of the inflammasome, which are key players in chronic metabolic disorders (Tilg 2010; Vezza et al. 2020). Two prevalent metabolic disorders in the modern world are obesity and diabetes (Tilg 2010; Fan and Pedersen 2021). Also, the combined adverse health effects of these diseases in the form of “diabesity” are the main concern of public health worldwide (Glatz et al. 2018; Farzi et al. 2019; Ng et al. 2021). Sedentary lifestyles and increased use of the western diet and minimized use of the Mediterranean diet in combination with a widespread polygenic susceptibility affect the gut intestinal microbiota and are one of the major causes of the diabesity (Turnbaugh et al. 2009b; Tilg 2010; Farzi et al. 2019; Dutta et al. 2022; Ng et al. 2021; Omar et al. 2022). Obesity is a multifactorial metabolic disorder that leads to excessive accumulation of adipose tissue in the body (Halmos and Suba 2016; Muscogiuri et al. 2019; Melit et al. 2022). Gut microbiota is crucial for energy harvesting, regulation of fat storage, and fat storage (Muscogiuri et al. 2019). Disruption of healthy microbiota in the human body affects the mechanisms regulating satiety/appetite, reduces

176

A. Gupta and A. Jha

metabolic energy consumption, and leads to an increase in insulin resistance as well as tissue inflammatory damage (Boroni Moreira et al. 2012; Khan et al. 2016; Muscogiuri et al. 2019). If we look at the microbiota of a healthy and an obese person, then one will find that the person with obesity encompasses deprived levels of Bacteroidetes and S. aureus, as well as higher proportions of Firmicutes as compared to the healthy person (Ley et al. 2005; Boroni Moreira et al. 2012; Gill et al. 2022). The presence of Bacteroidetes in a healthy person regulates the concentration of short-chain fatty acids (SCFAs) including acetate, butyrate, and propionate that interact with G-protein-coupled receptors (GPCRs) expressed in the gut, adipocytes, and reduces the release of inflammatory cytokines (Samuel et al. 2008; Choi et al. 2013; Rakhmat et al. 2022). People with obesity have an abundance of bacteria that are capable of increasing the rate of short-chain fatty acids biosynthesis and also reducing the expression of fasting-induced adipose factor (FIAF) (Backhed et al. 2004; Boroni Moreira et al. 2012). Further, an abundance of the presence of Gram-negative bacteria in the body also increases the absorption of lipopolysaccharides (LPS) by modulating the permeability of “tight junctions” (Backhed et al. 2004; de La Serre et al. 2010; Boroni Moreira et al. 2012). These changes in combination accelerate the process of white fat storage in the body which leads to the development of obesity (Backhed et al. 2004; Boroni Moreira et al. 2012). The role of microbiota in a normal and an obese person has been shown in Fig. 5. Recent research on the gut microbiome in obese and lean twins has also highlighted that despite having the same lineage, individuals from the same families show varying bacterial diversity and altered representation of bacterial genes in their microbiota (Turnbaugh et al. 2009a). These observed differences in the microbial community are mostly responsible for differences in physiological states and variations in metabolic pathways for individuals from the same families (Turnbaugh et al. 2009a).

3.2

Diabetes Mellitus

Diabetes mellitus (DM) is a chronic metabolic disorder accounting for 80% of premature mortality (Rawal et al. 2012). It is characterized by increased blood sugar levels, which can be due to decreased insulin production by the pancreas or decreased efficacy of the body to utilize the available insulin (Sapra and Bhandari 2022). Millions of people are affected by diabetes mellitus globally; among which a large number of cases remain undetected (Gifford et al. 2015; Roglic et al. 2016). Metabolic disorders can be understood as the combination of elevated fasting glucose levels in the blood, hypertension as a result of obesity, an increase in low-density lipoprotein (LDL), and a decrease in high-density lipoprotein (HDL) cholesterol in plasma (Alberti et al. 2005; Sapra and Bhandari 2022). The lifestyle changes in the past 3–4 decades include the change in dietary patterns, decreased physical activities, increased stress, and exposure to adverse environmental factors,

Human Microbiome and Lifestyle Disorders

177

Fig. 5 Role of gut microbiota in metabolism and development of obesity and type 2 diabetes. The figure shows a comparison of the gut microbiota of a normal and obese individual. An obese or diabetic person shows low tight junction integrity, high lipopolysaccharide, high insulin resistance, high levels of inflammation, etc. Changes in metabolism and high obesity and diabetes also increase the risk of cardiovascular disease. Here, IEC intestinal epithelial cells, LPS lipopolysaccharide, LDL-C low-density lipoproteins-cholesterol, SCFAs short-chain fatty acids, CVD cardiovascular disease, and TJ tight junction. (The figure was adapted from Vezza et al. (2020))

which together have contributed to the steep rise in DM cases seen in both developed and developing nations (Alberti et al. 2005; Gifford et al. 2015; Roglic et al. 2016). While the disease itself is multifactorial, one of the major factors is the diet itself and the change in the microflora (Farzi et al. 2019). The development and growth of the gut microbial environment begin in utero or during birth. The adult microbial profile is attained at around 2 years of age (Sharma

178

A. Gupta and A. Jha

and Tripathi 2019). Bacteria, eukaryotes, and archaea together comprise the gut microbial flora. Targeted metagenomics studies suggest that 90% of the bacterial species in the gut are made of the Bacteroidetes (gram-negative) and Firmicutes (gram-positive) species (Gevers et al. 2012; Human Microbiome Project Consortium 2012). This microbial environment competes for space and nutrition and thereby protects against pathogens. They also refine and improve the immune system and metabolic system of the host. The regular diet of an individual entails large portions of carbohydrates which can be simple or complex saccharide molecules. In the ileum, these complex polysaccharides are broken down into simple monosaccharides with the assistance of bacterial enzymes like glycosidases (Flint et al. 2012). With the impaired breakdown of sugar molecules, the ratio of Bacteroidetes: Firmicutes changes. The reduction of gut microbes leads to weak cell-to-cell integrity. This causes a “leaky” gut, which increases the permeability and causes inflammation of the intestine and reduced or disturbed immune response. These factors influence T cell-mediated immunity and are as a result seen in autoimmune diseases as well as type I DM (Paun et al. 2017; Farzi et al. 2019). Diabetes progression is also seen through both altered gut microbiota and changes in the subgingival bacterial flora (Yang et al. 2020). As the subgingival microflora grows and matures into a predominantly Gram-negative environment, it poses an important source of systemic challenge via the ulcerated gingival pocket epithelium. This, therefore, triggers an “infection-mediated” pathway of cytokine upregulation, especially with the secretion of IL1 and TNF-α, and a state of insulin resistance, affecting glucose-utilizing pathways (Li et al. 2000). The treatment approach toward DM also plays an important role in contributing to restoring the microbial environment (Fig. 6). The most popular choice of medicine against hyperglycemia is Metformin. Metformin is advantageous in controlling blood sugar levels without causing weight gain or added cardiovascular complications (Cefalu et al. 2014). Recent studies conducted by Lee H et al. and Hur KY et al. conclude that metformin suppresses the glucagon-like protein 1(GLP-1) and serum bile acid concentrations (Preiss et al. 2017; Bahne et al. 2018). This further correlates well with the changes in Bacteroidetes:Firmicutes ratio. Metformin also shows similarity with Akkermansia muciniphila, in improving the metabolic profile by lowering the tissue inflammation in cases of diet-induced obesity in DM patients (Lee et al. 2018). Another treatment modality is the introduction of probiotics. Infusion of species like Lactobacillus and Bifidobacterium through diet helps restore the gut microbial flora. The role of low-grade chronic inflammation is well understood in the progression of type II DM. Probiotic strains enhance the production of IL10 which helps in downregulating the pro-inflammatory cytokines such as IL1β and IL2 and thus helps in preventing the low-grade inflammation and onset of diabetes (REF: PMID: 23147032, PMID: 23418126). Some probiotic strains also help in the reduction of oxidative stress in pancreatic tissues and thus prevent pancreatic cell apoptosis (Ejtahed et al. 2012). However, regular intake of probiotics can cause a reduction of highly sensitive C-reactive proteins in pregnant women which may be implicated in type II DM (Asemi et al. 2013).

Fig. 6 Role of diet and gut microbiota in diabetes. This figure shows how the interplay between diet and microbial diversity affects metabolism. High lipopolysaccharide, high insulin resistance, high levels of inflammation, etc. in a diabetic person. Change in the intestinal barrier due to elevated concentrations of glucose is one of the major reasons for metabolic inflammation. LPS lipopolysaccharide, TLR toll-like receptor, GLUT2 glucose transporter 2. (This figure has been adapted from Yang et al. (2021))

Human Microbiome and Lifestyle Disorders 179

180

A. Gupta and A. Jha

One of the most important symptoms of diabetes mellitus is macrovascular changes. Patients with diabetes are susceptible to higher cholesterol levels and lipid abnormalities and have an elevated incidence of cardiovascular disease (Yang et al. 2021). To help reduce the chances of macrovascular diseases in type II DM patients with a history of previous cardiac disease, targeted lipid management is introduced to lower low-density lipoprotein cholesterol, raise high-density lipoprotein cholesterol, and reduce triglycerides (Davidson et al. 2000). Lifestyle intervention that aims at good glycemic control is necessary to control hypertriglyceridemia. Statins and Aspirin are the drugs of choice which are also known to restore and re-establish the oral microbial flora.

3.3

Preterm Low Birth Weight

Any birth before 37 weeks of gestation is defined as preterm birth by the WHO (Quinn et al. 2016; Xiong et al. 2021). The term very preterm is defined as delivery at below 32 weeks and extremely preterm is the delivery at less than 28 weeks. If the birth weight is below 2500 g it is considered to be low, 99%) of microbial species reject laboratory cultivation, interactions are constrained and imbalanced (Bakken 1985). “Recent advances in our knowledge of microbial diversity have been made possible by the application of 16S rRNA gene sequences”. These approaches circumvent the need to cultivate organisms by getting genetic material directly from environmental or biological sources. These techniques show an effect on microflora diversity (Ravel et al. 2011).

Lactobacillus-Dominated Vaginal Microbiota Lactobacillus members are frequently recognised as a sign of a normal or healthy vaginal environment. It has been assumed that this strain has a “vital character in defending the vaginal atmosphere from non-indigenous and putatively hazardous microbes” (Donders et al. 2000). This is performed via the generation of lactic acid, which results in a pH of 3.5–4.5, which is low and protective. Lactic acid, rather than acidity alone, has been demonstrated to be more effective as a microbicide against HIV and diseases like Neisseria gonorrhoea (Fichorova et al. 2011).

Other Types of Vaginal Microbiota “According to recent studies, 20–30% of unaffected, healthy women have vaginal ecosystems without Lactobacillus but with a wide variety of facultative or entirely anaerobic bacteria that are linked to a slightly higher pH (5.3–5.5)” (Ravel et al. 2011). Among Hispanic and Black women, this number of communities can approach 40% (Zhou et al. 2007). The extremely diverse microbial population may have allowed functional redundancy, allowing the ecosystem’s function to remain even when perturbed. Even though the makeup of these communities closely mimics that of symptomatic bacterial vaginosis, these forms of vaginal bacterial communities might be called as healthy (Ma et al. 2013).

3 COVID-19 “COVID-19” is a new-fangled coronavirus disease that emerged in 2019. It is caused by the severe acute “respiratory syndrome coronavirus 2 (SARS-CoV-2) and is characterised by systemic symptoms such as fever, muscle pain, and exhaustion, lung problems such as chronic cough, breathlessness, and autonomic dysfunction” (Wang et al. 2021). COVID-19 had been confirmed in over 418 million people globally as of “February 2022, with over 5 million deaths” (https://www. worldometers.info/coronavirus/). COVID-19 has no therapy now. In nutshell, this

Correlation of Human Microbiome and Immune Functioning with COVID-19. . .

207

epidemic has posed significant problems to humanity. There are still nations, such as India, that are in exceptionally harsh conditions. As a result, gaining a better knowledge of COVID-19 will aid in preventing and treatment of the illness (Wang et al. 2021).

3.1

Changes in Gut Microbiota in COVID-19

Analysis of faecal samples from COVID-19 patients by the method of metagenomic sequences, they discovered gastroenteric microflora was altered in patients, which was characterised by an abundance of harmful microbes such as “Campylobacter, Clostridium difficile, Enterococcus faecalis and a lower quantity of favourable microbes such as Bifidobacteria, Lactobacilli”, etc. (Zuo et al. 2020). Many severities of the disease are associated with Faecalibacterium prausnitzii, but not noticed in Coprobacillus, or Clostridium hathewayi in the faeces (an anti-inflammatory bacterium) (Wang et al. 2021).

Changes in Bacterial Community Individuals enduring COVID-19 have a limited bacterial diversity, which is characterised by a substantially lower abundance of helpful bacterial species but a greater abundance of “pathogenic organisms such as Actinomyces, and Streptococcus, among others. A decreased bacterial diversity and a distinct bacterial composition were found in H1N1 patients” (Gu et al. 2020), “Markers are linked with changes in the gut microbiota of COVID-19 and H1N1” (Yildiz et al. 2018). COVID-19 “patients showed significantly changed gut flora related to healthy controls, which may be one of the causes of many infectious diseases. Infection with COVID-19 is more common among older people, overweight, and resistant population” (Kassir 2020). Conversely, interchanging in gastroenteric microbiota is unquestionably prone to significant influencing variables (Kassir 2020).

Changes in the Fungal Community SARS-CoV-2 patients’ faeces fungal microbiomes were studied throughout their hospitalisation, and researchers noticed that the faecal microbiomes infected by the COVID virus were significantly different from the control group (Wang et al. 2021). Patients infected by this virus had more amount of Candida albicans and multiple mycobiome geography at the time of entrance. The faecal sample of COVID-19 patients had more diversity of fungus as compared to healthy humans (Zuo et al. 2020) (Fig. 4).

208

P. Khatri et al.

Fig. 4 Comparison of the healthy gut and healthy gut with COVID-19

3.2

Changes in the Gut–Lung Axis in COVID-19

“COVID-19” also engaged in the gastrointestinal and respiratory axis. The intensity of the sickness and microbial imbalance is linked to the gut–lung axis. If the intestinal barrier is breached by microbial imbalance, it may be clever to travel from the respiratory organs and lungs to the intestine via the blood circulatory system and lymphatic vessels. This may explain why some people with COVID19 suffer digestive problems. As people age, their gut flora may become less diverse, which might explain why severe COVID-19 is more common in the elderly (Aktas and Aslim 2020). The gut–lung axis is predominant in the immunological response to the COVID-19 virus. “Because of increased infection irritation in the lungs and bowels, as well as weakened regulatory or anti-inflammatory systems, intestinal malnutrition is linked to an increased risk of death from various respiratory diseases” (Aktas and Aslim 2020). A phenomenon known as organ crosstalk happens when organs from the same germ layer arise in different parts of the body during early development. Immunological studies have demonstrated that the mucosa of one’s digestive system can influence that of one’s respiratory system (Ichinohe et al. 2011). A pulmonary infection conveyed to the intestines via the GLA (gut–lung axis) might be the cause of the intestinal damage generated by this respiratory illness. In addition, studies have shown that the lungs play a part in the body’s immune response by harbouring pathogens. Some COVID-19 individuals died as a result of acute respiratory illness syndrome. As a result, these individuals have an even more severe dysbiosis in terms of gut flora, when gut flora loses beneficial microorganisms the amount of opportunistic microorganisms increases which causes dysbiosis and imbalance in gut microbiota (Al-Rashidi 2022). GLA moderates the inflammatory response of patients who are infected by COVID-19. Even though this chapter

Correlation of Human Microbiome and Immune Functioning with COVID-19. . .

209

revelations are primarily illustrative, and the specific pathophysiology of the COVID-19 virus remains unknown, they give crucial information and guidance for future study, as well as lay the groundwork for prospective treatment techniques (Fink and Delude 2005).

3.3

Changes in the Respiratory Tract Microbiome in COVID-19

“Current papers have examined the respirational region microbiota of COVID-19 patients. Samples collected from a nasopharyngeal area from individuals who have pneumonia were compared to individuals with other types of pneumonia, and an analysis of individuals with pneumonia revealed less diversity in individuals infected with COVID-19 virus” (Zhang et al. 2020a). Individuals which are infected by COVID-19 had a higher probability of bacterial and viral infection as compared to individuals without COVID-19 (Shen et al. 2020). The respiratory infection is mostly caused by the bacteria Acinetobacter, which can lead to pneumonia (Ramanathan et al. 2020). Many fungus species caused opportunistic infections mostly found in the individuals who have a smaller number of helpful bacteria. However, using 16S rRNA genome sequencing, “between patients with proven COVID-19 infection and those who were negative, they discovered no variations in the composition or variety of the microbiomes” (De Maio et al. 2020). “Like Minich et al., they evaluated the upper airway microbial populations of COVID-19 individuals but differentiated sample techniques and swab types, discovering that the sampling approach modified microbiome composition rather than swab type” (Minich et al. 2021).

4 Changes in Immune Functioning in COVID-19 Accumulating research supports the premise that obtaining a good knowledge of the immune system’s function during “SARS-COV-2” infection would significantly reduce COVID-19 mortality (Gusev et al. 2022). SARS is associated with an extensive variety of clinical manifestations, including severe hyper inflammation, leucocytosis, and multi-organ failure, ranging from mild to severe acute respiratory distress syndrome (ARDS) (Gibson et al. 2020). Through its spike protein, which is triggered by TMPRSS2, the virus connects with the receptor ACE2 on somatic cells. When the virus infects the nasopharyngeal area is set off the innate immune response, allowing the virus to propagate to the lower respiratory tract (LRT) (Qi et al. 2020). Innate immunity is set off by COVID viruses along with the production of immune responses and eosinophil filtration. “The TLR and RIG-I (retinoic acid-inducible gene I) receptors comprise pathogen recognition receptors

210

P. Khatri et al.

(PRRs) that recognise the formation of pathogen-associated molecular pattern molecules (PAMPs) in infected immune cells. such as alveolar macrophages. Phagocytise and signalling pathways are activated by intermolecular interactions between PRRs and PAMPs” (Fung and Liu 2019). Additionally, the antiviral signalling cascade recruits extra innate immune cells that all manufacture chemokines. These chemokines (MCP-1, MIG, and IP-10) can attract lymphocytes, which then recognise viral antigens presented by DCs. In COVID-19 most contributors innate cells, natural killer cells, dendritic cells and macrophages these cells are capable of production of cytokines, phagocytosis and apoptosis Additionally, these immune cells are accountable for distributing virus-related antigens to recruit adaptive immune responses. Cytokine storm can cause by a virus which infect the alveolar macrophages and damage multiple organs (Cyprian et al. 2021).

4.1

Changes in Innate Immunity

SARS-CoV-2 research is continuing and has provided insight into various aspects of the virus’s pathogenesis, including viral multiplication, dispersion, elimination or persistence, subsequent infection, and host immune responses. Interferon production is one of the early molecular executors of the host’s inherent resistance to viral infection (IFNs) (Schoggins 2019). These IFNs are potent cytokines with a variety of roles, including viral replication inhibition in innate immune cells and stimulation of adaptive immunological responses. Interferon responses like type I and III show less activation during COVID infected bronchial epithelial cells but the level of some chemokine and IL-6 was increased. Another study revealed that persons with severe “COVID-19 had defective many responses which were related to increased tumour necrosis factor (TNF) and interleukin (IL-6) levels” (Shen et al. 2020). “In fatal cases of severe COVID-19, involving the onset of ARDS and respiratory failure, toll-like receptors (TLR) activated by pathogen-associated molecular patterns (PAMPs) have been linked”.

4.2

Changes in Adaptive Immune Response

Numerous studies examined the people who had COVID-19 infection and their acquired immune system and used the in-depth immune constitution to see whether any correlations existed between immune responses and poor clinical outcomes. CD4+ and CD8+ T cells mainly tackled coronavirus infection by producing “IgG and IgA antibody titres in COVID-19 patients being highly correlated” (Mathew et al. 2020). Surprisingly, CD4+ T cells reactive to SARS-CoV-2 were attributed to people who had never been exposed to the virus, indicating that systemic virus infections and severe acute respiratory are cross-reactive (Wang et al. 2020). The level of IFN-g expressed by CD4+ T cells has also been reported to be decreased in

Correlation of Human Microbiome and Immune Functioning with COVID-19. . .

211

severe cases compared to mild instances. Loss of symbiotic organisms, together with low SCFA levels, can harm Treg levels, which help regulate an excessive immune system response. An earlier study found that 40% of the total patients had antibodies during the first week of illness onset, and that percentage rose to 100% for total antibodies, 94.3% for IgM, and 79.8% for IgG on day 15” (Wu et al. 2020). Tests of antibody levels in people who had SARS-CoV-2 and people who had recovered found that the level of antibodies dropped after 8 months, which raises questions about long-term immunity However, more research is needed to look into this (Forthal 2020).

5 Future Prospective 5.1

Faecal Microbial Transplantation for COVID-19

The clinical application of microflora therapeutics offers great potential. Many disorders have been proven to benefit from faecal microbiome transplantation, often known as faecal microbiota transplantation (FMT) (Cui et al. 2016). Toxic microbiota transplanting can restore epithelial viability and microbiota levels afterburn damage in a mouse model. The symptoms and diarrhoea of patients were significantly improved with FMT. Both body temperature and faeces production began to improve. A patient with sepsis and severe diarrhoea was treated with FMT following a vagotomy (Beccaria et al. 2018). As previously stated, the gastrointestinal system and airway system work with the immunological system to maintain equilibrium and prevent illness. The gastrointestinal and airway axis may regulate immune function. Changing the gut microflora may help COVID-19 modulate inflammation. An available outlets study was undertaken on COVID-19 individuals to analyse FMT function. This research included eleven COVID-19-positive patients in the hospital. For 4 days, each patient received ten FMT pills orally. In five of eleven individuals, gastrointestinal problems improved after FMT. The subsets of peripheral blood lymphocytes shifted, and the diversity of microbial communities grew. As a result, FMT might be used to treat COVID-19.

5.2

Uses Probiotics and Prebiotics for COVID-19

Microbes such as bacteria invade the living organism and transform the flora composition to benefit the host. The subdominant categories of the gut microbiota, respectively, are Bifidobacterium and Lactobacillus strains. Probiotics are now being studied for their involvement in a range of disorders (Knight and Girling 2003). Probiotics are beneficial in the treatment of throat infections (Guillemard et al. 2010). TLR3 activation causes inflammation coagulation, which can be influenced

212

P. Khatri et al.

by probiotics. “Controlling inflamed mediator, structural factor, and anticoagulant protein synthesis in the airways. Many research papers given an idea of that probiotic prophylaxis may successfully maintain the balance between respiratory viruses and immunological coagulation response regulation, allowing the normal function to withstand viral onslaught” (Zelaya et al. 2014). Some COVID-19 patients experience rapid deterioration and develop ARDS. Patients usually die of multiple organ failures after developing ARDS, which is caused by an infection-induced immunological response (known as the cytokine storm). As a result, if probiotics can be utilised to help treat COVID-19, the intemperate state generated by the immunological response will likely be reduced, as would the incidence of problems (Zhang et al. 2020b). Prebiotics are non-digestible and non-absorbable organic substances that benefit the host’s health by exhilarating the energy metabolism of good bacteria. Prebiotics transit undigested through the upper digestive system and thus can be metabolised by good microbiota. Instead of destructive or decomposing bacteria, prebiotics enhance their development. Considering the properties of prebiotics and probiotics on influenza contamination, probiotics and prebiotics may augment the final volume of haemolytic suppression antibodies following influenza vaccination. Prebiotics can help probiotics grow and survive, “which may improve the condition of patients having many severe diseases. Probiotics may improve the microbiota of patients’ lungs and intestines, as well as their immunity” (Olaimat et al. 2020).

6 Conclusion This chapter explored microflora and COVID-19 in terms of competence, pathogenesis, and medication. Up to this point, we have come to a few conclusions. Initially, the COVID-19 microbiota varies significantly from that of healthy people, particularly in the intestine and airways. Coronavirus relies on the gastroenteric and airways axis. FMT or edible microbiota may assist to decrease aggravation and COVID-19 concerns, potentially leading to substantial breakthroughs in preventive care. COVID-19 is still causing mayhem to people’s health. Despite the substantial research into the correlation involving microbiome and COVID19 disorders, the results in terms of causation, prevention, and therapy are primarily descriptive, which again is inadequate. These studies point towards new avenues for COVID19 prevention and therapy. To obtain a clearer conclusion, additional research is needed on this intriguing path. Research on COVID-19 and microbes is now attentive on the enteric microbiota, instead of throat microbiota, another important microecological topic. On the one hand, the gastrointestinal microbiota is quite stable, and several scientists have investigated the interaction was seen between intestinal flora and sickness; on the other hand, the digestive tract and COVID-19 have a particularly direct relationship. When it comes to COVID-19, a contagious illness transmitted by air, the oral microbiota should be examined as a possible link.

Correlation of Human Microbiome and Immune Functioning with COVID-19. . .

213

References Aktas B, Aslim B (2020) Gut-lung axis and dysbiosis in COVID-19. Turk J Biol 44:265–272. https://doi.org/10.3906/biy-2005-102 Al-Rashidi HE (2022) Gut microbiota and immunity relevance in eubiosis and dysbiosis. Saudi J Biol Sci 29:1628–1643. https://doi.org/10.1016/j.sjbs.2021.10.068 Arumugam M, Raes J, Pelletier E et al (2011) Erratum: enterotypes of the human gut microbiome (Nature (2011) 473 (174-180)). Nature 474:666. https://doi.org/10.1038/nature10187 Avoli M, Krnjević K (2015) The long and winding road to gamma-amino-butyric acid as neurotransmitter. Can J Neurol Sci 43:219–226. https://doi.org/10.1017/cjn.2015.333 Bakken LR (1985) Separation and purification of bacteria from soil. Appl Environ Microbiol 49: 1482–1487. https://doi.org/10.1128/aem.49.6.1482-1487.1985 Baradaran Ghavami S, Pourhamzeh M, Farmani M et al (2021) Cross-talk between immune system and microbiota in COVID-19. Expert Rev Gastroenterol Hepatol 15:1281–1294. https://doi.org/ 10.1080/17474124.2021.1991311 Beccaria et al (2018) 乳鼠心肌提取 HHS Public Access. Physiol Behav 176:139–148. https://doi. org/10.1097/SHK.0000000000000551.FECAL Belkaid Y, Hand T (2015) Role of the microbiota in immunity and inflammation. Cell 157:121– 141. https://doi.org/10.1016/j.cell.2014.03.011.Role Bik EM, Eckburg PB, Gill SR et al (2006) Molecular analysis of the bacterial microbiota in the human stomach. Proc Natl Acad Sci U S A 103:732–737. https://doi.org/10.1073/pnas. 0506655103 Bogaert D, Keijser B, Huse S et al (2011) Variability and diversity of nasopharyngeal microbiota in children: a metagenomic analysis. PloS One 6:e17035. https://doi.org/10.1371/journal.pone. 0017035 Booijink CCGM, El-Aidy S, Rajilić-Stojanović M et al (2010) High temporal and inter-individual variation detected in the human ileal microbiota. Environ Microbiol 12:3213–3227. https://doi. org/10.1111/j.1462-2920.2010.02294.x Bottari B, Castellone V, Neviani E (2021) Probiotics and Covid-19. Int J Food Sci Nutr 72:293– 299. https://doi.org/10.1080/09637486.2020.1807475 Chen Y, Ji F, Guo J et al (2016) Dysbiosis of small intestinal microbiota in liver cirrhosis and its association with etiology. Sci Rep 6:1–9. https://doi.org/10.1038/srep34055 Cleary DW, Clarke SC (2017) The nasopharyngeal microbiome. Emerg Top Life Sci 1:297–312. https://doi.org/10.1042/ETLS20170041 Costalonga M, Herzberg MC (2014) The oral microbiome and the immunobiology of periodontal disease and caries. Immunol Lett 162:22–38. https://doi.org/10.1016/j.imlet.2014.08.017 Cui B, Xu F, Zhang F (2016) Methodology, not concept of fecal microbiota transplantation, affects clinical findings. Gastroenterology 150:285–286. https://doi.org/10.1053/j.gastro.2015.05.065 Cussotto S, Sandhu KV, Dinan TG, Cryan JF (2018) The neuroendocrinology of the microbiotagut-brain axis: a behavioural perspective. Front Neuroendocrinol 51:80–101. https://doi.org/10. 1016/j.yfrne.2018.04.002 Cyprian F, Sohail MU, Abdelhafez I et al (2021) SARS-CoV-2 and immune-microbiome interactions: lessons from respiratory viral infections. Int J Infect Dis 105:540–550. https://doi.org/10. 1016/j.ijid.2021.02.071 Das S, Khanna C, Singh S et al (2020) Impact of human microbiome on health. Microb Divers Interv Scope 349–373. https://doi.org/10.1007/978-981-15-4099-8_20 De Maio F, Posteraro B, Ponziani FR et al (2020) Nasopharyngeal microbiota profiling of SARSCoV-2 infected patients 7:20–23. https://doi.org/10.21203/rs.3.rs-27326/v1 Dekaboruah E, Suryavanshi MV, Chettri D, Verma AK (2020) Human microbiome: an academic update on human body site specific surveillance and its possible role. Arch Microbiol 202:2147– 2167. https://doi.org/10.1007/s00203-020-01931-x

214

P. Khatri et al.

Dominguez-Bello MG, Costello EK, Contreras M et al (2010) Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proc Natl Acad Sci U S A 107:11971–11975. https://doi.org/10.1073/pnas.1002601107 Donders GGG, Bosmans E, Dekeersmaecker A et al (2000) Pathogenesis of abnormal vaginal bacterial flora. Am J Obstet Gynecol 182:872–878. https://doi.org/10.1016/S0002-9378(00) 70338-3 Fichorova RN, Yamamoto HS, Delaney ML et al (2011) Novel vaginal microflora colonization model providing new insight into microbicide mechanism of action. MBio 2:1–10. https://doi. org/10.1128/mBio.00168-11 Fink MP, Delude RL (2005) Epithelial barrier dysfunction: a unifying theme to explain the pathogenesis of multiple organ dysfunction at the cellular level. Crit Care Clin 21:177–196. https://doi.org/10.1016/j.ccc.2005.01.005 Forthal D (2020) Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID- 19. The COVID-19 resource centre is hosted on Elsevier Connect, the company’s public news and information Fung TS, Liu DX (2019) Human coronavirus: host-pathogen interaction. Annu Rev Microbiol 73: 529–557 Gibson PG, Qin L, Puah SH (2020) COVID-19 acute respiratory distress syndrome (ARDS): clinical features and differences from typical pre-COVID-19 ARDS. Med J Aust 213:54–56. e1. https://doi.org/10.5694/mja2.50674 Gomaa EZ (2020) Human gut microbiota/microbiome in health and diseases: a review. Antonie van Leeuwenhoek 113:2019–2040. https://doi.org/10.1007/s10482-020-01474-7 Gu S, Chen Y, Wu Z et al (2020) Alterations of the gut microbiota in patients with COVID-19 or H1N1 Influenza Silan. J Gerontol Ser A Biol Sci Med Sci 0813:1–11 Guillemard E, Tondu F, Lacoin F, Schrezenmeir J (2010) Consumption of a fermented dairy product containing the probiotic Lactobacillus casei DN-114001 reduces the duration of respiratory infections in the elderly in a randomised controlled trial. Br J Nutr 103:58–68. https://doi. org/10.1017/S0007114509991395 Gusev E, Sarapultsev A, Solomatina L, Chereshnev V (2022) Sars-Cov-2-specific immune response and the pathogenesis of COVID-19. Int J Mol Sci 23:1716. https://doi.org/10.3390/ ijms23031716 Hameed S, Hans S, Monasky R et al (2021) Understanding human microbiota offers novel and promising therapeutic options against candida infections. Pathogens 10:1–15. https://doi.org/10. 3390/pathogens10020183 Ichinohe T, Pang IK, Kumamoto Y et al (2011) Microbiota regulates immune defense against respiratory tract influenza a virus infection. Proc Natl Acad Sci U S A 108:5354–5359. https:// doi.org/10.1073/pnas.1019378108 Jovel J, Dieleman LA, Kao D et al (2018) The human gut microbiome in health and disease. Metagenomics Perspect Methods Appl 197–213. https://doi.org/10.1016/B978-0-08-102268-9. 00010-0 Kassir R (2020) Risk of COVID-19 for patients with obesity. Obes Rev 21:10–11. https://doi.org/ 10.1111/obr.13034 Kazor CE, Mitchell PM, Lee AM et al (2003) Diversity of bacterial populations on the tongue dorsa of patients with halitosis and healthy patients. J Clin Microbiol 41:558–563. https://doi.org/10. 1128/JCM.41.2.558-563.2003 Knight DJW, Girling KJ (2003) Gut flora in health and disease. Lancet 361:1831. https://doi.org/10. 1016/S0140-6736(03)13438-1 Lai P, Okin D, Drew D et al (n.d.) Metagenomic assessment of gut microbial communities and risk of severe COVID-19 Massachusetts General Hospital, pp 1–18 Le Chatelier E, Nielsen T, Qin J et al (2013) Richness of human gut microbiome correlates with metabolic markers. Nature 500:541–546. https://doi.org/10.1038/nature12506 Lloyd-Price J, Abu-Ali G, Huttenhower C (2016) The healthy human microbiome. Genome Med 8: 1–11. https://doi.org/10.1186/s13073-016-0307-y

Correlation of Human Microbiome and Immune Functioning with COVID-19. . .

215

Ma B, Forney L, Ravel J (2013) Orchard monitoring manual for pests, natural enemies, and diseases of apple, pear and cherry. 371–389. https://doi.org/10.1146/annurev-micro-092611-150157.The Mancabelli L, Milani C, Lugli GA et al (2017) Meta-analysis of the human gut microbiome from urbanized and pre-agricultural populations. Environ Microbiol 19:1379–1390. https://doi.org/ 10.1111/1462-2920.13692 Mathew D, Giles JR, Baxter AE et al (2020) Deep immune profiling of COVID-19 patients reveals patient heterogeneity and distinct immunotypes with implications for therapeutic interventions. bioRxiv Prepr Serv Biol https://doi.org/10.1101/2020.05.20.106401 Menni C, Jackson MA, Pallister T et al (2017) Gut microbiome diversity and high-fibre intake are related to lower long-term weight gain. Int J Obes (Lond) 41:1099–1105. https://doi.org/10. 1038/ijo.2017.66 Merenstein C, Liang G, Whiteside SA et al (2021) Signatures of COVID-19 severity and immune response in the respiratory tract microbiome. MBio 12:e0177721. https://doi.org/10.1128/mBio. 01777-21 Minich JJ, Ali F, Marotz C et al (2021) Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment. Microbiome 9:1–22. https://doi.org/10.1186/s40168-020-00960-4 Moffatt MF, Cookson WO (2017) CMJv17n6-Moffat.indd. Clin Med (Northfield Il) 17:525–534 Narayan Biswal B, Narayan Das S, Kumar Das B, Rath R (2017) Alteration of cellular metabolism in cancer cells and its therapeutic. J Oral Maxillofac Pathol 21:244–251. https://doi.org/10.4103/ jomfp.JOMFP Nelson KE, Peterson JL, Garges S (2011) Metagenomics of the human body. Metagenomics Hum Body 1–351. https://doi.org/10.1007/978-1-4419-7089-3 Olaimat AN, Aolymat I, Al-Holy M et al (2020) The potential application of probiotics and prebiotics for the prevention and treatment of COVID-19. NPJ Sci Food 4:17. https://doi.org/ 10.1038/s41538-020-00078-9 Qi F, Qian S, Zhang S, Zhang Z (2020) Single cell RNA sequencing of 13 human tissues identify cell types and receptors of human coronaviruses. bioRxiv. https://doi.org/10.1101/2020.02.16. 951913 Ramanathan K, Antognini D, Combes A et al (2020) Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-research that is available on the COVID-19 resource centre - including this for unrestricted research re-use a. 19–21 Ravel J, Gajer P, Abdo Z et al (2011) Vaginal microbiome of reproductive-age women. Proc Natl Acad Sci U S A 108:4680–4687. https://doi.org/10.1073/pnas.1002611107 Requena T, Velasco M (2021) The human microbiome in sickness and in health. Rev Clínica Española (English Ed) 221:233–240. https://doi.org/10.1016/j.rceng.2019.07.018 Rogers GB (2019) The nasopharyngeal microbiome and LRTIs in infants. Lancet Respir Med 7: 369–371. https://doi.org/10.1016/S2213-2600(18)30495-8 Schoggins JW (2019) Interferon-stimulated genes: what do they all do? Annu Rev Virol 6:567–584. https://doi.org/10.1146/annurev-virology-092818-015756 Scott NR, Mann B, Tuomanen EI, Orihuela CJ (2021) Multi-valent protein hybrid pneumococcal vaccines: a strategy for the next generation of vaccines. Vaccine 9:1–17. https://doi.org/10. 3390/vaccines9030209 Shapira M (2016) Gut microbiotas and host evolution: scaling up symbiosis. Trends Ecol Evol 31: 539–549. https://doi.org/10.1016/j.tree.2016.03.006 Shen Z, Xiao Y, Kang L et al (2020) Genomic diversity of SARS-CoV-2 in COVID-19 patients. J Infect Dis 1–27 Stearns JC, Davidson CJ, Mckeon S et al (2015) Culture and molecular-based profiles show shifts in bacterial communities of the upper respiratory tract that occur with age. ISME J 9:1246–1259. https://doi.org/10.1038/ismej.2014.250

216

P. Khatri et al.

Tye-Din JA, Galipeau HJ, Agardh D (2018) Celiac disease: a review of current concepts in pathogenesis, prevention, and novel therapies. Front Pediatr 6:1–19. https://doi.org/10.3389/ fped.2018.00350 Wang C, Xie J, Zhao L et al (2020) Alveolar macrophage dysfunction and cytokine storm in the pathogenesis of two severe COVID-19 patients. EBioMedicine 57:102833. https://doi.org/10. 1016/j.ebiom.2020.102833 Wang H, Wang H, Sun Y et al (2021) Potential associations between microbiome and COVID-19. Front Med 8:785496. https://doi.org/10.3389/fmed.2021.785496 Wu F, Zhao S, Yu B et al (2020) A new coronavirus associated with human respiratory disease in China. Nature 579:265–269. https://doi.org/10.1038/s41586-020-2008-3 Xavier-santos D, Padilha M, Alexandre G et al (2020) Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company’s public news and information Yildiz S, Mazel-Sanchez B, Kandasamy M et al (2018) Influenza A virus infection impacts systemic microbiota dynamics and causes quantitative enteric dysbiosis. Microbiome 6:1–17. https://doi. org/10.1186/s40168-017-0386-z Zelaya H, Tsukida K, Chiba E et al (2014) Immunobiotic lactobacilli reduce viral-associated pulmonary damage through the modulation of inflammation-coagulation interactions. Int Immunopharmacol 19:161–173. https://doi.org/10.1016/j.intimp.2013.12.020 Zhang Y, Wang X, Li H et al (2018) Human oral microbiota and its modulation for oral health. Biomed Pharmacother 99:883–893. https://doi.org/10.1016/j.biopha.2018.01.146 Zhang D, Li S, Wang N et al (2020a) The cross-talk between gut microbiota and lungs in common lung diseases. Front Microbiol 11:1–14. https://doi.org/10.3389/fmicb.2020.00301 Zhang S, Li L, Shen A et al (2020b) Rational use of tocilizumab in the treatment of novel coronavirus pneumonia. Clin Drug Investig 40:511–518. https://doi.org/10.1007/s40261-02000917-3 Zhou X, Brown CJ, Abdo Z et al (2007) Differences in the composition of vaginal microbial communities found in healthy Caucasian and black women. ISME J 1:121–133. https://doi.org/ 10.1038/ismej.2007.12 Zuo T, Zhan H, Zhang F et al (2020) Alterations in fecal fungal microbiome of patients with COVID-19 during time of hospitalization until discharge. Gastroenterology 159:1302–1310.e5. https://doi.org/10.1053/j.gastro.2020.06.048

Exploring the Pathoprofiles of SARS-COV-2 Infected Human Gut–Lungs Microbiome Crosstalks Sisir Nandi, Sarfaraz Ahmed, Aaruni Saxena, and Anil Kumar Saxena

Abstract There has been an unprecedented scientific exploration of post-COVID19 symptoms of the recovered patients put up with the novel coronavirus (nCoV), also called as SARS-CoV-2 infection. There have been reports of breathing difficulty, weakness, and gastrointestinal diarrhea, post SARS-CoV-2 infection recovery. Surprisingly, the thoracic computed tomography scan of the lungs and sonography of the whole abdomen appear normal in such patients. The microbiome of the body consists of all the microbes viz. bacteria, viruses, fungi, etc. and its dysbiosis often leads to depletion in immunity. Diverse microbial communities maintain the microecosystem of the gut and lungs. Therefore, it has been considered of interest to assess the studies on the effect of COVID-19 on the microbiota of the lungs and gut to ascertain its link with the escalation of post-infection symptoms and to explore the pathoprofiles of gut–lungs microbiome crosstalk due to novel coronavirus which negatively affects the host immunity. Although repurposing of several drugs has been carried out to tackle the COVID-19 disease, ever since its outbreak, there has been no evidence regarding the efficacy of any specific chemotherapeutic against the novel viral-induced host gut–lungs microbiome crosstalks. Keywords SARS-CoV-2 · COVID-19 · Gut–lungs microbiome · Crosstalk pathoprofiles

1 Introduction An unknown highly contagious novel strain of coronavirus was identified in human beings to cause COVID-19 disease. The disease originated in Wuhan, China in December 2019 and became a pandemic within a very short span, destroying the global health security and the world economy. Since the first reported case S. Nandi (✉) · S. Ahmed · A. K. Saxena (✉) Global Institute of Pharmaceutical Education and Research, Kashipur, India A. Saxena Department of Cardiovascular Medicine, University of Nottingham, Nottingham, UK © The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd. 2023 V. Kothari et al. (eds.), Probiotics, Prebiotics, Synbiotics, and Postbiotics, https://doi.org/10.1007/978-981-99-1463-0_12

217

218

S. Nandi et al.

(Gao et al. 2020), more than 225 countries including Italy, Germany, the USA, Canada, South Africa, India, and Peru have already faced several infection peaks and many lacs lives have been lost (Worldometer 2020). The first genetic sequences identified in China and USA are Wuhan-Hu1 and USA-WA1/2020, respectively. An unknown virus variant or sub-lineage may produce distinct mutations which differentiate it from the original sequences or prevailing virus variants already transmitting in the global population. The novel coronavirus has also produced various other genetic variants like delta and omicron which are the variant of concern (VOC) (https://www.fda.gov/medical-devices/coronavirus-covid-19-and-medical-devices/ sars-cov-2-viral-mutations-impact-covid-19-tests n.d.). The novel coronavirus belongs to the Coronaviridae family (Zhou et al. 2020). It is a strongly enveloped, positive-stranded RNA virus that infects amphibians, birds, and mammals. The possible modes of viral circulation are direct or indirect contact through the droplet, fomite, fecal–oral, airborne, blood borne, mother-to-child, and animal-to-human transmission (Belouzard et al. 2012). Similarly, symptoms of COVID-19 are SARS-associated bronchitis, pneumonia, shortness of the breath, high fever, dry cough, and multiple organ failure due to loss of immunity along with other minor symptoms like throat pain, pharyngitis, sinusitis, loss of taste and smell, and occasional diarrhea. Ever since its outbreak, there has been no evidence regarding the efficacy of any chemotherapeutic molecule against the novel virus. Several drugs have been under investigation as repurposed drugs to combat the COVID-19 disease (Chen et al. 2020). The breathing difficulty, diarrhea, and abdominal problems persist long due to disruption of the beneficial gut–lungs microbiome leading to the epithelium breakdown that triggers the pro-inflammatory cascades (Burchill et al. 2021).

1.1

SARS-CoV, MERS-CoV, and SARS-CoV-2 Associated Symptoms of the Human Gut and Lungs Infection

The SARS-CoV strain was first reported from China in 2002 and spread to more than 24 countries. Although it was controlled soon by the world health authorities but not before 8,098 individuals got infected and 774 people died with the severe symptoms of respiratory illness like dry cough, chills, pneumonia and breathing difficulty, hypoxia, and diarrhea in 10–20% of the patients (Hui and Zumla 2019). The Middle East respiratory syndrome (MERS) caused by an MERS-coronavirus was first detected in Saudi Arabia in the year of 2012 and quickly spread to over 27 countries with major outbreaks in the United Arab Emirates and South Korea in addition to its place of origin. The MERS claimed 866 lives with 2519 reported cases of infection (Alotaibi and Bahammam 2021). It was claimed that MERS-CoV was sourced in bats which then broaden it to dromedary camels and later passed it on to humans. In 2015, another MERS outbreak away from the Middle East infected 185 people in South Korea and 1 in China and led to 38 deaths. The commonly

Exploring the Pathoprofiles of SARS-COV-2 Infected Human Gut–Lungs. . .

219

reported symptoms of MERS were reported as fever, dry cough, along with shortness of breath. The infected people also reported gastrointestinal troubles like diarrhea, nausea, or vomiting (Ghimire et al. 2021). COVID-19 displays similar symptoms as that of SARS-CoV and MERS, such as severe dry cough, pneumonia, happy hypoxia, gastrointestinal problems like nausea, vomiting, abdominal pain, and diarrhea. Diarrhea is most commonly reported in patients with severe conditions (Guan et al. 2020a, b).

2 Pathoprofiles of SARS-CoV-2 Associated Disruption of the Human Gut–Lungs Microbiome Crosstalk The SARS-CoV-2 gains entry via the nose and mouth. It invades the trachea, tracheoles, and bronchi cells of the respiratory system followed by penetration into enterocytes through the esophagus. The novel coronavirus spike (S) contains two subunits such as S1 and S2. The S1 subunit helps in the recognition via N-terminal and C-terminal domains which help in the host angiotensin-converting enzyme-2 (ACE2) receptor (expressed in the respiratory and intestinal systems) binding, whereas the S2 subunit has repetitive heptapeptide comprising of the hydrophobic coiled-coil interlock strand to fuse the host ACE2 receptors (Nandi et al. 2021; Beniac et al. 2006; Li et al. 2006). After fusion, the SARS-CoV-2 incorporates antigenicity by replication and multiplication. The viral antigen stimulates the pro-inflammatory cytokines (PIC) and chemokines to produce a cytokine storm that activates the host macrophage-mediated phagocytosis (Zhang et al. 2021a; Huang et al. 2020a). Several clinical reports evidence that PIC and cytokine storm attack the microbiota of gut–lungs and change the normal physiology of the microbiome. It also destroys the epithelium and induces loss of the beneficial microbiome present in the gut and lungs. The microbiota crosstalk due to SARS-CoV-2 infection has been represented by a suitable figure showing role of pro-inflammatory cytokines (PIC) and chemokines, followed by the disruption of macrophages and lungs–gut microbiota (Fig. 1). It also triggers the inflammatory responses which cause chronic inflammatory bowel diseases and lung dysfunction (de Oliveira et al. 2021; Vignesh et al. 2020). Hence a superior thought of the pathoprofiles of virus–host microbiota interactions can give insights into the causes of disease progression and appropriate human health measures. The gut and the lungs are major organs closely associated with the immunological coordination and the microbiome makes a bridge between them (Fig. 2). It has been found that SARS-CoV-2 infection may lead to intestinal flora dysbiosis during a lung infection. It also increases levels of angiotensin-converting enzyme 2 (ACE2) occupied by the spike of SARS-CoV-2, which is expressed in the gut and lungs, and increases the gut–lungs permeability (Burchill et al. 2021) and calcium level perturbation (Chen et al. 2021). Further, the viral respiratory infection

220 Fig. 1 Disruption of epithelium and loss of lungs–gut microbiota by PIC and chemokines

S. Nandi et al.

SARS-CoV-2 ACE-2 receptor

Lungs microbiome

Gut microbiome i bi

alters the gut microbiome and the metabolome due to enhanced levels of CD8 + T cells and enhanced induction of lipid levels, respectively (Groves et al. 2020). The healthy inter-relationship and bidirectional interaction between gut–lungs microbiota are well balanced to maintain the host immunity. The fundamental maturation of the immune system is determined by the composition and function of the microbiota. Therefore, microbiota crosstalk due to nCoV may disrupt the integration of gut–lungs mutual understanding explained above (Vignesh et al. 2020).

3 SARS-CoV-2 Allied Disruption of the Human Gut Microbiome: Case Studies The novel coronavirus has been indicated for the disruption of the gut microbiome of the human, also called gut dysbiosis, which results in the loss of useful microbiomes. It triggers inflammatory cytokines due to the loss of intestinal flora and increased gut permeability (Petersen and Round 2014; Thevaranjan et al. 2017).

Exploring the Pathoprofiles of SARS-COV-2 Infected Human Gut–Lungs. . .

221

Fig. 2 SARS-CoV-2 invades and attacks lungs– gut microbiota

The enhanced gut permeability may leak the epithelium tissues stacking tight junction (TJ) proteins of the intestine like occludin, claudin-1, and ZO-1, disrupting the intestinal barricade (Lee et al. 2018). The intestinal mucosa becomes irritable or inflammatory bowel conditions developed under viral infection (Thevaranjan et al. 2017; Lv et al. 2021; Gu et al. 2020). Therefore, the mucosal barrier is expected to lose the integrity that breaks down the secretion and absorption homeostasis of the intestinal microenvironment. The ACE2 receptor is expressed in the intestinal epithelium where an amino acid transporter known as B0AT1 is present in the small intestinal epithelium. The uptake of the dietary tryptophan is dependent on B0AT1. The antimicrobial peptides secretion is regulated by levels of tryptophan which plays a role in the composition of the intestinal microbiota (Perlot and Penninger 2013). The attachment of SARS-CoV-2 to ACE2 receptors alters the gut–lungs microbiota conferring vulnerability to inflammation of the large intestine. The SARS-CoV-2 has been isolated from the stool samples of COVID-19 patients (Tang et al. 2020a; Mohan et al. 2021) and the changes in the intestinal flora have been seen for the COVID-infected patients who suffer from gastrointestinal disturbances (Dhar and Mohanty 2020). A study by Tang et al. on a set of cohort patients

222

S. Nandi et al.

with varying degrees of SARS-CoV-2 infection shows the occurrence of dysbiosis which depends on the severity of the disease. An increase in the opportunistic pathogens such as Enterococcus and Enterobacteriaceae in the critical patients may serve as biomarkers for COVID-19 (Tang et al. 2020b). Similarly, the results of another study suggest that microbiota disturbances play an important role in associated complications in COVID-19 (Schult et al. 2022). Several studies have also reported diarrhea to be an early indicator of SARS-CoV-2 infection (Song et al. 2020; D'Amico et al. 2020; Zhang et al. 2020).

4 SARS-CoV-2 Associated Disruption of the Human Lungs Microbiome: Case Studies Historically, the respiratory tract was considered free from microbes but this theory was discredited through high-throughput sequencing technology leading to the development of culture-independent techniques capable of detecting the microbiota which is specific to the lungs and associated respiratory tract (Project 2012; Charlson et al. 2010; Bassis et al. 2015). Propionibacteria, Corynebacteria, Staphylococcus, and Moraxella have been established as the common nasal microbiota (Rasmussen et al. 2000), and Propionibacterium acnes, Corynebacterium accolens, Corynebacterium kroppenstedtii, Staphylococcus aureus, and Staphylococcus Epidermidis (Huffnagle et al. 2017) as the major nasal organisms. According to the “Life in Antarctica” model of the lung microbiome, various factors outline the lung microbiome which include colonization and removal of the microbes as well as microbial population growth in the nasal airways (Dickson et al. 2014). Any variation in the microbiome may be attributed to the loss of balance between these factors. The microbial germination rates in the region depend on nutrient availability, pH, temperature, and oxygen tension which may be disturbed by any process causing inflammation. Diseases associated with the lungs, for example, cystic fibrosis, asthma, and chronic obstructive pulmonary disease (COPD) cause inflammation leading to the leakage in the airways providing nutrition to the microbes. The epithelial cell damage exposes the main membrane matrix which confers microbial adherence (Plotkowski et al. 1993). In addition, the damage to the epithelial cells can release major innate cytokines, such as TSLP, IL-25, and IL-33, as a response to bacterial components (Bartemes and Kita 2012) which induce ILC2s activation followed by the generation of IL-5 and IL-13 leading to the additional inflammation (Scanlon and McKenzie 2012). The hyperplasia of the Goblet cell, normally seen during allergies and chronic IL-13 production, results in excessive mucus levels in the deep airways forming anaerobic niches which inhibits phagocytosis and bacterial colonization is further enhanced (Lai and Rogers 2010). Catecholamines obtained from the inflammatory cells also modulate bacterial virulence (Flierl et al. 2007; Sperandio et al. 2003). The Bacteroidetes are found as the main constituent of a healthy lung microbiome which gradually shifts to the Gammaproteobacteria

Exploring the Pathoprofiles of SARS-COV-2 Infected Human Gut–Lungs. . .

223

microbiome (gram-negative pathogens) in the diseased individuals. The Gammaproteobacteria utilizes the conditions developed by the disease and associated inflammation (Huffnagle et al. 2017) to compete with other bacteria which do not have this adaptability. The respiratory tract which is in direct contact with the external environment is always vulnerable to microbial colonization. To protect against the same, the respiratory tract possesses a defense system to combat any potential infection, which includes a physical barrier in the form of a mucus coating comprising proteolytic enzymes, defense proteins such as immunoglobulins, lactoferrin, defensins, and lysozymes (Invernizzi et al. 2020). Pulmonary epithelial cells are also known to secrete a variety of cytokines and also express the pattern-recognition receptors (PRRs), which enable them to identify pathogen-associated molecular patterns (PAMPs) (Lloyd and Marsland 2017). In a healthy individual, the lung microbiome is involved in the determination of pulmonary immunity with the help of specific microbiota which enhances the innate and adaptative immunity assisting in respiratory functions and protecting the lungs from harmful pathogens (RamírezLabrada et al. 2020). The normal healthy microbiota prevents the growth of harmful pathogens entering into the lungs. The activation of the pulmonary immune system is dependent on the exposure to pathogens (Sommariva et al. 2020) as evidenced by the development of innate immunity in neonates exposed to microbes (Stein et al. 2016). As explained in the earlier sections, ACE2 is the prime target of nCoV, which is expressed in a variety of cells and is involved in regulating inflammatory and fibrotic pathways. The ACE2 protects against severe acute lung failure (Imai et al. 2005). An infection with the novel coronavirus begins a process of hyper-inflammation presenting as a cytokine storm, in which the levels of IL-6, IL-10, and tumor necrosis factor (TNFα) increase significantly causing multiorgan failure leading to sepsis and death (Huang et al. 2020a). COVID-19 may manifest itself as asymptomatic or with severe pneumonia. In a very early study when the pandemic was beginning to spread, it was reported that the main manifestations of COVID-19 included acute respiratory distress syndrome (ARDS) and hypoxemia. The levels of initial plasma IL1B, IL1RA, IL7, IL8, IL9, IL10, TNFα, and VEGF were found to be high in both intensive care unit (ICU) and non-ICU patients (Huang et al. 2020b). There have been evidences indicating the effects on both the lung and gut microbiota in COVIDinfected patients and it impacts the immunity and disease virulence. In this section, we are describing some of the important case studies stating the changes in the lung microbiome in COVID-19. In a study by Shen et al. conducted on bronchoalveolar lavage fluid of COVID-19 on pneumonia (community-acquired) patients, as well as healthy individuals, it was found that there was a substantial difference in the composition of microbiota in both COVID-19 and community-acquired pneumonia patients showing a surge in the pathogenic and commensal bacteria. The study certainly points toward microbial dysbiosis in both the diseased states (Shen et al. 2020). In another study conducted on the post-mortem biopsies of the COVID19 lung, it was revealed that the both bacterial (Acinetobacter, Chryseobacterium, Burkholderia, Brevundimonas, Sphingobium, and Enterobacteriaceae) and fungal

224

S. Nandi et al.

(Cutaneotrichosporon, followed by Issatchenkia, Wallemia, Cladosporium, Alternaria, Dipodascus, Mortierella, Aspergillus, Naganishia, Diutina, and Candida) infections took place again suggesting dysbiosis (Fan et al. 2020). In yet another study by Zhong et al. (Zhong et al. 2021) conducted on 23 hospitalized patients with SARS-CoV-2 infection, confirmed using ultra-deep metatranscriptomic sequencing and clinical laboratory diagnosis, it was found that the Burkholderia cepacia complex (BCC) bacteria, S. epidermidis, and Mycoplasma spp. (including M. hominis and M. orale) were the most prevalent respiratory bacteria. These bacterial species were different from infectious bacteria found in previous coronavirus outbreaks and influenza pandemics (e.g., Streptococcus pneumoniae, Staphylococcus aureus, Klebsiella pneumoniae, and Mycoplasma pneumoniae) (Peiris et al. 2003; Morris et al. 2017; Gill et al. 2010). The human oral microbiome has also been shown to inhibit infections by enhancing immunity (Wilks and Golovkina 2012). In another important autopsy study (Zacharias et al. 2022) on COVID-19 and control cases, it was found that either dominant diffuse alveolar damage (DAD) or secondary infections of the lungs was the most prominent cause of death in the infected individuals. In addition, lung microbiome alterations in terms of reduction in biodiversity and increase in the presence of prototypical bacterial and fungal pathogens were present in secondary infections cases. Moreover, in this study, several signs of immunity impairment were found in COVID-19 lungs including strong introduction of inhibitory immune checkpoints. Liu et al. also reported a depletion in nasopharyngeal commensal bacteria such as Gemella morbillorum, Gemella haemolysans, and Leptotrichia hofstadii in COVID-19 patients (Liu et al. 2021). The very recent and important study carried out by Sulaiman et al. has shown that the total load and taxonomic identification of lower respiratory tract bacteria characterized by bronchoalveolar lavage have been the indicators of death and prolonged mechanical ventilation in COVID-19 (Sulaiman et al. 2021).

5 Disruption of Host Immunity Due to Loss of Human Gut–Lungs Microbiome Crosstalks The gut microbiome shows more variations compared to the lung microbiome. The intestinal microbiome performs various functions viz. establishing intestinal morphology, metabolism, and supply of essential nutrients including the most important one of providing defense against infections by opportunistic pathogens (Yamashiro 2017). Gut dysbiosis is associated with various disorders, such as obesity, inflammatory bowel syndrome (IBS), and type II diabetes (Walters et al. 2014; Yassour et al. 2016). The gut-associated lymphoid tissues (GALTs) being the part of mucosaassociated lymphoid tissues (MALTs) perform a dual role in the gut and is connected with providing innate immunity by recognizing the pathogens and is also responsible for the maintenance of the immune tolerance to commensal flora (Brandtzaeg et al.

Exploring the Pathoprofiles of SARS-COV-2 Infected Human Gut–Lungs. . .

225

2008). Innate lymphoid cells (ILCs) are the vital components of the innate compartment of GALTs that possess several surface (activating, inhibitory, and cytokine) receptors (Chiossone et al. 2018). In addition to the GALTs and ILCs, phagocytes (macrophages, dendritic cells, and other non-immune cells like IECs) are also closely related to immune cells of gut microbiota. The gut phagocytes uphold gut homeostasis, especially during the development of immune tolerance to symbiotic bacteria and immune recognition of pathogenic bacteria as it can be seen that the gut is an immunological organ and its microbiota has been known to modulate host immune response. It may be assumed that gut microbiota plays a vital role in host inflammatory immune responses in COVID-19 (Schirmer et al. 2016). The same can be gauged by several works of literature where SARS-CoV-2 infection and subsequent replication has been reported in human small intestine enterocytes (Lamers et al. 2020) as detected in virus RNA in fecal samples (Wölfel et al. 2020; Xu et al. 2020a) and altered gut microbiota in SARS-CoV-2 infected individuals (Zuo et al. 2020a; Gu et al. 2020). There have been numerous studies stating the effects of change in the microbiota as a consequence of COVID-19 infection. Microbiome characterization by rRNA gene sequencing in a study by Gu et al. on 30 COVID-19 patients revealed reduction of the bacterial diversity and a rise in opportunistic pathogens, such as Streptococcus, Rothia, Veillonella, and Actinomyces (Gu et al. 2020). In a series of studies conducted by Zuo et al. on COVID-19 patients, it was ascertained through whole-genome sequencing that i) patients with antibiotic abuse had an increase in opportunistic pathogens, ii) infected patients had alterations in the microbiome with an increase in Candida albicans, and iii) Stool with high SARS CoV-2 infectivity had a higher abundance of bacterial species, including Collinsella aerofaciens, Collinsella tanakaei, Streptococcus infantis, and Morganella morganii (Zuo et al. 2020a; Zuo et al. 2020b; Zuo et al. 2021). An increase in opportunistic pathogens, including Candida albicans was also reported in a study conducted on COVID-19 patients by Zhang et al. (Zhang et al. 2021b). A study by Tao et al. reported that COVID-19 patients had abundant Streptococcus, Clostridium, Lactobacillus, and Bifidobacterium in gut microbiota in contrast to lower levels of Bacteroides, Roseburia, Faecalibacterium, Coprococcus, Parabacteroides (Tao et al. 2020). Xu et al. reported that COVID-19 patients had intestinal dysbiosis with decreased Lactobacillus and Bifidobacterium (Xu et al. 2020b). A study by Soffritti et al. (Soffritti et al. 2021) conducted on 75 COVID and non-COVID patients revealed that oral dysbiosis is involved with symptom rigorousness and increased local inflammation. In addition, a decreased mucosal IgA response was observed in symptomatic patients, signifying that local immune response is crucial in the initial control of virus infection and that its right development is influenced by the human oral microbiome profile. A well-maintained microbiota, comprising microbial species and metabolites is required for immune homeostasis. Factors such as environment, diet, antibiotics, and stress affect the microbiome environment (Dong and Gupta 2019). The promising evidences show a gut–lung axis, this allows for bidirectional crosstalk in between the gut and lung microbiota. There have been studies suggesting an association of altered microbiomes with pulmonary diseases (Aan et al. 2022). Gut microbiota by

226

S. Nandi et al.

regulating innate and adaptive immune responses plays an important protective role in viral and pulmonary infections (Schuijt et al. 2016a; Yitbarek et al. 2018). A broad network connects both the lung and gut microbiome throughout the life span of a human (Grier et al. 2018). The role of both the lung and gut microbiota in local immunity has been reviewed by Enaud et al. (Enaud et al. 2020). A study by Ichinohe et al. suggests that treatment of influenza-infected mice with antibiotics reduces the immune response to the disease (Ichinohe et al. 2011). The same results were also obtained in different studies on lung infection mouse models (Schuijt et al. 2016b; Robak et al. 2018). The lung microbiota protects against Streptococcus pneumoniae and Klebsiella pneumonia by the production of granulocytemacrophage colony-stimulating factor (GM-CSF) through IL-17 and nucleotidebinding oligomerization domain protein-2 (Nod2) stimulation at pulmonary sites (Brown et al. 2017). The gut microbiota vis-à-vis commands a similar role in bacterial lung infections. A microbiome free mouse showed increased fatality in the case of Streptococcus pneumoniae, Klebsiella pneumoniae, or Pseudomonas aeruginosa infection (Fagundes et al. 2012; Fox et al. 2012; Brown et al. 2017). In the case of chronic infectious lung diseases such as tuberculosis, the severity of the disease can be related to the gut microbiota (Namasivayam et al. 2018). The gut microbiota plays an important role in the production of virus-specific CD4+ and CD8+ T cells, in addition to eliciting antibody actions in response to an influenza virus infection (Ichinohe et al. 2011) and any change in gut microbiota can lead to respiratory viral infections (Berger and Mainou 2018; Hanada et al. 2018; Li et al. 2019).

6 Role of Probiotics in COVID-19 COVID-19 has been an unconquered disease by the use of any specific therapeutic agent. Apart from the few vaccines approved for emergency use, the world still awaits the novel molecule specifically designed to treat the disease. In search of finding, alternative prophylactic and therapeutic measures, the probiotics may be considered a worthy candidate for safeguarding the human health during SARS CoV-2 infection. As per the Food and Agriculture Organization (FAO) of the United Nations and the World Health Organization (WHO), a probiotic is defined as live microorganisms which when administered in adequate amounts confer a health benefit to the host (Hill et al. 2014). The majority of the probiotic bacteria belong to the same family as gut microbiota and have been implicated in affecting immunity by altering microbiota metabolism (Maldonado Galdeano et al. 2019). Studies have also revealed that non-living entities present in the probiotics such as bacterial exopolysaccharides and spores have immunogenic and immunomodulatory properties (Jung et al. 2017; Tonetti et al. 2020), while some have antimicrobial properties in addition to their action on neurological and endocrine systems by inhibiting the overgrowth of pathogenic bacteria through short-chain fatty acids (SCFAs) secretions and in increasing the pathogen resistance in the intestine by improving the

Exploring the Pathoprofiles of SARS-COV-2 Infected Human Gut–Lungs. . .

227

functionality of the epithelium (Hill et al. 2014). There are several studies implicating the use of probiotics in respiratory tract infections (Wang et al. 2016). Hence, the use of probiotics in COVID-19 should be seen in the light of the gut–lung axis. This is an important aspect since the gut–lung axis is severely affected during SARSCoV-2 infection as exemplified in the above sections. One of the studies indicated low levels of beneficial Lactobacillus and Bifidobacterium in COVID-19 patients (Venegas-Borsellino et al. 2021). Another study demonstrated the effectiveness of probiotic lactobacilli such as Lactobacillus acidophilus, Lactobacillus brevis, and Lactobacillus plantarum in inducing immunity in COVID-19 (d'Ettorre et al. 2020; Lundstrom 2020). An oral recombinant Lactobacillus vaccine has been planned for COVID-19 (Jiang et al. 2016) and a more detailed review concerning probiotic vaccines has been recently published (Taghinezhad-S et al. 2021). In yet another study, bacteriocins such as Plantaricin BN, Plantaricin JLA-9, Plantaricin W, and Plantaricin D were evaluated computationally for their probiotic activity by blocking the entry of the virus by binding with RNA-dependent RNA polymerase (RdRp), receptor-binding domain (RBD), and ACE2 (Anwar et al. 2021). Hence, because of increasing the natural immunity and also ameliorating gut dysbiosis, probiotics warrant its role in COVID-19.

7 Conclusion The release of various cytokines such as interleukins (IL-1 and IL-6), chemokines, and pro-inflammatory cytokines may produce cytokine storms that damage the microbiota present in the gut and lungs. These inflammatory mediators produce cytotoxicity to the pneumocytes and enterocytes dismantling the healthy environments of the gut–lungs microbiome. Also, the excessive use of antibiotics and antiviral chemotherapeutics may disrupt the gut–lungs microbiomes. Maintenance of both the lung and the gut microbiome is important for regulating the immune system and overall good health. The gut microbiome is more diverse than the lung microbiome and it has been shown that the gut microbiome exerts a protective effect on the lung microbiome through the lung–gut axis. Any dysbiosis in either lung or gut microbiome has a definitive impact on the immune responses and may increase the chances of infection. COVID-19 has become a serious pandemic in a very short space of time. Its severity and sometimes death can be attributed to dysbiosis. In various studies as mentioned in the above sections, it was important to note that any disruption in the microbiome had a detrimental effect on the treatment outcomes. Since there is still no sure-shot treatment for this disease, it is imperative to boost an individual’s immunity through the maintenance of the microbiome. Some allopathic preparations are formulated with a probiotic composition containing Streptococcus faecalis, Clostridium butyricum, Bacillus mesentericus, and Lactobacillus sporogenes that normalize gut flora, boost immunity, and protect gastrointestinal health. But there are hardly any formulations to normalize the lungs flora available to date. The development of this formulation would be a great challenge. Therefore, we

228

S. Nandi et al.

may rely on naturopathies like natural prebiotics, probiotics, synbiotics, and postbiotics which can contribute to adequate security measures to combat the postCOVID-19 symptoms like weakness, breathlessness, and gastrointestinal problems. Conflict of Interest None to declare.

References Aan FJ, Glibetic N, Montoya-Uribe V, Matter ML (2022) 2.34 - COVID-19 and the microbiome: the gut-lung connection. In: Glibetic M (ed) Comprehensive gut microbiota. Elsevier, Oxford, pp 442–458. https://doi.org/10.1016/B978-0-12-819265-8.00048-6 Alotaibi MH, Bahammam SA (2021) Determining the correlation between comorbidities and MERS-CoV mortality in Saudi Arabia. J Taibah Univ Medical Sci 16(4):591–595. https://doi. org/10.1016/j.jtumed.2021.02.003 Anwar F, Altayb HN, Al-Abbasi FA, Al-Malki AL, Kamal MA, Kumar V (2021) Antiviral effects of probiotic metabolites on COVID-19. J Biomol Struct Dyn 39(11):4175–4184. https://doi.org/ 10.1080/07391102.2020.1775123 Bartemes KR, Kita H (2012) Dynamic role of epithelium-derived cytokines in asthma. Clin Immunol 143(3):222–235. https://doi.org/10.1016/j.clim.2012.03.001 Bassis CM, Erb-Downward JR, Dickson RP, Freeman CM, Schmidt TM, Young VB, Beck JM, Curtis JL, Huffnagle GB (2015) Analysis of the upper respiratory tract microbiotas as the source of the lung and gastric microbiotas in healthy individuals. mBio 6(2):e00037. https://doi.org/10. 1128/mBio.00037-15 Belouzard S, Millet JK, Licitra BN, Whittaker GR (2012) Mechanisms of coronavirus cell entry mediated by the viral spike protein. Viruses 4(6):1011–1033. https://doi.org/10.3390/v4061011 Beniac DR, Andonov A, Grudeski E, Booth TF (2006) Architecture of the SARS coronavirus prefusion spike. Nat Struct Mol Biol 13(8):751–752. https://doi.org/10.1038/nsmb1123 Berger AK, Mainou BA (2018) Interactions between enteric bacteria and eukaryotic viruses impact the outcome of infection. Viruses 10(1):19. https://doi.org/10.3390/v10010019 Brandtzaeg P, Kiyono H, Pabst R, Russell MW (2008) Terminology: nomenclature of mucosaassociated lymphoid tissue. Mucosal Iimmunol 1(1):31–37. https://doi.org/10.1038/mi.2007.9 Brown RL, Sequeira RP, Clarke TB (2017) The microbiota protects against respiratory infection via GM-CSF signaling. Nat Commun 8(1):1512. https://doi.org/10.1038/s41467-017-01803-x Burchill E, Lymberopoulos E, Menozzi E, Budhdeo S, McIlroy JR, Macnaughtan J, Sharma N (2021) The unique impact of COVID-19 on human gut microbiome research. Front Med 8: 652464. https://doi.org/10.3389/fmed.2021.652464 Charlson ES, Chen J, Custers-Allen R, Bittinger K, Li H, Sinha R, Hwang J, Bushman FD, Collman RG (2010) Disordered microbial communities in the upper respiratory tract of cigarette smokers. PLoS One 5(12):e15216. https://doi.org/10.1371/journal.pone.0015216 Chen PL, Lee NY, Cia CT, Ko WC, Hsueh PR (2020) A review of treatment of coronavirus disease 2019 (COVID-19): therapeutic repurposing and unmet clinical needs. Front Pharmacol 11: 584956. https://doi.org/10.3389/fphar.2020.584956 Chen Z, Lv Y, Xu H, Deng L (2021) Herbal medicine, gut microbiota, and COVID-19. Front Pharmacol 12:646560–646560. https://doi.org/10.3389/fphar.2021.646560 Chiossone L, Dumas P-Y, Vienne M, Vivier E (2018) Natural killer cells and other innate lymphoid cells in cancer. Nature Rev Immunol 18(11):671–688. https://doi.org/10.1038/s41577-0180061-z D'Amico F, Baumgart DC, Danese S, Peyrin-Biroulet L (2020) Diarrhea during COVID-19 infection: pathogenesis, epidemiology, prevention, and management. Clin Gastroenterol Hepatol 18(8):1663–1672. https://doi.org/10.1016/j.cgh.2020.04.001

Exploring the Pathoprofiles of SARS-COV-2 Infected Human Gut–Lungs. . .

229

de Oliveira GLV, Oliveira CNS, Pinzan CF, de Salis LVV, Cardoso CRB (2021) Microbiota modulation of the gut-lung Axis in COVID-19. Front Immunol 12:635471. https://doi.org/10. 3389/fimmu.2021.635471 d’Ettorre G, Ceccarelli G, Marazzato M, Campagna G, Pinacchio C, Alessandri F, Ruberto F, Rossi G, Celani L, Scagnolari C, Mastropietro C, Trinchieri V, Recchia GE, Mauro V, Antonelli G, Pugliese F, Mastroianni CM (2020) Challenges in the management of SARSCoV2 infection: the role of Oral bacteriotherapy as complementary therapeutic strategy to avoid the progression of COVID-19. Front Med 7:389. https://doi.org/10.3389/fmed.2020.00389. eCollection.2020 Dhar D, Mohanty A (2020) Gut microbiota and Covid-19- possible link and implications. Virus Res 285:198018. https://doi.org/10.1016/j.virusres.2020.198018 Dickson RP, Erb-Downward JR, Huffnagle GB (2014) Toward an ecology of the lung: new conceptual models of pulmonary microbiology and pneumonia pathogenesis. The Lancet Respir Med 2(3):238–246. https://doi.org/10.1016/s2213-2600(14)70028-1 Dong TS, Gupta A (2019) Influence of early life, diet, and the environment on the microbiome. Clin Gastroenterol Hepatol 17(2):231–242. https://doi.org/10.1016/j.cgh.2018.08.067 Enaud R, Prevel R, Ciarlo E, Beaufils F, Wieërs G, Guery B, Delhaes L (2020) The gut-lung Axis in health and respiratory diseases: a place for inter-organ and inter-kingdom Crosstalks. Front Cell Infect Microbiol 10:9. https://doi.org/10.3389/fcimb.2020.00009 Fagundes CT, Amaral FA, Vieira AT, Soares AC, Pinho V, Nicoli JR, Vieira LQ, Teixeira MM, Souza DG (2012) Transient TLR activation restores inflammatory response and ability to control pulmonary bacterial infection in germfree mice. J Immunol 188(3):1411. https://doi. org/10.4049/jimmunol.1101682 Fan J, Li X, Gao Y, Zhou J, Wang S, Huang B, Wu J, Cao Q, Chen Y, Wang Z, Luo D, Zhou T, Li R, Shang Y, Nie X (2020) The lung tissue microbiota features of 20 deceased patients with COVID-19. J Infect 81(3):e64–e67. https://doi.org/10.1016/j.jinf.2020.06.047 Flierl MA, Rittirsch D, Nadeau BA, Chen AJ, Sarma JV, Zetoune FS, McGuire SR, List RP, Day DE, Hoesel LM, Gao H, Van Rooijen N, Huber-Lang MS, Neubig RR, Ward PA (2007) Phagocyte-derived catecholamines enhance acute inflammatory injury. Nature 449(7163): 721–725. https://doi.org/10.1038/nature06185 Fox AC, McConnell KW, Yoseph BP, Breed E, Liang Z, Clark AT, O'Donnell D, Zee-Cheng B, Jung E, Dominguez JA, Dunne WM, Burd EM, Coopersmith CM (2012) The endogenous bacteria alter gut epithelial apoptosis and decrease mortality following Pseudomonas aeruginosa pneumonia. Shock 38(5):508–514. https://doi.org/10.1097/SHK.0b013e31826e47e8 Gao K, Nguyen DD, Chen J, Wang R, Wei G-W (2020) Repositioning of 8565 existing drugs for COVID-19. J Phys Chem Lett 11(13):5373–5382. https://doi.org/10.1021/acs.jpclett.0c01579 Ghimire S, Sharma S, Patel A, Budhathoki R, Chakinala R, Khan H, Lincoln M, Georgeston M (2021) Diarrhea is associated with increased severity of disease in COVID-19: systemic review and Metaanalysis. SN Compr Clin Med 3(1):28–35. https://doi.org/10.1007/s42399-02000662-w Gill JR, Sheng ZM, Ely SF, Guinee DG, Beasley MB, Suh J, Deshpande C, Mollura DJ, Morens DM, Bray M, Travis WD, Taubenberger JK (2010) Pulmonary pathologic findings of fatal 2009 pandemic influenza a/H1N1 viral infections. Arch Path Lab Med 134(2):235–243. https://doi. org/10.5858/134.2.235 Grier A, McDavid A, Wang B, Qiu X, Java J, Bandyopadhyay S, Yang H, Holden-Wiltse J, Kessler HA, Gill AL, Huyck H, Falsey AR, Topham DJ, Scheible KM, Caserta MT, Pryhuber GS, Gill SR (2018) Neonatal gut and respiratory microbiota: coordinated development through time and space. Microbiome 6(1):193. https://doi.org/10.1186/s40168-018-0566-5 Groves HT, Higham SL, Moffatt MF, Cox MJ, Tregoning JS (2020) Respiratory viral infection alters the gut microbiota by inducing inappetence. mBio 11(1):e03236-19. https://doi.org/10. 1128/mBio.03236-19 Gu S, Chen Y, Wu Z, Chen Y, Gao H, Lv L, Guo F, Zhang X, Luo R, Huang C, Lu H, Zheng B, Zhang J, Yan R, Zhang H, Jiang H, Xu Q, Guo J, Gong Y, Tang L, Li L (2020) Alterations of the

230

S. Nandi et al.

gut microbiota in patients with coronavirus disease 2019 or H1N1 influenza. Clin Infect Dis 71(10):2669–2678. https://doi.org/10.1093/cid/ciaa709 Guan W-J, Liang W-H, Zhao Y, Liang H-R, Chen Z-S, Li Y-M, Liu X-Q, Chen R-C, Tang C-L, Wang T, Ou C-Q, Li L, Chen P-Y, Sang L, Wang W, Li J-F, Li C-C, Ou L-M, Cheng B, Xiong S, Ni Z-Y, Xiang J, Hu Y, Liu L, Shan H, Lei C-L, Peng Y-X, Wei L, Liu Y, Hu Y-H, Peng P, Wang J-M, Liu J-Y, Chen Z, Li G, Zheng Z-J, Qiu S-Q, Luo J, Ye C-J, Zhu S-Y, Cheng L-L, Ye F, Li S-Y, Zheng J-P, Zhang N-F, Zhong N-S, He J-X, China Medical Treatment Expert Group for C (2020b) Comorbidity and its impact on 1590 patients with COVID-19 in China: a nationwide analysis. Eur Respir J 55(5):2000547. https://doi.org/10.1183/13993003. 00547-2020 Guan W-J, Ni Z-Y, Hu Y, Liang W-H, Ou C-Q, He J-X, Liu L, Shan H, Lei C-l, Hui DSC, Du B, Li L-J, Zeng G, Yuen K-Y, Chen R-C, Tang C-l, Wang T, Chen P-Y, Xiang J, Li S-Y, Wang J-l, Liang Z-J, Peng Y-X, Wei L, Liu Y, Hu Y-H, Peng P, Wang J-M, Liu J-Y, Chen Z, Li G, Zheng Z-J, Qiu S-Q, Luo J, Ye C-J, Zhu S-Y, Zhong N-S (2020a) Clinical characteristics of coronavirus disease 2019 in China. New Engl J Med 382(18):1708–1720. https://doi.org/10.1056/ NEJMoa2002032 Hanada S, Pirzadeh M, Carver KY, Deng JC (2018) Respiratory viral infection-induced microbiome alterations and secondary bacterial pneumonia. Front Immunol 9:2640 Hill C, Guarner F, Reid G, Gibson GR, Merenstein DJ, Pot B, Morelli L, Canani RB, Flint HJ, Salminen S, Calder PC, Sanders ME (2014) The international scientific Association for Probiotics and Prebiotics consensus statement on the scope and appropriate use of the term probiotic. Nat Rev Gastroenterol Hepatol 11(8):506–514. https://doi.org/10.1038/nrgastro. 2014.66 https://www.fda.gov/medical-devices/coronavirus-covid-19-and-medical-devices/sars-cov-2-viralmutations-impact-covid-19-tests, n.d. Huang C, Wang Y, Li X, Ren L, Zhao J, Hu Y, Zhang L, Fan G, Xu J, Gu X, Cheng Z, Yu T, Xia J, Wei Y, Wu W, Xie X, Yin W, Li H, Liu M, Xiao Y, Gao H, Guo L, Xie J, Wang G, Jiang R, Gao Z, Jin Q, Wang J, Cao B (2020a) Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China. Lancet (London, England) 395(10223):497–506. https://doi.org/ 10.1016/s0140-6736(20)30183-5 Huang C, Wang Y, Li X, Ren L, Zhao J, Hu Y, Zhang L, Fan G, Xu J, Gu X, Cheng Z, Yu T, Xia J, Wei Y, Wu W, Xie X, Yin W, Li H, Liu M, Xiao Y, Gao H, Guo L, Xie J, Wang G, Jiang R, Gao Z, Jin Q, Wang J, Cao B (2020b) Clinical features of patients infected with 2019 novel coronavirus in Wuhan. China Lancet 395(10223):497–506. https://doi.org/10.1016/S01406736(20)30183-5 Huffnagle GB, Dickson RP, Lukacs NW (2017) The respiratory tract microbiome and lung inflammation: a two-way street. Mucosal Immunol 10(2):299–306. https://doi.org/10.1038/mi. 2016.108 Hui DSC, Zumla A (2019) Severe acute respiratory syndrome: historical, epidemiologic, and clinical features. Infect Dis Clin N Am 33(4):869–889. https://doi.org/10.1016/j.idc.2019. 07.001 Human Microbiome Project Consortium (2012) Structure, function and diversity of the healthy human microbiome. Nature 486(7402):207–214. https://doi.org/10.1038/nature11234 Ichinohe T, Pang IK, Kumamoto Y, Peaper DR, Ho JH, Murray TS, Iwasaki A (2011) Microbiota regulates immune defense against respiratory tract influenza a virus infection. PNAS 108(13): 5354–5359. https://doi.org/10.1073/pnas.1019378108 Imai Y, Kuba K, Rao S, Huan Y, Guo F, Guan B, Yang P, Sarao R, Wada T, Leong-Poi H, Crackower MA, Fukamizu A, Hui CC, Hein L, Uhlig S, Slutsky AS, Jiang C, Penninger JM (2005) Angiotensin-converting enzyme 2 protects from severe acute lung failure. Nature 436(7047):112–116. https://doi.org/10.1038/nature03712 Invernizzi R, Lloyd CM, Molyneaux PL (2020) Respiratory microbiome and epithelial interactions shape immunity in the lungs. Immunol 160(2):171–182. https://doi.org/10.1111/imm.13195

Exploring the Pathoprofiles of SARS-COV-2 Infected Human Gut–Lungs. . .

231

Jiang X, Hou X, Tang L, Jiang Y, Ma G, Li Y (2016) A phase trial of the oral lactobacillus casei vaccine polarizes Th2 cell immunity against transmissible gastroenteritis coronavirus infection. Appl Microbiol Biotechnol 100(17):7457–7469. https://doi.org/10.1007/s00253-016-7424-9 Jung Y-J, Lee Y-T, Ngo VL, Cho Y-H, Ko E-J, Hong S-M, Kim K-H, Jang J-H, Oh J-S, Park M-K, Kim C-H, Sun J, Kang S-M (2017) Heat-killed lactobacillus casei confers broad protection against influenza a virus primary infection and develops heterosubtypic immunity against future secondary infection. Sci Rep 7(1):17360. https://doi.org/10.1038/s41598-017-17487-8 Lai HY, Rogers DF (2010) Mucus hypersecretion in asthma: intracellular signalling pathways as targets for pharmacotherapy. Current Opin Allergy Clin Immunol 10(1):67–76. https://doi.org/ 10.1097/ACI.0b013e328334643a Lamers MM, Beumer J, van der Vaart J, Knoops K, Puschhof J, Breugem TI, Ravelli RBG, Paul van Schayck J, Mykytyn AZ, Duimel HQ, van Donselaar E, Riesebosch S, Kuijpers HJH, Schipper D, van de Wetering WJ, de Graaf M, Koopmans M, Cuppen E, Peters PJ, Haagmans BL, Clevers H (2020) SARS-CoV-2 productively infects human gut enterocytes. Science 369(6499):50–54. https://doi.org/10.1126/science.abc1669 Lee B, Moon KM, Kim CY (2018) Tight junction in the intestinal epithelium: its association with diseases and regulation by phytochemicals. J Immunol Res 2018:2645465. https://doi.org/10. 1155/2018/2645465 Li F, Berardi M, Li W, Farzan M, Dormitzer PR, Harrison SC (2006) Conformational states of the severe acute respiratory syndrome coronavirus spike protein ectodomain. J Virol 80(14): 6794–6800. https://doi.org/10.1128/jvi.02744-05 Li N, Ma W-T, Pang M, Fan Q-L, Hua J-L (2019) The commensal microbiota and viral infection: a comprehensive review. Front Immunol 10:1551 Liu J, Liu S, Zhang Z, Lee X, Wu W, Huang Z, Lei Z, Xu W, Chen D, Wu X, Guo Y, Peng L, Lin B, Chong Y, Mou X, Shi M, Lan P, Chen T, Zhao W, Gao Z (2021) Association between the nasopharyngeal microbiome and metabolome in patients with COVID-19. Synth Syst Biotechnol 6(3):135–143. https://doi.org/10.1016/j.synbio.2021.06.002 Lloyd CM, Marsland BJ (2017) Lung homeostasis: influence of age, microbes, and the immune system. Immunity 46(4):549–561. https://doi.org/10.1016/j.immuni.2017.04.005 Lundstrom K (2020) Coronavirus pandemic—therapy and vaccines. Biomedicine 8(5):109. https:// doi.org/10.3390/biomedicines8050109 Lv L, Gu S, Jiang H, Yan R, Chen Y, Chen Y, Luo R, Huang C, Lu H, Zheng B, Zhang H, Xia J, Tang L, Sheng G, Li L (2021) Gut mycobiota alterations in patients with COVID-19 and H1N1 infections and their associations with clinical features. Commun Biol 4(1):480. https://doi.org/ 10.1038/s42003-021-02036-x Maldonado Galdeano C, Cazorla SI, Lemme Dumit JM, Vélez E, Perdigón G (2019) Beneficial effects of probiotic consumption on the immune system. Ann Nutr Metab 74(2):115–124. https://doi.org/10.1159/000496426 Mohan SV, Hemalatha M, Kopperi H, Ranjith I, Kumar AK (2021) SARS-CoV-2 in environmental perspective: occurrence, persistence, surveillance, inactivation and challenges. Chem Eng J 405: 126893. https://doi.org/10.1016/j.cej.2020.126893 Morris DE, Cleary DW, Clarke SC (2017) Secondary bacterial infections associated with influenza pandemics. Fron Microbiol 8:1041. https://doi.org/10.3389/fmicb.2017.01041 Namasivayam S, Sher A, Glickman MS, Wipperman MF (2018) The microbiome and tuberculosis: early evidence for cross talk. mBio 9(5):e01420-18. https://doi.org/10.1128/mBio.01420-18 Nandi S, Roy H, Gummadi A, Saxena AK (2021) Exploring spike protein of novel coronavirus and to inhibit the viability utilizing natural agents. Curr Drug Targets 22:2006–2020 Peiris JS, Chu CM, Cheng VC, Chan KS, Hung IF, Poon LL, Law KI, Tang BS, Hon TY, Chan CS, Chan KH, Ng JS, Zheng BJ, Ng WL, Lai RW, Guan Y, Yuen KY (2003) Clinical progression and viral load in a community outbreak of coronavirus-associated SARS pneumonia: a prospective study. Lancet 361(9371):1767–1772. https://doi.org/10.1016/s0140-6736(03)13412-5 Perlot T, Penninger JM (2013) ACE2 - from the renin-angiotensin system to gut microbiota and malnutrition. Microbes Infect 15(13):866–873. https://doi.org/10.1016/j.micinf.2013.08.003

232

S. Nandi et al.

Petersen C, Round JL (2014) Defining dysbiosis and its influence on host immunity and disease. Cell Microbiol 16(7):1024–1033. https://doi.org/10.1111/cmi.12308 Plotkowski MC, Bajolet-Laudinat O, Puchelle E (1993) Cellular and molecular mechanisms of bacterial adhesion to respiratory mucosa. Eur Respir J 6(6):903–916 Ramírez-Labrada AG, Isla D, Artal A, Arias M, Rezusta A, Pardo J, Gálvez EM (2020) The influence of lung microbiota on lung carcinogenesis, immunity, and immunotherapy. Trends Cancer 6(2):86–97. https://doi.org/10.1016/j.trecan.2019.12.007 Rasmussen TT, Kirkeby LP, Poulsen K, Reinholdt J, Kilian M (2000) Resident aerobic microbiota of the adult human nasal cavity. APMIS 108(10):663–675. https://doi.org/10.1034/j.1600-0463. 2000.d01-13.x Robak OH, Heimesaat MM, Kruglov AA, Prepens S, Ninnemann J, Gutbier B, Reppe K, Hochrein H, Suter M, Kirschning CJ, Marathe V, Buer J, Hornef MW, Schnare M, Schneider P, Witzenrath M, Bereswill S, Steinhoff U, Suttorp N, Sander LE, Chaput C, Opitz B (2018) Antibiotic treatment–induced secondary IgA deficiency enhances susceptibility to Pseudomonas aeruginosa pneumonia. J Clin Investig 128(8):3535–3545. https://doi.org/10. 1172/JCI97065 Scanlon ST, McKenzie AN (2012) Type 2 innate lymphoid cells: new players in asthma and allergy. Current Opin Immunol 24(6):707–712. https://doi.org/10.1016/j.coi.2012.08.009 Schirmer M, Smeekens SP, Vlamakis H, Jaeger M, Oosting M, Franzosa EA, Ter Horst R, Jansen T, Jacobs L, Bonder MJ, Kurilshikov A, Fu J, Joosten LAB, Zhernakova A, Huttenhower C, Wijmenga C, Netea MG, Xavier RJ (2016) Linking the human gut microbiome to inflammatory cytokine production capacity. Cell 167(4):1125–1136.e1128. https://doi.org/10.1016/j.cell. 2016.10.020 Schuijt TJ, Lankelma JM, Scicluna BP, de Sousa e Melo F, JJTH R, de Boer JD, Hoogendijk AJ, de Beer R, de Vos A, Belzer C, de Vos WM, van der Poll T, Wiersinga WJ (2016b) The gut microbiota plays a protective role in the host defence against pneumococcal pneumonia. Gut 65(4):575. https://doi.org/10.1136/gutjnl-2015-309728 Schuijt TJ, Lankelma JM, Scicluna BP, de Sousa e Melo F, Roelofs JJ, de Boer JD, Hoogendijk AJ, de Beer R, de Vos A, Belzer C, de Vos WM, van der Poll T, Wiersinga WJ (2016a) The gut microbiota plays a protective role in the host defence against pneumococcal pneumonia. Gut 65(4):575–583. https://doi.org/10.1136/gutjnl-2015-309728 Schult D, Reitmeier S, Koyumdzhieva P, Lahmer T, Middelhoff M, Erber J, Schneider J, Kager J, Frolova M, Horstmann J, Fricke L, Steiger K, Jesinghaus M, Janssen K-P, Protzer U, Neuhaus K, Schmid RM, Haller D, Quante M (2022) Gut bacterial dysbiosis and instability is associated with the onset of complications and mortality in COVID-19. Gut Microbes 14(1): 2031840. https://doi.org/10.1080/19490976.2022.2031840 Shen Z, Xiao Y, Kang L, Ma W, Shi L, Zhang L, Zhou Z, Yang J, Zhong J, Yang D, Guo L, Zhang G, Li H, Xu Y, Chen M, Gao Z, Wang J, Ren L, Li M (2020) Genomic diversity of severe acute respiratory syndrome-coronavirus 2 in patients with coronavirus disease 2019. Clinical Infect Dis 71(15):713–720. https://doi.org/10.1093/cid/ciaa203 Soffritti I, D’Accolti M, Fabbri C, Passaro A, Manfredini R, Zuliani G, Libanore M, Franchi M, Contini C, Caselli E (2021) Oral microbiome dysbiosis is associated with symptoms severity and local immune/inflammatory response in COVID-19 patients: a cross-sectional study. Front Microbiol 12:687513. https://doi.org/10.3389/fmicb.2021.687513 Sommariva M, Le Noci V, Bianchi F, Camelliti S, Balsari A, Tagliabue E, Sfondrini L (2020) The lung microbiota: role in maintaining pulmonary immune homeostasis and its implications in cancer development and therapy. Cell Mol Life Sci 77(14):2739–2749. https://doi.org/10.1007/ s00018-020-03452-8 Song Y, Liu P, Shi XL, Chu YL, Zhang J, Xia J, Gao XZ, Qu T, Wang MY (2020) SARS-CoV-2 induced diarrhoea as onset symptom in patient with COVID-19. Gut 69(6):1143–1144. https:// doi.org/10.1136/gutjnl-2020-320891 Sperandio V, Torres AG, Jarvis B, Nataro JP, Kaper JB (2003) Bacteria-host communication: the language of hormones. PNAS USA 100(15):8951–8956. https://doi.org/10.1073/pnas. 1537100100

Exploring the Pathoprofiles of SARS-COV-2 Infected Human Gut–Lungs. . .

233

Stein MM, Hrusch CL, Gozdz J, Igartua C, Pivniouk V, Murray SE, Ledford JG, Marques Dos Santos M, Anderson RL, Metwali N, Neilson JW, Maier RM, Gilbert JA, Holbreich M, Thorne PS, Martinez FD, von Mutius E, Vercelli D, Ober C, Sperling AI (2016) Innate immunity and asthma risk in Amish and Hutterite farm children. New Engl J Med 375(5):411–421. https://doi. org/10.1056/NEJMoa1508749 Sulaiman I, Chung M, Angel L, Tsay J-CJ, Wu BG, Yeung ST, Krolikowski K, Li Y, Duerr R, Schluger R, Thannickal SA, Koide A, Rafeq S, Barnett C, Postelnicu R, Wang C, Banakis S, Pérez-Pérez L, Shen G, Jour G, Meyn P, Carpenito J, Liu X, Ji K, Collazo D, Labarbiera A, Amoroso N, Brosnahan S, Mukherjee V, Kaufman D, Bakker J, Lubinsky A, Pradhan D, Sterman DH, Weiden M, Heguy A, Evans L, Uyeki TM, Clemente JC, de Wit E, Schmidt AM, Shopsin B, Desvignes L, Wang C, Li H, Zhang B, Forst CV, Koide S, Stapleford KA, Khanna KM, Ghedin E, Segal LN (2021) Microbial signatures in the lower airways of mechanically ventilated COVID-19 patients associated with poor clinical outcome. Nature Microbiol 6(10):1245–1258. https://doi.org/10.1038/s41564-021-00961-5 Taghinezhad-S S, Mohseni AH, Bermúdez-Humarán LG, Casolaro V, Cortes-Perez NG, Keyvani H, Simal-Gandara J (2021) Probiotic-based vaccines may provide effective protection against COVID-19 acute respiratory disease. Vaccine 9(5):466. https://doi.org/10.3390/ vaccines9050466 Tang A, Tong ZD, Wang HL, Dai YX, Li KF, Liu JN, Wu WJ, Yuan C, Yu ML, Li P, Yan JB (2020a) Detection of novel coronavirus by RT-PCR in stool specimen from asymptomatic child. China Emerg Infectious Dis 26(6):1337–1339. https://doi.org/10.3201/eid2606.200301 Tang L, Gu S, Gong Y, Li B, Lu H, Li Q, Zhang R, Gao X, Wu Z, Zhang J, Zhang Y, Li L (2020b) Clinical significance of the correlation between changes in the major intestinal bacteria species and COVID-19 severity. Engineering 6(10):1178–1184. https://doi.org/10.1016/j.eng.2020. 05.013 Tao W, Zhang G, Wang X, Guo M, Zeng W, Xu Z, Cao D, Pan A, Wang Y, Zhang K, Ma X, Chen Z, Jin T, Liu L, Weng J, Zhu S (2020) Analysis of the intestinal microbiota in COVID-19 patients and its correlation with the inflammatory factor IL-18. Med Microecol 5:100023. https://doi.org/10.1016/j.medmic.2020.100023 Thevaranjan N, Puchta A, Schulz C, Naidoo A, Szamosi JC, Verschoor CP, Loukov D, Schenck LP, Jury J, Foley KP, Schertzer JD, Larché MJ, Davidson DJ, Verdú EF, Surette MG, Bowdish DME (2017) Age-associated microbial dysbiosis promotes intestinal permeability, systemic inflammation, and macrophage dysfunction. Cell Host Microbe 21(4):455–466.e454. https:// doi.org/10.1016/j.chom.2017.03.002 Tonetti FR, Islam MA, Vizoso-Pinto MG, Takahashi H, Kitazawa H, Villena J (2020) Nasal priming with immunobiotic lactobacilli improves the adaptive immune response against influenza virus. Int Immunopharmacol 78:106115. https://doi.org/10.1016/j.intimp.2019.106115 Venegas-Borsellino C, Sankararaman S, Roche K, Burns J, Landis RM (2021) Impact of COVID19 on the intestinal microbiome. Curr Nutr Rep 10(4):300–306. https://doi.org/10.1007/s13668021-00375-z Vignesh R, Swathirajan CR, Tun ZH, Rameshkumar MR, Solomon SS, Balakrishnan P (2020) Could perturbation of gut microbiota possibly exacerbate the severity of COVID-19 via cytokine storm? Front Immunol 11:607734. https://doi.org/10.3389/fimmu.2020.607734 Walters WA, Xu Z, Knight R (2014) Meta-analyses of human gut microbes associated with obesity and IBD. FEBS Lett 588(22):4223–4233. https://doi.org/10.1016/j.febslet.2014.09.039 Wang Y, Li X, Ge T, Xiao Y, Liao Y, Cui Y, Zhang Y, Ho W, Yu G, Zhang T (2016) Probiotics for prevention and treatment of respiratory tract infections in children: a systematic review and meta-analysis of randomized controlled trials. Medicine 95(31):e4509 Wilks J, Golovkina T (2012) Influence of microbiota on viral infections. PLoS Pathog 8(5): e1002681. https://doi.org/10.1371/journal.ppat.1002681 Wölfel R, Corman VM, Guggemos W, Seilmaier M, Zange S, Müller MA, Niemeyer D, Jones TC, Vollmar P, Rothe C, Hoelscher M, Bleicker T, Brünink S, Schneider J, Ehmann R, Zwirglmaier K, Drosten C, Wendtner C (2020) Virological assessment of hospitalized patients with COVID-2019. Nature 581(7809):465–469. https://doi.org/10.1038/s41586-020-2196-x

234

S. Nandi et al.

Worldometer. 2020. https://www.worldometers.info/coronavirus/ Xu K, Cai H, Shen Y, Ni Q, Chen Y, Hu S, Li J, Wang H, Yu L, Huang H, Qiu Y, Wei G, Fang Q, Zhou J, Sheng J, Liang T, Li L (2020b) Management of COVID-19: the Zhejiang experience. Zhejiang Da Xue Xue Bao Yi Xue Ban 49(2):147–157. https://doi.org/10.3785/j.issn. 1008-9292.2020.02.02 Xu Y, Li X, Zhu B, Liang H, Fang C, Gong Y, Guo Q, Sun X, Zhao D, Shen J, Zhang H, Liu H, Xia H, Tang J, Zhang K, Gong S (2020a) Characteristics of pediatric SARS-CoV-2 infection and potential evidence for persistent fecal viral shedding. Nat Med 26(4):502–505. https://doi. org/10.1038/s41591-020-0817-4 Yamashiro Y (2017) Gut microbiota in health and disease. Ann Nutr Meta 71(3–4):242–246. https://doi.org/10.1159/000481627 Yassour M, Lim MY, Yun HS, Tickle TL, Sung J, Song Y-M, Lee K, Franzosa EA, Morgan XC, Gevers D, Lander ES, Xavier RJ, Birren BW, Ko G, Huttenhower C (2016) Sub-clinical detection of gut microbial biomarkers of obesity and type 2 diabetes. Genome Med 8(1):17. https://doi.org/10.1186/s13073-016-0271-6 Yitbarek A, Taha-Abdelaziz K, Hodgins DC, Read L, Nagy É, Weese JS, Caswell JL, Parkinson J, Sharif S (2018) Gut microbiota-mediated protection against influenza virus subtype H9N2 in chickens is associated with modulation of the innate responses. Sci Rep 8(1):13189. https://doi. org/10.1038/s41598-018-31613-0 Zacharias M, Kashofer K, Wurm P, Regitnig P, Schütte M, Neger M, Ehmann S, Marsh LM, Kwapiszewska G, Loibner M, Birnhuber A, Leitner E, Thüringer A, Winter E, Sauer S, Pollheimer MJ, Vagena FR, Lackner C, Jelusic B, Ogilvie L, Durdevic M, Timmermann B, Lehrach H, Zatloukal K, Gorkiewicz G (2022) Host and microbiome features of secondary infections in lethal covid-19. medRxiv:2022.2002.2018.22270995. https://doi.org/10.1101/ 2022.02.18.22270995 Zhang H, Ai JW, Yang W, Zhou X, He F, Xie S, Zeng W, Li Y, Yu Y, Gou X, Li Y, Wang X, Su H, Zhu Z, Xu T, Zhang W (2021b) Metatranscriptomic characterization of coronavirus disease 2019 identified a host transcriptional classifier associated with immune signaling. Clin Infect Dis 73(3):376–385. https://doi.org/10.1093/cid/ciaa663 Zhang J, Wu H, Yao X, Zhang D, Zhou Y, Fu B, Wang W, Li H, Wang Z, Hu Z, Ren Y, Sun R, Tian Z, Bian X, Wei H (2021a) Pyroptotic macrophages stimulate the SARS-CoV-2-associated cytokine storm. Cell Mol Immunol 18(5):1305–1307. https://doi.org/10.1038/s41423-02100665-0 Zhang Y, Lu Z, Wang B, Cang J, Ma Y (2020) Gastrointestinal tract symptoms in coronavirus disease 2019: analysis of clinical symptoms in adult patients. medRxiv:2020.2003.2023.20040279. https://doi.org/10.1101/2020.03.23.20040279 Zhong H, Wang Y, Shi Z, Zhang L, Ren H, He W, Zhang Z, Zhu A, Zhao J, Xiao F, Yang F, Liang T, Ye F, Zhong B, Ruan S, Gan M, Zhu J, Li F, Li F, Wang D, Li J, Ren P, Zhu S, Yang H, Wang J, Kristiansen K, Tun HM, Chen W, Zhong N, Xu X, Li Y-m, Li J, Zhao J (2021) Characterization of respiratory microbial dysbiosis in hospitalized COVID-19 patients. Cell Discov 7(1):23. https://doi.org/10.1038/s41421-021-00257-2 Zhou P, Yang XL, Wang XG, Hu B, Zhang L, Zhang W, Si HR, Zhu Y, Li B, Huang CL, Chen HD, Chen J, Luo Y, Guo H, Jiang RD, Liu MQ, Chen Y, Shen XR, Wang X, Zheng XS, Zhao K, Chen QJ, Deng F, Liu LL, Yan B, Zhan FX, Wang YY, Xiao GF, Shi ZL (2020) A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature 579(7798):270–273. https://doi.org/10.1038/s41586-020-2012-7 Zuo T, Liu Q, Zhang F, Lui GC, Tso EY, Yeoh YK, Chen Z, Boon SS, Chan FK, Chan PK, Ng SC (2021) Depicting SARS-CoV-2 faecal viral activity in association with gut microbiota composition in patients with COVID-19. Gut 70(2):276–284. https://doi.org/10.1136/gutjnl2020-322294 Zuo T, Zhan H, Zhang F, Liu Q, Tso EYK, Lui GCY, Chen N, Li A, Lu W, Chan FKL, Chan PKS, Ng SC (2020b) Alterations in fecal fungal microbiome of patients with COVID-19 during time of hospitalization until discharge. Gastroenterol 159(4):1302–1310.e1305. https://doi.org/10. 1053/j.gastro.2020.06.048

Exploring the Pathoprofiles of SARS-COV-2 Infected Human Gut–Lungs. . .

235

Zuo T, Zhang F, Lui GCY, Yeoh YK, Li AYL, Zhan H, Wan Y, Chung ACK, Cheung CP, Chen N, Lai CKC, Chen Z, Tso EYK, Fung KSC, Chan V, Ling L, Joynt G, Hui DSC, Chan FKL, Chan PKS, Ng SC (2020a) Alterations in gut microbiota of patients with COVID-19 during time of hospitalization. Gastroenterol 159(3):944–955.e948. https://doi.org/10.1053/j.gastro.2020. 05.048

Role of Human Microbiome in Cardiovascular Disease: Therapeutic Potential and Challenges Sathiya Maran, Wendy Wai Yeng Yeo, Kok Song Lai, and Swee Hua Erin Lim

Abstract Cardiovascular diseases (CVDs) are the most prevalent cause of morbidity and morbidity worldwide. The human microbiome has been reported to have a role in the development of human disorders, most notably in cardiovascular diseases. Modifications in gut microbiota are reflected in the increasing number of human and animal studies which precipitate the start of CVDs. In addition, intestinal flora transforms the host’s food into metabolites such as trimethylamine N-oxide, shortchain fatty acids, secondary bile acid, and indoxyl sulphate, influence the physiological processes by triggering several signalling pathways. This comprehensive review summarises the role of gut microbiota in CVD pathogenesis, emphasising human metabolites, prospective CVD therapy options, and problems in addressing flora composition and functions. Keywords Cardiovascular diseases · Microbiome · Trimethylamine N-oxide · Short-chain fatty acids

1 Introduction Lederberg and McCray (2001) introduced the term ‘microbiome’ to describe the population of beneficial and pathogenic microorganisms that live in the human host, predominantly bacteria but also viruses, protozoa, and fungus. Consisting of more than 1500 species of bacteria, viruses, and some eukaryotes (Gomaa 2020) and dominated 90% by Bacteroidetes and Firmicutes, other populations include the Proteobacteria, Fusobacteria, Tenericutes, Actinobacteria, and Verrucomicrobia (Jethwani and Grover 2019) (Fig. 1). The human microbiome has been indicated S. Maran · W. W. Y. Yeo School of Pharmacy, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Selangor Darul Ehsan, Malaysia K. S. Lai · S. H. Erin Lim (✉) Health Sciences Division, Abu Dhabi Women’s College, Higher Colleges of Technology, Abu Dhabi, United Arab Emirates e-mail: [email protected] © The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd. 2023 V. Kothari et al. (eds.), Probiotics, Prebiotics, Synbiotics, and Postbiotics, https://doi.org/10.1007/978-981-99-1463-0_13

237

238

S. Maran et al.

Fig. 1 Phylogenetic tree representing human gut microbiota (Andersson and Vasan 2018)

to have a key role in digestion, metabolism, epithelial cell proliferation and differentiation, as well as in regulation of insulin, and modulation of brain–gut communication (Mills et al. 2019; Rothschild et al. 2018; Wiley et al. 2017; Zheng et al. 2019). As a result, maintaining a healthy microbiome is critical for living an optimal lifestyle. Worldwide, CVDs are the main cause of morbidity and mortality and the most common cause of death (Townsend et al. 2022). The Global Burden of Diseases study reported 17.8 million deaths globally due to CVD previously in 2017 (Roth et al. 2018). Research focussing on the human microbiome in several disciplines of medicine have grown in popularity (Huttenhower et al. 2012). These research have revealed the importance of human microbiome in determining risk towards autoimmune, inflammatory (Belkaid and Harrison 2017; Opazo et al. 2018), neurodegenerative (Endres and Schäfer 2018), infectious diseases (Lazar et al. 2018), and cancer (Villéger et al. 2019).

Role of Human Microbiome in Cardiovascular Disease: Therapeutic. . .

239

Imbalances in intestinal flora have been linked to multiple CVD types. Present evidence confirms inflammation, apoptosis, and other signalling pathways metabolites’ heavy involvement in governing the progression of CVDs (Zhu et al. 2016; Perez et al. 2020). To ensure and support regular blood circulatory function, important metabolites are produced by gut flora (Zhu et al. 2020). Microbiome research to better understand its association with CVD holds assuring promises (Kazemian et al. 2020). This chapter will discuss the physiologic and pathophysiologic elements of the human microbiome with CVD. In addition, this chapter will also address the therapeutic potentials and caveats of the human microbiome in determining the risk towards cardiovascular disease.

2 Gut Microbiota and the Risk of CVD Atherosclerosis is a prominent predisposition for CVD, mainly caused by cholesterol build-up and macrophage migration into arterial walls, both of which lead to atherosclerotic plaques (Gui et al. 2012). Atherosclerosis remains as one of the most pressing issues in medicine and is the leading cause of prevalent disorders such as myocardial infarction, stroke, and sudden death (Kirichenko et al. 2020). The gut microbiota is predicted to have a key function in the pathways of metabolism that lead to atherosclerosis (Ahmed and Spence 2021). Several research and clinical investigations have also recently looked into the involvement of the microbiome and metabolic processes involved in the progression of atherosclerosis. Figure 2 depicts microbiome influences in fundamental atherogenesis processes. The human microbiome influences the development of obesity and type 2 diabetes; these diseases contribute towards an increased risk of atherosclerosis (Komaroff 2018). Metabolites generated from the gut microbiota play a critical function in the development of atherosclerosis (Brown and Hazen 2015; Bergeron et al. 2016). The human gut microbiota produces a range of metabolites, including amines, methylamines, polyamines, SCFAs, TMAO, secondary BAs, and co-metabolism BAs (Ma and Li 2018). Intestinal microorganisms contribute to the digestive functions and intestinal well-being and play a key role in metabolism related to the breakdown of carbohydrate and protein (Macfarlane and Macfarlane 2012). The gut microbiome controls digestion, further influencing the host’s physiology (Tang et al. 2017). Metabolites that are low molecular weight generated by gut flora are absorbed by the intestinal tract and released systemically. They are key in determining the risks of cardiovascular disease (CVD) (Lam et al. 2016). The stomach flora can be categorised into three categories: beneficial, dangerous, and neutral bacteria (Grabherr et al. 2019). To execute host metabolism, the gut microbiota interacts with TMA or TMAO, SCFA, primary and secondary BA, and phosphatidylcholine pathways (Skye et al. 2018). Brown and Hazen reported that choline- and TMAO-rich diets enhance atherosclerosis and cholesterol pathways in mouse models (Li et al. 2017). According to

240

S. Maran et al.

Fig. 2 Microbiome effects in basic mechanisms of atherogenesis. (Adapted from Kirichenko et al. (2020))

the study, reverse transfer of cholesterol and its catabolism are the critical mechanisms of TMAO in promoting atherosclerosis. This was further revealed with an autopsy showing that atherosclerotic plaques carried substantial bacterial DNA levels (Liu et al. 2015; Ott et al. 2006). This research demonstrates that gut florainduced chronic inflammation enhances the development of atherosclerotic plaques. In a study of 1159 types 1 diabetics, Winther and colleagues concluded that more significant plasma TMAO concentrations elevated the risk of cardiovascular events, renal vascular disease, and death, implying that TMAO had an effect on the microand microvasculature (Wang et al. 2015). TMAO is a proatherogenic molecule produced by microbial processing of phosphatidylcholine, found in shellfish, red meat, and eggs (Andersson and Vasan 2018). The gut microbiota converts phosphatidylcholine to trimethylamine (TMA), processed by flavin monooxygenases in the liver, resulting in TMAO. TMAOproducing compounds, such as L-carnitine and -butyrobetaine, have been linked to an elevated risk of cardiovascular disease (Andersson and Vasan 2018). The significance of TMAO towards the risk of atherosclerosis has been widely investigated. TMA lyases in the gut convert choline and carnitine to TMA, which eventually diffuses into the bloodstream and is converted to tTMAO by enzyme flavine monooxygenase 3 (FMO3) (Brown and Hazen 2015). Several factors alter circulating plasma TMAO levels, including the absorption of metabolic initiators, medicine, and liver flavin monooxygenase activity (Janeiro et al. 2018). It is reported that

Role of Human Microbiome in Cardiovascular Disease: Therapeutic. . .

241

TMAO triggers atherosclerosis, and TMAO plasma levels have been linked to the occurrence of CVDs (Zhu et al. 2016). A study investigating the expression of CD36 and steroid receptor RNA activator 1 (SR-A1) showed that TMAO-treated animals had higher levels of CD36 and SR-A1 in their macrophages as compared to the untreated group; meanwhile, antibiotic treatment decreased the development of foam cells by lowering TMA synthesis (Wang et al. 2011). TMAO was seen to cause atherosclerosis by reducing reverse cholesterol translocation and altering cholesterol action. TMAO administration also showed suppression of liver BAs synthetase (Cyp7a1 and Cyp27a1) and BAs transporters including Oatp1, Oatp4, Mrp2, and Ntcp, resulting in atherosclerosis, indicating TMAO’s atherosclerotic-promoting effect (Koeth et al. 2013). A recent study investigated the potential effect of allicin (found in garlic juice) against atherosclerosis; TMAO-producing capacity was significantly reduced through carnitine metabolism in normal populations who are TMAO-producing (Panyod et al. 2022). Thus summarising the potential effect of TMAO in causing atherosclerosis can be potentially reduced by the anti-atherosclerotic activity of allicin. Another study by Liu et al. (2022) reported that A positive feedback loop between TMAO and lncRNA enriched the ubiquitous transcript 1/miR-370-3p/STAT3/FMO3 aggravating AS severity. This unique feedback loop could be a valuable treatment point for atherosclerosis. Table 1 summarises studies that investigated gut microbiome in the progression of atherosclerosis. The synthesis of BA metabolites by the gut microbiota has shown correlation on the development of cardiovascular diseases (Kazemian et al. 2020). Tseui and colleagues (Tsuei et al. 2014) reported that BA is a metabolic regulator of signalling molecules and plays important roles in lipid and glucose breakdown as well as energy consumption. The rate-limiting enzyme cholesterol 7-alpha-hydroxylase (CYP7A1) generates BAs, which are crucial for the control of lipid, glucose, and energy metabolism as well as the absorption of fats, nutrients, and lipophilic vitamins (Chiang 2009; Ferrell et al. 2016). Gut bacteria regulate the expression of the farnesoid X receptor (FXR) and G protein-coupled receptors, which control BA production (GPRs). BAs restrict the formation of intestinal flora via activation of FXR target system, which may hinder intestinal flora transfer (Lin et al. 2019). BAs are reported to exhibit different effects on cardiomyocytes, primarily through modifying sodium, potassium, and calcium concentrations (Zhu et al. 2020). Hydrophilic BAs (such as ursodeoxycholic acid) may help keep the cell membrane potential stable (Fedorova et al. 2015). Lipophilic BAs cause rapid modifications in the membrane, causing harmful electrophysiological effects on cell membranes, leading to arrhythmias (Rainer et al. 2013). Free BAs activate FXR and caspase-9/caspase-3, regulating BCL-2/BAX expression, causing mitochondrial malfunction, and eventually causing ischemia-reperfusion damage in cardiac cells, leading to cardiomyocyte death (Pu et al. 2013). By inhibiting the choline-TMA pathway, antibodies limit TMAO formation, lowering the risk of atherosclerosis (Chen et al. 2016). The exchange occurring between BAs and gut intestinal flora has crucial regulatory implications.

242

S. Maran et al.

Table 1 The overview of the bacterial challenge studies in mouse models relating to the gut microbiome and the progression of atherosclerosis Mouse model ApoE-/-

Diet and treatment protocol(s) Fed on HFD for 12 weeks followed by traditional Chinese medicines for 12 weeks

ApoE KO mice

Given standard chow (control) or adenine diets with optional addition of iodomethylcholine for a fortnight

LDLr-/-

Western diet (no chow)

ApoE-/-

Purified diet low in fibre

Apoe-/(gnotobiotic)

Chow, Roseburia intestinalis administration

Apoe-/-

Chow, chow added with 1.2% choline, Western diet, or Western diet added with 1% choline for 12 weeks

Apoe-/(GF by abx)

Chow without/with choline

Apoe-/(GF and CONV-R)

Chow without/with cholesterol

Apoe-/(GF and CONV-R)

HFD

Findings Anti-atherosclerosis effect by regulating the level of TG, TC, LDL-C, and HDL-C and inhibiting cholesterol deposition in aorta Bacterial choline TMA lyase activity inhibited and reduced amount of TMAO in the blood; # atherosclerotic lesions Reduced plasma total cholesterol levels and atherosclerotic plaques; reduced atherosclerotic lesions Reduced vascular inflammation, atherosclerotic lesion burden, and cardiac remodelling Reduced lesions and inflammation in R. intestinalis vs. control Atherosclerotic lesion size and plasma cholesterol levels lower conventionally raised mice Choline supplementation promoted TMAO levels in conventionally raised mice ApoE interacts with ABCA1/ ABCG1 gene, causing cholesterol efflux Germ-free ApoE-/- aortic plaques found in animals ingesting the same low cholesterol standard diet compared to the traditionally maintained ApoE-deficient mice No significant differences in atherosclerosis between germfree animals compared to those reared with low levels of microbial challenge

References Andersson and Vasan (2018)

Zhang et al. (2021)

Chen et al. (2020)

Bartolomaeus et al. (2019)

Kasahara et al. (2018) Lindskog Jonsson et al. (2018)

Murphy et al. (2011) Stepankova et al. (2010)

Wright et al. (2000)

HFD high fed diet, TG triglycerides, TC total cholesterol, LDL-C low-density lipoprotein-cholesterol, HDL-C high density lipoprotein-cholesterol, ApoE KO mice apolipoprotein E (Apoe) knockout (Apoe-/-), TMA trimethylamine, TMAO trimethylamine N-oxide, LDLr-/- low-density lipoprotein receptor null, abx broad spectrum antibiotic, GF germ-free, CONV-R conventionally raised

Role of Human Microbiome in Cardiovascular Disease: Therapeutic. . .

243

Emerging research investigating human microbiome reported that gut dysbiosis damages intestinal mucosal barriers (Li et al. 2022). It increases intestinal permeability, allowing the persistence of harmful bacteria and translocation of their metabolites into the plasma through the gut–heart axis, further initiating chronic inflammation of blood vessels. A research focusing on the preventive benefits of dietary FO intervention on HFD-induced AS and the gut microbiota-inflammationartery axis reported that FO could reduce AS pathological damage in atherosclerotic ApoE/mice. It was postulated that FO might significantly regulate the gut microbiota by lowering the phylum level of prevalent Firmicutes/Bacteroidetes, implying that FO could significantly impact the gut microbiota (Wu et al. 2018). Glycolipids, phospholipids, and neutral fats are components of fatty acids (FAs), which are normally linked to increase risk of CVDs (Pu et al. 2013). Lactobacillus and Bifidobacteria, an anaerobic bacteria that create SCFAs are important in (1) providing energy to the host’s intestinal microflora and epithelial cells; (2) inhibiting the development of dangerous bacteria; (3) maintaining the pH balance in the intestine; (4) reducing inflammatory reactions; and (5) regulating the host’s gut immunity. Meanwhile, acetic acid, butyric acid, and propionic acid make up 90% of the intestinal SCFAs (Wu et al. 2018). Thus, SCFA-producing bacteria such as Lachnospiraceae, Bacteroides plebeius, and Bacteroides coprocola have been associated with hypertensive people. Studies have reported a favourable relationship between systolic and diastolic blood pressure. Short-chain fatty acid (SCFA) produced by anaerobes provides energy for the host’s intestinal microflora and epithelial cells, not only in preventing the proliferation of harmful bacteria and maintaining the pH balance in the gut, but also reduces inflammatory response, all these contribute to regulating host intestinal immunity. Ninety percent of the intestinal SCFAs are butyric acid, acetic acid, and propionic acid (Wu et al. 2018). The Lachnospiraceae, Bacteroides plebeius, and Bacteroides coprocola are SCFA-producing microbes that were reported to be abundant in hypertensive subjects. Studies have reported a favourable relationship with systolic and diastolic blood pressure. Many research projects have demonstrated the role of SCFAs in immune system function. Nagpal and colleagues (Lee et al. 2022) reported that Lactobacillus and Enterococcus strains from the new-born gut increased the quantity of SCFAs in faeces and moderated digestive microbiome disturbance, resulting in a decrease in inflammation in mouse and human models. A recent study investigating SCFA supplementation reported no significant reduction in colon inflammation; however, the increased regulatory T cell and IL-17-producing T cell expression showed protective and aggressive gut microbiota (Li et al. 2022). Another study investigating the effects in atherosclerotic Apolipoprotein E (ApoE)-/- mice reported that the gut microbiota-inflammation-artery nexus, dietary ALA-rich FO alleviated atherosclerosis (Hosseinkhani et al. 2021). SCFAs influence immune cells’ cytolytic activity, cytokine generation, and regulation of gene expression. SCFAs exert their anti-inflammatory effects via two key signalling pathways: (1) inhibition of histone deacetylases (HDAC) and (2) stimulation of G-protein-coupled receptor signalling (GPCR) (Hosseinkhani et al. 2021).

244

2.1

S. Maran et al.

Pro-, Pre-, and Synbiotics from the View of Gut Microbiome in CVD

Probiotics, prebiotics, and synbiotics may be associated with the protection against CVDs. Probiotics are a group of beneficial bacteria, mainly Lactobacillus, Bifidobacterium, Lactococcus, Streptococcus, and Enterococcus, while oligosaccharides, fructo-oligosaccharides (FOS), inulin, and galactans (galactooligosaccharides (GOS)) are prebiotics (Nagpal et al. 2018; Wu and Chiou 2021). It is believed that the probiotics which are the live bacterial cultures may protect against CVDs by lowering cholesterol levels (Olas 2020). However, the prebiotics, composed of substances which can only be metabolised by gut microbiome, protect the host against CVD such as fructans and galactans (Wu et al. 2021a). The synbiotics containing both probiotics and prebiotics have showed promising results of reducing blood cholesterol in a recent clinical trial using a combination of Lactiplantibacillus plantarum strains CECT7527, CECT7528, and CECT7529 together with Monacolin K (Guerrero-Bonmatty et al. 2021). Probiotics on human health were reported to positively influence: (1) improved epithelial barrier function; (2) competition against pathogens for nutrients and adhesion sites; (3) immune system and neurotransmitter production effect on other tissues; and (4) immunomodulation (Sánchez et al. 2017). A significant relationship between pro- and prebiotic gut microbiota alterations and atherosclerotic heart disease was reported by Karlsson et al. (2012). Lactobacillus was reported to be high among CHD patients, whereas Bacteroidetes such as Bifidobacterium and Prevotella was seen to decrease significantly (Yamashita et al. 2016; Emoto et al. 2017). Furthermore, gut microbiome indicated decreased diversity and increased Bacteroidetes phylum was also observed among ischemic stroke patients (Stanley et al. 2018). A recent study by Cai et al. (2022) showed that high levels of Lactobacillus exhibited an improved prognosis and quality of life for patients with acute myocardial infractions. A recent study carried out on 2037 adults with hypertension showed that probiotics might reduce systolic and diastolic pressure (Wu et al. 2021b). The beneficial effects of prebiotics, especially inulin, have been extensively investigated. Inulin supplementation was reported to lower cholesterol levels, including total and LDL cholesterol, CRP and inflammatory cytokines, and improve antioxidant parameters and gut microbial dysregulation. The administration of a prebiotic complex was also observed to restore intestinal dysbiosis and endotoxemia in female rats with modelled heart failure (Vlasov et al. 2020). It has been reported that chitosan oligosaccharides (COS) exhibit protective effects against CHD by increasing antioxidant capacities and enhancing lipid profiles, achieved through promoting the growth of probiotics in the gut flora (Jiang et al. 2019). It can be summarised that prebiotics plays an essential role in CVD via several pathways implicated in inflammation, antioxidant capacity, and rebalancing of the dysregulated gut microbiota (Wu et al. 2021a) (Fig. 3).

Role of Human Microbiome in Cardiovascular Disease: Therapeutic. . .

245

Fig. 3 Summary of the positive role of probiotics, prebiotics, and synbiotics in cardiovascular diseases via digestive microbiome. (Figure was modified using servier medical art templates, which are licenced under a creative commons attribution 3.0 unported licence. https://creativecommons. org/licenses/by/3.0/)

3 Therapeutic Potentials of Digestive Microbiome in Cardiovascular Diseases The digestive microbiome has been explored as a diagnostic tool for early diagnosis and disease-risk prediction. The influence of gut microbiome has been recognised as a vital environmental driving force of various metabolic diseases (Boulangé et al. 2016). The emerging microbiome-based therapeutics basically works on the manipulation of the bacteria in the gut as this diverse microbial ecosystem functions as communicators between gut microbiome and host metabolism in physiological and various dysregulated states including cardiovascular diseases (Fan and Pedersen 2021).

246

S. Maran et al.

It has been drawn to attention that microbiota-related biomarkers such as trimethylamine-N-oxide (TMAO), butyrate, bile acids, and uremic toxins potentially work as a biomarker for coronary artery disease and heart failure (Trøseid et al. 2020). A study from Gózd-Barszczewska et al. (2017) reported that intestinal microbiome of different bacterial genera including Prevotella, Bacteroides, Clostridium, and Faecalibacterium may involve in the pathogenesis of atherosclerosis via its role in lipid breakdown. Meanwhile, microbiota richness was observed in patients with coronary heart disease (CHD) with Bacteroidetes and Bacteroidia as the dominant bacteria as compared to healthy control group (Wan et al. 2021). Therefore, this indicates microbiota detection may open up as an avenue to predict the risk of cardiovascular events between CHD and healthy populations. Human microbiome is the potential candidate interventions for precision medicine with personalised approaches in treating cardiovascular diseases. The intra- and inter-individual differences within the microbiota which has effects on drug usefulness and the potential adverse outcome profiles are important aspects in order to develop personalised treatment strategies (Behrouzi et al. 2019; Talmor-Barkan et al. 2022). The inter-individual variation to statins as the cholesterol-lowering drugs such as simvastatin, rosuvastatin, and atorvastatin revealed that gut microbiota may influence drug outcomes (Tuteja and Ferguson 2019). In addition, precision medicine strategy has gained wide interest as these studies focus on microbiome modulation by targeting microbial metabolism instead of the host. The correlation of existing gut microbiome with cardiovascular diseases leads towards the modulation of microbiome variations in response to drugs that might help to improve the effectiveness of the drugs’ action target and disposition in the current emerging field of pharmacomicrobiomics (Curini and Amedei 2021; Chen et al. 2022).

3.1

Challenges and Caveats of Using Gut Microbiome to Determine Risk Towards Cardiovascular Diseases

When considering gut microbiome as the therapeutic therapy for cardiovascular diseases, there is a rise of concern related to the safety and drug interactions as patients are often prescribed with different types of drugs. This poses another question whether the gut microbiota can affect the drug efficacy, bioavailability, bioactivity, or even cause any toxicity, either via significant conversion of drugs or microbial interactions with the host immune system (Kazemian et al. 2020). Nevertheless, there is more to explore about the external modifications in the gut microbiota ecology such as diet, drug intake, stress, genetics, immune system, age, physical activities, and circadian cycles (Boulangé et al. 2016; Olofsson and Bäckhed 2022) to have better understanding role of microbiome in the pathophysiology of cardiovascular diseases. Meanwhile, improvement of protocols such as increasing sample size, conformation of microbiome engraftment, mechanistic

Role of Human Microbiome in Cardiovascular Disease: Therapeutic. . .

247

insight is vital to provide more robust and reproducible studies to better elucidate the function of the gut microbiome–drug interactions (Olofsson and Bäckhed 2022). Impediment faced by individuals with atherosclerosis who are highly medicated is to distinguish between authentic atherosclerosis signals in the gut microbiota and signals triggered by medications as well as pre-morbidities and co-morbidities (Almeida et al. 2021). It should be taken note that drug–microbiome interactions influence the ability of the drug metabolism as these gut microbiota can alter the drug pharmacokinetics and pharmacodynamics which subsequently affect the drug response (Talmor-Barkan et al. 2022; Chen et al. 2022). Findings from VieiraSilva et al. (2020) reported that usage of statins is linked with lower prevalence of gut microbiota dysbiosis. Amidst modernisation, there has been a receding of gut microbiota diversity alongside with the use of broad spectrum of antibiotics to overcome infectious diseases (Janeiro et al. 2018; Yang et al. 2021). Therefore, it is crucial to explore the correlation of the gut microbiome with different cardiovascular diseases; this is to enable the discovery of potential of microbiome intervention on drug efficacy and side effects profiles for individualised use or even as a reference in clinical settings application. Findings have indicated that gut ecosystem has a direct influence on hypercholesterolemia through metabolites such as bile acids, coprostanol, and short-chain fatty acids (Kazemian et al. 2020). Various studies have indicated that rising TMAO levels is correlated with cardiovascular diseases which promotes vascular inflammation including enhancing platelet hyperreactivity and thrombosis risk (Skye et al. 2018; Kazemian et al. 2020). This shows that changes in diet can alter the gastrointestinal environment which is required for optimal functions of the metabolite that may render the host vulnerable to disease. Aside from that, the malnutrition issue that is associated with food and water security is one of the main adverse contributors in relation to the maturation of healthy gut microbiota (Almeida et al. 2021). This new microbiome field may face changes especially in the clinical development and commercialisation of microbiome-based therapeutics. Challenges remain in this area as limited studies have evidenced mechanistic or direct evidence of a direct involvement of gut microbiota in the progression to atherosclerosis (Tang et al. 2017). In addition, most studies focused on cross-sectional observations which only analyse the differences of the gut microbiome presence between patients and healthy volunteers at specific time points are unable to delineate the overall role of microbiome during the disease development (Olofsson and Bäckhed 2022). Other limitations include the geographical constraint, sample size, and also a strictly controlled inclusion and exclusion criteria, which results in limited participation that is occurring in most clinical trials whereby they study the role of microbiome and their risk of cardiovascular diseases (Fig. 4).

248

S. Maran et al.

Fig. 4 Therapeutic potential and challenges in using human microbiome for cardiovascular diseases. (Figure was modified using servier medical art templates, which are licenced under a creative commons attribution 3.0 unported licence. https://creativecommons.org/licenses/by/3.0/)

4 Future Perspectives and Conclusion Increasing number of studies on human microbiome suggests that modulation of gut microbiome can be further explored together with their potential functions and roles in treating cardiovascular diseases. Moving forward, current advancement in bioinformatics and shotgun sequencing technologies has enabled researchers to look into a more extensive view of the entire gut microorganism community. The availability of these massive genetic data facilitates the sharing of information among the researchers to further provide insights into the effects of genetic variation of human microbiome and their potential roles associated with cardiovascular diseases. In summary, the gut microbiome-dependent of various types of metabolites including trimethylamine-N-oxide (TMAO), bile acids (BAs) and short-chain fatty

Role of Human Microbiome in Cardiovascular Disease: Therapeutic. . .

249

acids (SCFA) could be potentially utilised as biomarkers in precision medicine for diagnosis purposes and prognosis reporting in the near future. Thus, it is pivotal to look into investigations relating to microbiome-based biomarkers across distinct populations to fully grasp the function of the human digestive microbiome in cardiovascular diseases.

References Ahmed S, Spence JD (2021) Sex differences in the intestinal microbiome: interactions with risk factors for atherosclerosis and cardiovascular disease. Biol Sex Differ 12(1):35. https://doi.org/ 10.1186/s13293-021-00378-z Almeida C, Barata P, Fernandes R (2021) The influence of gut microbiota in cardiovascular diseases—a brief review. Porto Biomed J 6(1):e106. https://doi.org/10.1097/j.pbj. 0000000000000106 Andersson C, Vasan RS (2018) Epidemiology of cardiovascular disease in young individuals. Nat Rev Cardiol 15(4):230–240 Bartolomaeus H, Balogh A, Yakoub M, Homann S, Markó L, Höges S et al (2019) Short-chain fatty acid propionate protects from hypertensive cardiovascular damage. Circulation 139(11): 1407–1421. https://doi.org/10.1161/CIRCULATIONAHA.118.036652 Behrouzi A, Nafari AH, Siadat SD (2019) The significance of microbiome in personalized medicine. Clin Transl Med 8(1):16. https://doi.org/10.1186/s40169-019-0232-y Belkaid Y, Harrison OJ (2017) Homeostatic immunity and the microbiota. Immunity 46(4): 562–576 Bergeron N, Williams PT, Lamendella R, Faghihnia N, Grube A, Li X et al (2016) Diets high in resistant starch increase plasma levels of trimethylamine-N-oxide, a gut microbiome metabolite associated with CVD risk. Br J Nutr 116(12):2020–2029 Boulangé CL, Neves AL, Chilloux J, Nicholson JK, Dumas ME (2016) Impact of the gut microbiota on inflammation, obesity, and metabolic disease. Genome Med 8(1):1–12. https:// doi.org/10.1186/s13073-016-0303-2 Brown JM, Hazen SL (2015) The gut microbial endocrine organ: bacterially derived signals driving cardiometabolic diseases. Annu Rev Med 66:343–359 Cai JJ, Liu Y, Wang J, Wang JX, Wang Y, Xu SB et al (2022) Lactobacillus levels and prognosis of patients with acute myocardial infarction. J Geriatr Cardiol 19(2):101–114. https://doi.org/10. 11909/j.issn.1671-5411.2022.02.009 Chen M-l, Yi L, Zhang Y, Zhou X, Ran L, Yang J et al (2016) Resveratrol attenuates trimethylamine-N-oxide (TMAO)-induced atherosclerosis by regulating TMAO synthesis and bile acid metabolism via remodeling of the gut microbiota. MBio 7(2):e02210–e02215 Chen PB, Black AS, Sobel AL, Zhao Y, Mukherjee P, Molparia B et al (2020) Directed remodeling of the mouse gut microbiome inhibits the development of atherosclerosis. Nat Biotechnol 38(11):1288–1297. https://doi.org/10.1038/s41587-020-0549-5 Chen HQ, Gong JY, Xing K, Liu MZ, Ren H, Luo JQ (2022) Pharmacomicrobiomics: exploiting the drug-microbiota interactions in antihypertensive treatment. Front Med (Lausanne) 8: 742394. https://doi.org/10.3389/fmed.2021.742394 Chiang JY (2009) Bile acids: regulation of synthesis: thematic review series: bile acids. J Lipid Res 50(10):1955–1966 Curini L, Amedei A (2021) Cardiovascular diseases and pharmacomicrobiomics: a perspective on possible treatment relevance. Biomedicine 9(10):1–13. https://doi.org/10.3390/ biomedicines9101338 Emoto T, Yamashita T, Kobayashi T, Sasaki N, Hirota Y, Hayashi T et al (2017) Characterization of gut microbiota profiles in coronary artery disease patients using data mining analysis of

250

S. Maran et al.

terminal restriction fragment length polymorphism: gut microbiota could be a diagnostic marker of coronary artery disease. Heart Vessels 32(1):39–46 Endres K, Schäfer K-H (2018) Influence of commensal microbiota on the enteric nervous system and its role in neurodegenerative diseases. J Innate Immun 10(3):172–180 Fan Y, Pedersen O (2021) Gut microbiota in human metabolic health and disease. Nat Rev Microbiol 19(1):55–71. https://doi.org/10.1038/s41579-020-0433-9 Fedorova OV, Zernetkina VI, Shilova VY, Grigorova YN, Juhasz O, Wei W et al (2015) Synthesis of an endogenous steroidal Na pump inhibitor marinobufagenin, implicated in human cardiovascular diseases, is initiated by CYP27A1 via bile acid pathway. Circ Cardiovasc Genet 8(5): 736–745 Ferrell JM, Boehme S, Li F, Chiang JY (2016) Cholesterol 7α-hydroxylase-deficient mice are protected from high-fat/high-cholesterol diet-induced metabolic disorders [S]. J Lipid Res 57(7):1144–1154 Gomaa EZ (2020) Human gut microbiota/microbiome in health and diseases: a review. Antonie Van Leeuwenhoek 113(12):2019–2040. https://doi.org/10.1007/s10482-020-01474-7 Gózd-Barszczewska A, Kozioł-Montewka M, Barszczewski P, Młodzińska A, Humińska K (2017) Gut microbiome as a biomarker of cardiometabolic disorders. Ann Agric Environ Med 24(3): 416–422. https://doi.org/10.26444/aaem/75456 Grabherr F, Grander C, Effenberger M, Adolph TE, Tilg H (2019) Gut dysfunction and non-alcoholic fatty liver disease. Front Endocrinol 10:611 Guerrero-Bonmatty R, Gil-Fernández G, Rodríguez-Velasco FJ, Espadaler-Mazo J (2021) A combination of Lactiplantibacillus plantarum strains CECT7527, CECT7528, and CECT7529 plus monacolin K reduces blood cholesterol: results from a randomized, double-blind, placebocontrolled study. Nutrients 13(4):1206 Gui T, Shimokado A, Sun Y, Akasaka T, Muragaki Y (2012) Diverse roles of macrophages in atherosclerosis: from inflammatory biology to biomarker discovery. Mediators Inflamm 2012: 693083 Hosseinkhani F, Heinken A, Thiele I, Lindenburg PW, Harms AC, Hankemeier T (2021) The contribution of gut bacterial metabolites in the human immune signaling pathway of non-communicable diseases. Gut Microbes 13(1):1–22. https://doi.org/10.1080/19490976. 2021.1882927 Huttenhower C, Gevers D, Knight R, Abubucker S, Badger JH, Chinwalla AT et al (2012) Structure, function and diversity of the healthy human microbiome. Nature 486(7402):207–214 Janeiro MH, Ramírez MJ, Milagro FI, Martínez JA, Solas M (2018) Implication of trimethylamine N-oxide (TMAO) in disease: potential biomarker or new therapeutic target. Nutrients 10(10): 1398 Jethwani P, Grover K (2019) Gut microbiota in health and diseases—a review. Int J Curr Microbiol App Sci 8(8):1586–1599 Jiang T, Xing X, Zhang L, Liu Z, Zhao J, Liu X (2019) Chitosan oligosaccharides show protective effects in coronary heart disease by improving antioxidant capacity via the increase in intestinal probiotics. Oxid Med Cell Longev 2019:7658052 Karlsson FH, Fåk F, Nookaew I, Tremaroli V, Fagerberg B, Petranovic D et al (2012) Symptomatic atherosclerosis is associated with an altered gut metagenome. Nat Commun 3(1):1–8 Kasahara K, Krautkramer KA, Org E, Romano KA, Kerby RL, Vivas EI et al (2018) Interactions between Roseburia intestinalis and diet modulate atherogenesis in a murine model. Nat Microbiol 3(12):1461–1471 Kazemian N, Mahmoudi M, Halperin F, Wu JC, Pakpour S (2020) Gut microbiota and cardiovascular disease: opportunities and challenges. Microbiome 8(1):36. https://doi.org/10.1186/ s40168-020-00821-0 Kirichenko TV, Markina YV, Sukhorukov VN, Khotina VA, Wu W-K, Orekhov AN (2020) A novel insight at atherogenesis: the role of microbiome. Front Cell Dev Biol 8:586189. https:// doi.org/10.3389/fcell.2020.586189

Role of Human Microbiome in Cardiovascular Disease: Therapeutic. . .

251

Koeth RA, Wang Z, Levison BS, Buffa JA, Org E, Sheehy BT et al (2013) Intestinal microbiota metabolism of L-carnitine, a nutrient in red meat, promotes atherosclerosis. Nat Med 19(5): 576–585 Komaroff AL (2018) The microbiome and risk for atherosclerosis. JAMA 319(23):2381–2382. https://doi.org/10.1001/jama.2018.5240 Lam V, Su J, Hsu A, Gross GJ, Salzman NH, Baker JE (2016) Intestinal microbial metabolites are linked to severity of myocardial infarction in rats. PloS One 11(8):e0160840 Lazar V, Ditu L-M, Pircalabioru GG, Gheorghe I, Curutiu C, Holban AM et al (2018) Aspects of gut microbiota and immune system interactions in infectious diseases, immunopathology, and cancer. Front Immunol 9:1830 Lederberg J, McCray AT (2001) Ome sweet omics—a genealogical treasury of words. Sci J 15(7):8 Lee JG, Lee J, Lee AR, Jo SV, Park CH, Han DS et al (2022) Impact of short-chain fatty acid supplementation on gut inflammation and microbiota composition in a murine colitis model. J Nutr Biochem 101:108926. https://doi.org/10.1016/j.jnutbio.2021.108926 Li XS, Obeid S, Klingenberg R, Gencer B, Mach F, Räber L et al (2017) Gut microbiota-dependent trimethylamine N-oxide in acute coronary syndromes: a prognostic marker for incident cardiovascular events beyond traditional risk factors. Eur Heart J 38(11):814–824. https://doi.org/10. 1093/eurheartj/ehw582 Li Y, Yu Z, Liu Y, Wang T, Liu Y, Bai Z et al (2022) Dietary α-linolenic acid-rich flaxseed oil ameliorates high-fat diet-induced atherosclerosis via gut microbiota-inflammation-artery axis in ApoE (-/-) mice. Front Cardiovasc Med 9:830781. https://doi.org/10.3389/fcvm.2022.830781 Lin S, Yang X, Yuan P, Yang J, Wang P, Zhong H et al (2019) Undernutrition shapes the gut microbiota and bile acid profile in association with altered gut-liver FXR signaling in weaning pigs. J Agric Food Chem 67(13):3691–3701 Lindskog Jonsson A, Caesar R, Akrami R, Reinhardt C, Fåk Hållenius F, Borén J et al (2018) Impact of gut microbiota and diet on the development of atherosclerosis in Apoe-/- mice. Arterioscler Thromb Vasc Biol 38(10):2318–2326 Liu T-X, Niu H-T, Zhang S-Y (2015) Intestinal microbiota metabolism and atherosclerosis. Chin Med J (Engl) 128(20):2805–2811 Liu A, Zhang Y, Xun S, Sun M (2022) Trimethylamine N-oxide promotes atherosclerosis via regulating the enriched abundant transcript 1/miR-370-3p/signal transducer and activator of transcription 3/flavin-containing monooxygenase-3 axis. Bioengineered 13(1):1541–1553. https://doi.org/10.1080/21655979.2021.2010312 Ma J, Li H (2018) The role of gut microbiota in atherosclerosis and hypertension. Front Pharmacol 9:1082. https://doi.org/10.3389/fphar.2018.01082 Macfarlane GT, Macfarlane S (2012) Bacteria, colonic fermentation, and gastrointestinal health. J AOAC Int 95(1):50–60 Mills S, Stanton C, Lane JA, Smith GJ, Ross RP (2019) Precision nutrition and the microbiome, part I: current state of the science. Nutrients 11(4):923 Murphy AJ, Akhtari M, Tolani S, Pagler T, Bijl N, Kuo C-L et al (2011) ApoE regulates hematopoietic stem cell proliferation, monocytosis, and monocyte accumulation in atherosclerotic lesions in mice. J Clin Invest 121(10):4138–4149 Nagpal R, Wang S, Ahmadi S, Hayes J, Gagliano J, Subashchandrabose S et al (2018) Humanorigin probiotic cocktail increases short-chain fatty acid production via modulation of mice and human gut microbiome. Sci Rep 8(1):1–15 Olas B (2020) Probiotics, prebiotics and synbiotics—a promising strategy in prevention and treatment of cardiovascular diseases? Int J Mol Sci 21(24):9737 Olofsson LE, Bäckhed F (2022) The metabolic role and therapeutic potential of the microbiome. Endocr Rev 43:1–20. https://doi.org/10.1210/endrev/bnac004 Opazo MC, Ortega-Rocha EM, Coronado-Arrázola I, Bonifaz LC, Boudin H, Neunlist M et al (2018) Intestinal microbiota influences non-intestinal related autoimmune diseases. Front Microbiol 9:432

252

S. Maran et al.

Ott SJ, El Mokhtari NE, Musfeldt M, Hellmig S, Freitag S, Rehman A et al (2006) Detection of diverse bacterial signatures in atherosclerotic lesions of patients with coronary heart disease. Circulation 113(7):929–937 Panyod S, Wu W-K, Chen P-C, Chong K-V, Yang Y-T, Chuang H-L et al (2022) Atherosclerosis amelioration by allicin in raw garlic through gut microbiota and trimethylamine-N-oxide modulation. NPJ Biofilms Microbiomes 8(1):4. https://doi.org/10.1038/s41522-022-00266-3 Perez NB, Dorsen C, Squires A (2020) Dysbiosis of the gut microbiome: a concept analysis. J Holist Nurs 38(2):223–232 Pu J, Yuan A, Shan P, Gao E, Wang X, Wang Y et al (2013) Cardiomyocyte-expressed farnesoidX-receptor is a novel apoptosis mediator and contributes to myocardial ischaemia/reperfusion injury. Eur Heart J 34(24):1834–1845 Rainer PP, Primessnig U, Harenkamp S, Doleschal B, Wallner M, Fauler G et al (2013) Bile acids induce arrhythmias in human atrial myocardium—implications for altered serum bile acid composition in patients with atrial fibrillation. Heart 99(22):1685–1692 Roth GA, Abate D, Abate KH, Abay SM, Abbafati C, Abbasi N et al (2018) Global, regional, and national age-sex-specific mortality for 282 causes of death in 195 countries and territories, 1980–2017: a systematic analysis for the global burden of disease study 2017. Lancet 392(10159):1736–1788 Rothschild D, Weissbrod O, Barkan E, Kurilshikov A, Korem T, Zeevi D et al (2018) Environment dominates over host genetics in shaping human gut microbiota. Nature 555(7695):210–215 Sánchez B, Delgado S, Blanco-Míguez A, Lourenço A, Gueimonde M, Margolles A (2017) Probiotics, gut microbiota, and their influence on host health and disease. Mol Nutr Food Res 61(1):1600240 Skye SM, Zhu W, Romano KA, Guo C-J, Wang Z, Jia X et al (2018) Microbial transplantation with human gut commensals containing CutC is sufficient to transmit enhanced platelet reactivity and thrombosis potential. Circ Res 123(10):1164–1176 Stanley D, Moore RJ, Wong CH (2018) An insight into intestinal mucosal microbiota disruption after stroke. Sci Rep 8(1):1–12 Stepankova R, Tonar Z, Bartova J, Nedorost L, Rossman P, Poledne R et al (2010) Absence of microbiota (germ-free conditions) accelerates the atherosclerosis in ApoE-deficient mice fed standard low cholesterol diet. J Atheroscler Thromb 17(8):796–804 Talmor-Barkan Y, Bar N, Shaul AA, Shahaf N, Godneva A, Bussi Y et al (2022) Metabolomic and microbiome profiling reveals personalized risk factors for coronary artery disease. Nat Med 28(2):295–302. https://doi.org/10.1038/s41591-022-01686-6 Tang WW, Kitai T, Hazen SL (2017) Gut microbiota in cardiovascular health and disease. Circ Res 120(7):1183–1196 Townsend N, Kazakiewicz D, Lucy Wright F, Timmis A, Huculeci R, Torbica A et al (2022) Epidemiology of cardiovascular disease in Europe. Nat Rev Cardiol 19(2):133–143. https://doi. org/10.1038/s41569-021-00607-3 Trøseid M, Andersen GØ, Broch K, Hov JR (2020) The gut microbiome in coronary artery disease and heart failure: current knowledge and future directions. EBioMedicine 52:102649. https:// doi.org/10.1016/j.ebiom.2020.102649 Tsuei J, Chau T, Mills D, Wan Y-JY (2014) Bile acid dysregulation, gut dysbiosis, and gastrointestinal cancer. Exp Biol Med 239(11):1489–1504 Tuteja S, Ferguson JF (2019) Gut microbiome and response to cardiovascular drugs. Circ Genom Precis Med 12(9):421–429. https://doi.org/10.1161/CIRCGEN.119.002314 Vieira-Silva S, Falony G, Belda E, Nielsen T, Aron-Wisnewsky J, Chakaroun R, Forslund SK, Assmann K, Valles-Colomer M, Nguyen TTD, Proost S, Prifti E, Tremaroli V, Pons N, Le Chatelier E, Andreelli F, Bastard JP, Coelho LP, Galleron N, Hansen TH et al (2020) Statin therapy is associated with lower prevalence of gut microbiota dysbiosis. Nature 581(7808):310– 315. https://doi.org/10.1038/s41586-020-2269-x Villéger R, Lopès A, Carrier G, Veziant J, Billard E, Barnich N et al (2019) Intestinal microbiota: a novel target to improve anti-tumor treatment? Int J Mol Sci 20(18):4584

Role of Human Microbiome in Cardiovascular Disease: Therapeutic. . .

253

Vlasov A, Shperling M, Terkin D, Bystrova O, Osipov G, Salikova S et al (2020) Effect of prebiotic complex on gut microbiota and endotoxemia in female rats with modeled heart failure. Bull Exp Biol Med 168(4):435–438 Wan C, Zhu C, Jin G, Zhu M, Hua J, He Y (2021) Analysis of gut microbiota in patients with coronary artery disease and hypertension. Evid Based Complement Alternat Med 2021: 7195082. https://doi.org/10.1155/2021/7195082 Wang Z, Klipfell E, Bennett BJ, Koeth R, Levison BS, DuGar B et al (2011) Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease. Nature 472(7341):57–63 Wang Z, Roberts AB, Buffa JA, Levison BS, Zhu W, Org E et al (2015) Non-lethal inhibition of gut microbial trimethylamine production for the treatment of atherosclerosis. Cell 163(7): 1585–1595 Wiley N, Dinan T, Ross R, Stanton C, Clarke G, Cryan J (2017) The microbiota-gut-brain axis as a key regulator of neural function and the stress response: implications for human and animal health. J Anim Sci 95(7):3225–3246 Wright SD, Burton C, Hernandez M, Hassing H, Montenegro J, Mundt S et al (2000) Infectious agents are not necessary for murine atherogenesis. J Exp Med 191(8):1437–1442 Wu H, Chiou J (2021) Potential benefits of probiotics and prebiotics for coronary heart disease and stroke. Nutrients 13(8):2878 Wu S, Hu R, Nakano H, Chen K, Liu M, He X et al (2018) Modulation of gut microbiota by Lonicera caerulea L. berry polyphenols in a mouse model of fatty liver induced by high fat diet. Molecules 23(12):3213 Wu J, Wang K, Wang X, Pang Y, Jiang C (2021a) The role of the gut microbiome and its metabolites in metabolic diseases. Protein Cell 12(5):360–373. https://doi.org/10.1007/ s13238-020-00814-7 Wu Y, Xu H, Tu X, Gao Z (2021b) The role of short-chain fatty acids of gut microbiota origin in hypertension. Front Microbiol 12:730809. https://doi.org/10.3389/fmicb.2021.730809 Yamashita T, Emoto T, Sasaki N, Hirata K-i (2016) Gut microbiota and coronary artery disease. Int Heart J 57(6):663–671 Yang L, Bajinka O, Jarju PO, Tan Y, Taal AM, Ozdemir G (2021) The varying effects of antibiotics on gut microbiota. AMB Express 11(1):116. https://doi.org/10.1186/s13568-021-01274-w Zhang W, Miikeda A, Zuckerman J, Jia X, Charugundla S, Zhou Z et al (2021) Inhibition of microbiota-dependent TMAO production attenuates chronic kidney disease in mice. Sci Rep 11(1):518. https://doi.org/10.1038/s41598-020-80063-0 Zheng P, Zeng B, Liu M, Chen J, Pan J, Han Y et al (2019) The gut microbiome from patients with schizophrenia modulates the glutamate-glutamine-GABA cycle and schizophrenia-relevant behaviors in mice. Sci Adv 5(2):eaau8317 Zhu W, Gregory JC, Org E, Buffa JA, Gupta N, Wang Z et al (2016) Gut microbial metabolite TMAO enhances platelet hyperreactivity and thrombosis risk. Cell 165(1):111–124 Zhu Y, Shui X, Liang Z, Huang Z, Qi Y, He Y et al (2020) Gut microbiota metabolites as integral mediators in cardiovascular diseases (review). Int J Mol Med 46(3):936–948. https://doi.org/10. 3892/ijmm.2020.4674

The Human Microbiome and Respiratory Diseases Oksana Zolnikova

and Vladimir Ivashkin

Abstract The composition of the respiratory tract microbiota has been actively studied around the world. In this article, we have analyzed and summarized the data published over the last 20 years (PubMed/Medline, RSCI/e-library databases) and presented the results of our research of the intestinal and respiratory tract microbiota in patients with bronchial asthma. There is currently no standardized methodology for collecting samples for studies. Nasopharyngeal swab, oropharyngeal swab, bronchi-alveolar lavage, brush biopsy, and induced sputum are most commonly examined. The composition of the respiratory microbiota is determined by a balance of three factors. The first factor is microbial immigration, the second factor is microbial elimination, and the third is the local condition of bacterial growth into the respiratory tract. The interaction between biotopes is being studied for the microbiota–gut–lung axis. It is known that the composition of the gut microbiota and the lung microbiota varies in patients with bronchial asthma significantly. The microbiota differs and depends on the severity of bronchial asthma and sensitivity to steroid therapy. In bronchial asthma, the metabolic activity of the microbiota changes, with a decrease in the content of SCFAs and their ratio. Conclusion: The significant pathogenic role of the microbiota is confirmed by a lot of the accumulated research data. Microbiota is a marker and a possible target in bronchial asthma therapy. All of the above data indicate the existing need for and interest in more substantial research in this direction in the future. Keywords Microbiota · Bronchial asthma · Dysbiosis · 16S rRNA · Gut–lung axis · Short-chain fatty acids · Probiotics · Bacterial metabolism

O. Zolnikova (✉) · V. Ivashkin Department of Propedeutics of Internal Diseases, Gastroenterology and Hepatology, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russian Federation © The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd. 2023 V. Kothari et al. (eds.), Probiotics, Prebiotics, Synbiotics, and Postbiotics, https://doi.org/10.1007/978-981-99-1463-0_14

255

256

O. Zolnikova and V. Ivashkin

1 Introduction Scientific interest to study human microbiome is growing around the world. On having a wide range of differences as in genome as in a metabolic activity, the human microbiome is involved in a health supporting process. It has been established that the microbiota contributes to maintaining the integrity of the mucosa, providing nutrients, protecting against pathogens, etc. In addition, the interaction between the microbiota and mucosal immune system is crucial for providing adequate immune function. The existence of the lung microbiome is now also generally recognized. The lung microbiome, apparently, affects not only disease susceptibility but also disease activity and treatment response. Lung and gut microbiota can interact through the gut–lung axis. According to this scientific concept, intestinal bacteria have a significant impact on the maintenance of normal respiratory tract biocenosis and the functional status of the lungs. Today, there is a very serious rethinking of the human biology and the process of development of various diseases. A new vision is forming on the development of various pathologies that are related to the composition and metabolic functions of the human microbiota. It is likely that understanding the human microbiota can be directed toward better diagnosis and rational treatment of many diseases in the future.

2 Lung Microbiota Study The pre-existing dogma that healthy human lungs are sterile has led to a long time lack of research on the microbiota of the respiratory tract. One of the first studies on the microbiota of the lungs was carried out by the Charlesson’s group in 2011. They conducted comprehensive quantitative and qualitative analyses of the microbiota composition of the upper and lower respiratory tract in healthy volunteers in their study (Charlson et al. 2011). Having sequenced the bacterial genomes, the authors noticed that the lungs of healthy people contain diverse microbial communities with important functional features. The maximal number of bacteria was found in the upper respiratory tract. So, up to 103/ml viable bacteria were detected in the nasal cavity and nasopharynx, and similar number of the viable bacteria (up to 106/ml) was found in the oropharynx (Charlson et al. 2012; Bassis et al. 2015). In the trachea and lungs, the quantity of bacteria is lower and is up to 102 bacterial cells per ml (Man et al. 2017; Huang et al. 2013). The lung microbiota is diverse and contains various types of bacteria, like Firmicutes, Proteobacteria, Bacteroides, Fusobacteria, Acidobacteria, and Actinobacteria (Bassis et al. 2015; Man et al. 2017; Huang et al. 2013; Segal and Blaser 2014). Today, there is no standard sampling methodology for the respiratory microbiota study. Nasopharyngeal swab, oropharyngeal swab, bronchoalveolar lavage, brush biopsy, induced sputum are most commonly used as research material (Ozdemir 2018; Hogan et al. 2016). Each of the sampling methods has had its own advantages

The Human Microbiome and Respiratory Diseases

257

and disadvantages. When analyzing the results, it should be specified what biological materials were studied. A balance of the three main factors was shown to influence the respiratory microbiota composition (O’Dwyer et al. 2016; Gallaracher and Kotecha 2016; Dickson and Huffnagle 2015). Firstly, it is microbial immigration (by inhalation of environmental air with bacteria, viruses, and fungus), microaspiration of ones and then, a dispersion of bacteria along the respiratory mucosa. Secondly, it is microbial elimination (mucociliary clearance, cough, and the antimicrobial mechanisms of innate and adaptive immunity). The third factor is determined by the local bacterial growth conditions in the bronchopulmonary system (the distinctions in temperature, pH, mucus production, etc. in the different parts of the respiratory tract). Epithelial characteristics and mucociliary clearance play an important role, as well as the oxygen concentration and the availability of nutrients, which significantly influence the reproduction of bacterial communities (Yaung et al. 2014; Zolnikova et al. 2018). In healthy persons, the lung microbiota is much more similar to the oropharynx microbiota. It is represented by the Firmicutes, Bacteroidetes, and Proteobacteria types predominate (Integrative HMP (iHMP) Research Network Consortium 2019) and Prevotella, Veillonella and Streptococcus bacteria at the genus bacteria level (Dickson and Huffnagle 2015; Dickson et al. 2017; Dickson et al. 2013). The similarity of the microbiota of the lungs and oropharynx has been explained by the systematic approach of R. Dickson et al. in their study (Dickson and Huffnagle 2015; Dickson et al. 2017; Dickson et al. 2013). They have demonstrated that microaspiration from the oral cavity is the main pathway for the bacterial immigration to healthy lungs. So, the lungs of healthy people are a habitat with a low bacterial biomass, which is constantly renewed (Dickson and Huffnagle 2015; Dickson et al. 2017; Dickson et al. 2013). The nasopharyngeal microbiota is the second main entry route for bacteria into the lungs and contributes relatively little to the lung microbiota. The microbiota of the nasopharynx has a microbial composition more characteristic of the skin (Dickson et al. 2017; Dickson et al. 2013). One of the first studies on the bacterial composition of the respiratory tract in patients with bronchial asthma (BA) and chronic obstructive pulmonary disease (COPD) was carried out by M. Hilty et al. in 2010. The authors studied brush biopsies and samples of Bronchoalveolar lavage from the lower respiratory tract. It was found that the Proteobacteria type and most notably the Haemophilus species are contained in patients with BA and COPD more frequently than in healthy individuals (Hilty et al. 2010). It is likely that a number of conditions contribute to changes in the lung microbiota in chronic pulmonary diseases (Dickson and Huffnagle 2015; Dickson et al. 2017; Dickson et al. 2013; Wu et al. 2003): • Hyperventilation: the influx of bacteria from air is accelerated, and the incoming air temperature is reduced significantly; • Cough: the microbial elimination and the inflammatory cells activity are increased;

258

O. Zolnikova and V. Ivashkin

• Hyperproduction of proinflammatory cytokines, catecholamine, glucose, and the free forms of oxygen that create favorable conditions for the growth of some bacteria; • Bronchoconstriction: it is associated with changes in the oxygen concentration and pH; • Higher vascular permeability and mucus production, which enhance the nutritional support of bacteria and also create additional gradients of local hypoxia and hyperthermia. In addition, in response to trigger agents (viruses, bacteria, allergens), a cascade of the inflammatory reactions is launched with the involvement of alveolar macrophages, neutrophils, eosinophils, dendritic cells, and lymphocytes, which dramatically changes microbial growth. For example, the excessive production of proinflammatory cytokines (TNF-α, IL-1, IL-6, IL-8) directly activates the growth of such bacteria as P. aeruginosa, S. aureus, S. pneumonia, B. cepacia (Wu et al. 2003; Tanoue et al. 2016; Sivan et al. 2015; Schmidt 2011; Schmidt et al. 2014). It is important to note that some of the microbes have modified virulence factors, which makes them more aggressive and increases their immunogenicity. The abovementioned factors contribute to the further development of inflammation by increasing the expression of pathogen-associated molecular structures (lipopolysaccharides, flagellins) activating the pathogen-bound receptors (e.g., toll-like receptors) (Rabe et al. 2020; Lin and Zhang 2017). For example, there is a very active discussion in the literature about the colonization of the bronchial tree by gram-negative bacteria of the Prevotella spp. genus that constitute the human commensal microbiota. It has been noted that some strains of Prevotella cause neutrophilic infiltration of the bronchial tree associated with TLR2 activation (Larsen et al. 2015). Moreover, Prevotella bacteria were more frequently detected in individuals with severe COPD and in patients receiving glucocorticosteroids (Bassis et al. 2015). So, the result of the Prevotella influence to the immune response needs additional clarification. As it was obtained in experiments that Prevotella can reduce the level of the IL-12p70 induced by the Haemophilus infection, but it does not affect the IL-10 level. According to the authors, this fact could indicate a possible connection between the subclinical course of inflammatory changes in the lungs and Prevotella spp. (Bassis et al. 2015; Larsen et al. 2015). The studies available to date tend to focus on the bacterial component of the microbiota. However, it should be taken into account that the stability and diversity of the microbial population are also maintained by the symbiotic relationships of viruses and fungi, not just by bacteria only. Thus, the viral–bacterial interaction can affect the composition of the resident microbiota to launch a transition from the colonizing potential pathogens to infectious agents (Zolnikova et al. 2018; Bosch et al. 2013). The presence of respiratory viruses increases the frequency of colonization of the bronchopulmonary system by S. pneumoniae, H. influenza, M. catarrhalis bacteria. For example, it was found that he rhinovirus and respiratory syncytial viruses are associated with an increasing risk of the H. influenza

The Human Microbiome and Respiratory Diseases

259

colonization (Avadhanula et al. 2006). The potential mechanisms underlying virusinduced changes in the bacterial spectrum were investigated in vitro and in experimental animal models. The obtained results demonstrate that the bacterial adhesion and translocation increase because of the direct damage to the epithelial barrier that suppresses various components of the innate immune system (Avadhanula et al. 2006; Bosch et al. 2008; Van de Flier et al. 1995; McNamee and Harmsen 2006; Small et al. 2010; Sun and Metzger 2008).

3 Gut–Lung Axis The literature discusses the hypothesis that the lungs and intestines could have a similar bacterial spectrum formed during the early postnatal period, which contributes to the development of some diseases of the bronchopulmonary system (Frati et al. 2018). However, there are no convincing evidences to support the hypothesis. The possibility of interaction between the intestine and the lungs through the microbiota has now been established. This kind of “the human organs dialogue” is named the “gut–lung” axis (Frati et al. 2018) and suggests that the changes in one of the biotopes can affect the other, both in terms of the microbial composition and functional activity of the respiratory and the gastrointestinal tracts. An interaction of the compartments may be realized by the next pathway. The microbiota and the products of its metabolism (short-chain fatty acids), as well as the immune cells, are activated in the lamina propria of the intestinal mucosa, migrate to the mesenteric lymph nodes followed by activation and changes in the differentiation of the T-regulatory lymphocytes and B-cells (Zolnikova et al. 2018; Clemente et al. 2012; Kåhrström et al. 2016; Kumar et al. 2016; Kuwahara 2014). Later on, due to the systemic circulation (with blood and lymph flow), the immune cells get a direct access both to the lymph nodes of the lungs and to the lung parenchyma. In addition, it leads to an activation of the dendritic cells, macrophages, and T lymphocytes and changes their differentiation. Thus, the effects of the gut microbiota reach the bronchial epithelium and modify the immune response that depends on the profile of the activated cells (Th1, Th2) (Zolnikova et al. 2018; Clemente et al. 2012; Kåhrström et al. 2016; Kumar et al. 2016; Kuwahara 2014) (Fig. 1). It has been established that the pulmonary dendritic cells interact with leukocyte translocation receptors (integrins) that determine the migration of cells to the intestinal mucosa and the associated lymphoid, thus participating in formatting and support of mucosal immunity (Huang et al. 2013; Kåhrström et al. 2016; Christensen and Pestka 2002; Parker et al. 2016). Coopersmith et al. (2003) and He et al. (2017) have demonstrated that pneumonia caused by Pseudomonas aeruginosa decreases a proliferation of the intestinal epithelium and blocks the M-phase of the epithelial cell cycle (Coopersmith et al. 2003; He et al. 2017). The obtained experimental results demonstrated the increasing numbers of Enterobacteriacea and the decreasing numbers of Lactobacillus and

260

O. Zolnikova and V. Ivashkin

Fig. 1 Model of the regulatory effect of short-chain fatty acids on the immunological response of the respiratory tract. Butyrate, propionate, and acetate bind to the G-protein receptors GPR43 and GPR41. Butyrate also interacts with GPR109A and receptors that activate peroxisome proliferation (PPAR-γ). All SCFAs affect the function of nuclear transcription factor (NF-kB) and dendritic cells (DC), thereby modulating the activity of Treg lymphocytes and various regulatory cytokines (IL-10, TGF-α, INF-γ, IL-6). Systemic circulation with the bloodstream and lymph provides access of regulatory cytokines and SCFAs to the lungs where they participate in immune and antiinflammatory reactions, thereby maintaining the gut–lung axis connection

Lactococcus in the intestinal microbiota in mice infected with the influenza virus (Looft and Allen 2012). The administration of lipopolysaccharide by inhalation to mice has also led to changes in the taxonomic spectrum of the gut microbiota (Sze et al. 2014). Interesting data were obtained regarding IgA. It was found that the commensal bacteria regulate the synthesis of IgA maintaining a harmonious interaction between the bacteria and the host. The role of IgA has been extensively studied in the gastrointestinal tract (Pabst and Slack 2020; Huus et al. 2021), but the recent results allow to suggest that similar mechanisms also exist in the bronchopulmonary system (Evsyutina et al. 2017; Daniel et al. 2021). Ichiohe et al. (2011) have demonstrated the participation of bacteria from the intestinal biotope in the antiviral immune response of the respiratory tract. The altered gut microbiota, which was obtained by long-term antibiotic administration (for 3 weeks), decreased the resistance of the tested laboratory animals to the influenza A virus infection (Ichiohe et al. 2011). This manifested in high viral titers and decreased IgA, IgG, CD8+, and CD4+ T cells. The administration of peptidoglycans of the commensal bacteria, which served as the TLR ligands, restored the antiviral immune response in those laboratory animals (Ichiohe et al. 2011).

The Human Microbiome and Respiratory Diseases

261

So, all of the above-mentioned results confirm that the gut–lung axis is a bond in two directions, which is accompanied by changes in the immune response of both biotopes.

4 Bronchial Asthma and Microbiota The pathogenesis of bronchial asthma (BA) has been studied for more than one century. It has been confirmed that this disease develops as a result of the complex interactions of the genetic factors and environment which have determined the different phenotypes of the disease. Recently, scientists have focused on the study of the role of the human microbiota in the origin and development of bronchial asthma. Epidemiological studies have shown that the influence of microbes on the organism in childhood is a factor determining the development of atopic diseases (Olszak et al. 2012; Ownby et al. 2002; Riedler et al. 2001; Thursby and Juge 2017). Atopy in childhood, with a polarization of the immune response toward the type 2 T-helpers (Th2), is a risk factor for the development of bronchial asthma (Tanoue et al. 2016; Russel et al. 2013; Sullivan et al. 2016; Van De Pol et al. 2010). This includes both the intestinal microbiota and the respiratory microbiota. At some point, this led to the development of the so-called hygienic hypothesis (Kåhrström et al. 2016; Looft and Allen 2012; Olszak et al. 2012; Russel et al. 2013; Stiemsma and Turvey 2017; Cani 2018; Clemente et al. 2012). The essence of the hypothesis is that reduced exposure to pathogens leads to the inadequate immune response. Also, it is known that the use of antibiotics at an early age potentiates the development of allergies, sensitization, and bronchial asthma (Fig. 2). It is confirmed by a lot of experimental studies (van Tilburg and Arrieta 2017; Russell et al. 2012; Kaiser 2015; Crane and Wickens 2014). One of the first clinical studies to confirm the role of the microbiota in the development of bronchial asthma was carried out in Denmark. It revealed a correlation between the presence of M. catarrhalis, H. influenzae, S. pneumoniae in the oropharynx of newborns and the subsequent development of BA in result of the studies (Thursby and Juge 2017; Russel et al. 2013; Bisgaard et al. 2007; Bisgaard et al. 2010; Simpson et al. 2016).

Fig. 2 Relationship between the development of microbiota and asthma. Environmental exposures affect the composition of the microbiota; the microbiota shape the rate and nature of immune function development; differences in immune function determine the nature and intensity of response to allergens and viruses encountered

262

O. Zolnikova and V. Ivashkin

A few years later, by sequencing 16S ribosomal RNA, it was found that the number of pathogenic Proteobacteria (for example, Haemophilus) was significantly higher and the number of Bacteroidetes, especially the bacteria of the Prevotella genus, was significantly lower in patients with BA compared to healthy individuals (Hilty et al. 2010; Huang et al. 2011). Another study demonstrated a correlation of the bronchial hyperactivity to the increase in the Comamonadaceae, Sphingomonadaceae, and Oxalobacteraceae families (belonging to the Proteobacteria type) (Huang et al. 2011). It is interesting that the colonization process by some pathogenic bacteria is clearly associated with immune response (Ege et al. 2011; Fujimura and Lynch 2015; Mukhopadhya et al. 2012). So, with a high number of M. catarrhalis and H. influenza, the production of IL-1, IL-17 increases, which indicates the development of Th1 and Th17 immune responses. The increase of S. aureus bacteria number is associated with a hyperproduction of IL-17 (Mukhopadhya et al. 2012; Følsgaard et al. 2013). In connection with that, it was assumed that the bacterial communities play a role in the determination of the asthma endotype by regulating the balance between the Th2 and Th17 cell patterns (Adami and Bracken 2016). The microbiota composition was found to vary different in patients depending on the disease severity. Thus, in patients with severe persistent BA compared to those with mild and moderate severity of the disease, increased content (by 7–8 times) of the Klebsiella (Proteobacteria type) was observed (Denner et al. 2016). In another study, patients with non-severe BA had a higher number of Fusobacteria and Bacteroidetes compared to healthy volunteers. The number of Bacteroidetes (odds ratio = 0.62) and Fusobacteria (odds ratio = 0.38) were reduced in severe BA. In patients with BA, the twofold increase of the pathogenic Proteobacteria (Neisseria, Moraxella spp.) was observed. A positive correlation was found for the asthma severity to the Streptococcus (Streptococcus spp., Streptococcus_23, Streptococcus_155) level and the opposite correlation was to the number of Prevotella spp. (Zhang et al. 2016). It was found that the microbiota composition of the respiratory tract is associated with the degree of obstruction and hypersensitivity in patients with BA. Neisseriaceae, Comamonadaceae, Pseudomonadaceae, and Sphingomonadaceae have been reported to correlate with the degree of bronchial hypersensitivity, and a low bacterial diversity correlates with severe disturbances of airflow (Huang et al. 2015; Huang et al. 2017). An increase in the Actinobacteria content in the respiratory microbiota correlates with the ventilation function improvement of the lungs (Huang et al. 2017). The microbiota composition varies depending on the disease phenotype in patients. The microbiota in sputum samples, which were obtained from patients with the poorly controlled neutrophilic asthma, was less diverse compared to the taxonomic composition of the microbiota of patients with an IgE-mediated (atopic) asthma phenotype (Denner et al. 2016). To date, it is discussed that the microbiota composition determines sensitivity to glucocorticosteroid therapy (Durack et al. 2016; Durack et al. 2017). Thus,

The Human Microbiome and Respiratory Diseases

263

Haemophilus, Campylobacter, and Leptotrichia were detected in the microbiota of the low respiratory tract in patients with corticosteroid-resistant BA, while these bacteria were not observed in patients with a sensitivity to corticosteroids (Goleva et al. 2013). According to the authors, bronchoalveolar lavage macrophages activated by H. influenzae induce the production of the proinflammatory cytokines IL-8 formatting a reduced response to corticosteroid therapy (Goleva et al. 2013). The induction of the H. influenza steroid resistance was also demonstrated in the mouse model of asthma (Essilfie et al. 2012; Green et al. 2014). It is interesting to note that the treatment with corticosteroids also has a direct effect on the activity of H. influenza by causing the formation of biofilm by the microorganism and resistance of microorganisms to azithromycin (Earl et al. 2015a, b; Slater et al. 2014). It has been demonstrated that the use of the inhaled and oral corticosteroids for the disease treatment is associated with an increase in the number of Proteobacteria and Pseudomonas and a decrease in Bacteroidetes, Fusobacteria, and Prevotella (Stokholm et al. 2018). However, some studies have demonstrated that the number of Proteobacteria increases in asthmatics, regardless of the ongoing drug therapy (Ozdemir 2018; Mukhopadhya et al. 2012; Huang et al. 2015; Park et al. 2014). Thus, it can be concluded that the increase in the Proteobacteria number is associated with the disease itself and not with the effect of corticosteroids. Recently, researchers have detected a mechanism which allows the commensal microbiota to regulate basophil function influencing the susceptibility of the Th2 immune response. It was also found that oral antibiotics increase IgE concentrations and the level of circulated basophil in serum, which causes excessive Th2 inflammation. The expression of the mitogen-activated protein kinase MyD88 by B-cells serves as an important step in increasing serum levels of IgE and basophils by activation of Toll-like receptors and nuclear transcription factor (NF-kB). Usually, the MyD88 expression is blocked by healthy microbiota and the allergic inflammation development of airways does not occur (Herbst et al. 2011; Hill et al. 2012). Canadian researchers have identified four bacterial taxa in newborns, which prevent the asthma development in adulthood, in their opinion. They have reported changes in the Faecalibacterium, Lachnospira, Veillonella, and Rothia (FLVR) content (Arrieta 2015). The addition of those bacteria to the experimental animals showed a reduction in the allergic inflammation of airways compared to the control group. Intestine colonization by FLVR promotes an increase in the short-chain fatty acids (SCFA) content, predominantly acetate, and is likely to prevent the BA development (Trompette et al. 2014). The role of Faecalibacterium, Lachnospira in the BA development was discussed by Stokholm et al. 2018. They have concluded that those microorganisms have a high prognostic significance for that (Stokholm et al. 2018). The mechanism by which the microbiota-produced SCFAs reduce hyperreactivity and allergic inflammation of the respiratory tract is not always clear. It was found that low levels of acetate in three-month-old infants’ feces were associated with an increased risk of the BA development (Theiler et al. 2019). Clear correlations were found between the SCFA values and the eosinophils levels and

264

O. Zolnikova and V. Ivashkin

also between the production level of proinflammatory cytokines and the degree of bronchoconstriction in the presented experimental models (Venkataraman et al. 2015). Some authors suggest that all SCFAs have the same effect on protection against allergic inflammation because of their interaction with GPR41 (Theiler et al. 2019; Kim et al. 2016). According to other data, butyric acid (butyrate) has a more pronounced antiallergic effect (Trompette et al. 2014; Theiler et al. 2019). Also known is the influence of SCFAs on the changing cytokines level and on the expression of the co-stimulated molecules of the dendritic cells (CD80, CD86, CD40), which leads to a changing ability of the latter to interact with regulatory T lymphocytes (Larsen et al. 2012). There is information in the published articles on the participation of intestinal bacteria in the metabolism of biogenic amines, particularly of histamine. It has been demonstrated that in dysbiosis the number of bacteria with high decarboxylation activity, i.e., ones are able to produce histamine from histidine in the intestines, increases in patients with asthma (Jutel et al. 2009; MacGlashan 2003). It is also known that the changed intestinal mucosa against the background of dysbiosis does not produce histaminase or diamine oxidase, i.e., the enzymes involved in the metabolism of dietary histamine, in the required amount (Jutel et al. 2009; MacGlashan 2003). Against the background of increased intestinal permeability, histamine is absorbed actively. An increase of the histamine level in patients with BA is also facilitated by a decrease in the enzyme histamine-N-methyltransferase activity, which is responsible for the catabolism of histamine in the bronchial epithelium (MacGlashan 2003; Smolinska et al. 2014). However, it is not clear yet, which of the receptors (H1, H2, H3, H4) could interact with this histamine and what effect could be there (MacGlashan 2003). Some authors suggest its participation in the development and intensification of bronchospasm in asthmatics against the background of a violation of the microflora composition (MacGlashan 2003). The results of our studies of the microbiota composition in patients with BA were published earlier (Sánchez-Pérez et al. 2022; Costa et al. 2022; Mou et al. 2021; Hu et al. 2021). We have found changes in the intestinal microbiota composition, namely the increased number of bacteria of the Proteobacteria type (Zolnikova et al. 2020a). There was a marked decrease in the content of bacteria produced by short-chain fatty acids Faecalibacterium and Anaerostipes (Firmicutes type) and Bacteroidetes (Alistipes, p < 0.05). In patients with BA, the metabolic activity of the intestinal microbiota was reduced: the total content of SCFAs in feces was reduced ( p < 0.001) and the absolute concentrations of acetate, propionate, and butyrate were reduced also ( p < 0.001) (Ivashkin et al. 2018; Ivashkin et al. 2019). A decrease in the metabolic activity of bacteria in the intestinal biotope was correlated to the level of the immune response. An abnormality of the gut microbiota in the form of SIBO (small intestinal bacterial overgrowth) was associated with a more severe atopic BA (Ivashkin et al. 2019; Potskhverashvili et al. 2018; Zolnikova et al. 2020b). In the oropharyngeal microbiota of patients with bronchial asthma, changes of the Firmicutes type, Bacteroidetes type, and Fusobacteria type were observed ( p < 0.05) (Zolnikova et al. 2020c).

The Human Microbiome and Respiratory Diseases

265

An important factor requiring a separate discussion is the change of the ventilation-perfusion ratios in the lung of patients with BA. In that case, the decreased carbon dioxide and hydrogen excretion leads to its reabsorption, which affects the value of the redox potential of the intraluminal medium (Eh) (Charlson et al. 2011; Charlson et al. 2012; Bassis et al. 2015). It is known from literature that the existence and active development of the certain bacteria type occurs at the appropriate values of the redox potential of the intraluminal medium. Thus, a decrease or increase of the Eh value determines the growth of the specific microorganisms. The redox potential is an important feature of the human internal space, influenced both by the host organism and the microbial environment. In the large intestine, as in an “anaerobic organ,” the negative Eh value is supported by a number of factors. Its value is determined by the sodium pumps that work on the epithelial cells’ plasma membrane, surface glycoproteins, as well as various gaseous molecular bacterial metabolites (N2, O2, H2, CH4, CO2, H2S, NH3, CO). It is known that the shift of the Eh of the intraluminal medium to the more negative values direction creates a favorable environment for the anaerobic microorganisms’ growth, while the small negative Eh values are preferred for aerobes. Thus, the redox potential determines the stability and growth of bacteria in the intestinal biotope and its biological activity direction (Fig. 3).

Fig. 3 Model of changes in the redox potential of the intraluminal medium (Eh) in patients with bronchial asthma. The value of Eh is influenced by both host and microbiota metabolites. The value of Eh is determined by the work of sodium pumps on the epithelial cells’ plasma membrane, surface glycoproteins, gaseous molecular bacterial metabolites (N2, O2, H2, CH4, CO2, H2S, NH3, CO). Сhanges in Еh are accompanied by aerobic or anaerobic bacterial predominance

266

O. Zolnikova and V. Ivashkin

In patients with bronchial asthma, the changing Eh could be a significant factor that aggravates the abnormalities of the microbiota. The noted pathogenic mechanism is not to be underestimated. However, it should be clarified because there are no studies of that subject in the published data yet. The published results demonstrate the influence of microbiota on the human circadian rhythms (Liang and Bushman 2015). In this connection, it has been suggested that they are related to the disease course, as well as to the formatting of sensitivity of the patients to the ongoing standard BA therapy (Gibbs et al. 2014).

5 Conclusion The discovery of the role of the microbiota in the vital functions of the human body allows getting a novel look at the pathogenesis of multiple diseases including bronchial asthma. However, the researches do not yet have a clear understanding of which biological samples and specimens should be investigated for a deeper study of the lung microbiota. There are still a lot of questions like: How does the gut–lung axis form in a newborn, and how could its dynamics be unaffected by the changing life style? Moreover, the microbiota composition in adults and children with different BA duration and phenotype has not been sufficiently studied. Studies on the efficacy of probiotics in adults are scarce. There is no answer yet regarding the most effective strains of microorganisms that should be used in treatment. When should treatment be started? What should be the duration of therapy? Looking for answers to these questions prompts new research to substantiate and better understand the potential of administration of probiotic cultures to patients with bronchial asthma.

References Adami AJ, Bracken SJ (2016) Breathing better through bugs: asthma and the microbiome. Yale J Biol Med 89(3):309–324. PMID: 27698615 Arrieta M (2015) Early infancy microbial and metabolic alterations affect risk of childhood asthma. Sci Transl Med 7:307–312. https://doi.org/10.1126/scitranslmed.aab2271 Avadhanula V, Rodriguez CA, Devincenzo JP (2006) Respiratory viruses augment the adhesion of bacterial pathogens to respiratory epithelium in a viral species- and cell type-dependent manner. J Virol 6:1629–1636. https://doi.org/10.1128/JVI.80.4.1629-1636.2006 Bassis CM, Erb-Downward JR, Dickson RP (2015) Analysis of the upper respiratory tract microbiotas as the source of the lung and gastric microbiota in healthy individuals. mBio 6 (2):e00037-15. https://doi.org/10.1128/mBio.00037-15 Bisgaard H, Hermansen MN, Bønnelykke K et al (2010) Association of bacteria and viruses with wheezy episodes in young children: prospective birth cohort study. BMJ 341:c4978. https://doi. org/10.1136/bmj.c4978 Bisgaard H, Hermansen MN, Buchvald F et al (2007) Childhood asthma after bacterial colonization of the airway in neonates. N Engl J Med 357:1487–1495. https://doi.org/10.1056/ NEJMoa052632

The Human Microbiome and Respiratory Diseases

267

Bosch A, Biesbroek G, Trzcinski K (2013) Viral and bacterial interactions in the upper respiratory tract. PLoS Pathog 9:e1003057. https://doi.org/10.1371/journal.ppat.1003057 Bosch A, Sajjan U, Wang Q et al (2008) Rhinovirus disrupts the barrier function of polarized airway epithelial cells. Am J Respir Crit Care Med 178:1271–1281. https://doi.org/10.1164/rccm. 200801-136OC Cani P (2018) Human gut microbiome: hopes, threats and promises. Gut 0:1–10. https://doi.org/10. 1136/gutjnl-2018-316723 Charlson ES, Bittinger K, Haas AR (2011) Topographical continuity of bacterial populations in the healthy human respiratory tract. Am J Respir Crit Care Med 184:957–963. https://doi.org/10. 1164/rccm.201104-0655OC Charlson ES, Diamond JM, Bittinger K et al (2012) Lung-enriched organisms and aberrant bacterial and fungal respiratory microbiota after lung transplant. Am J Respir Crit Care Med 186:536– 545. https://doi.org/10.1164/rccm.201204-0693OC Christensen HR, Pestka J (2002) Lactobacilli differentially modulate expression of cytokines and maturation surface markers in murine dendritic cells. J Immunol 168:171–178. https://doi.org/ 10.4049/jimmunol.168.1.171 Clemente JC, Ursell LK, Parfrey LW et al (2012) The impact of the gut microbiota on human health: an integrative view. Cell 148(6):1258–1270. https://doi.org/10.1016/j.cell.2012.01.035 Coopersmith CM, Stromberg PE, Davis CG et al (2003) Sepsis from Pseudomonas aeruginosa pneumonia decreases intestinal proliferation and induces gut epithelial cell cycle arrest. Crit Care Med 31:1630–1637. https://doi.org/10.1097/01.CCM.0000055385.29232.11 Costa A, Rani B, Bastiaanssen TFS et al (2022) Diet prevents social stress-induced maladaptive Neurobehavioural and gut microbiota changes in a histamine-dependent manner. Int J Mol Sci 23(2):862. https://doi.org/10.3390/ijms23020862 Crane J, Wickens K (2014) Antibiotics and asthma: a tricky tributary of the hygiene hypothesis. Lancet Respir Med 2(8):595–597. https://doi.org/10.1016/S2213-2600(14)70109-2 Daniel S, Pusadkar V, McDonald J et al (2021) Traffic generated emissions alter the lung microbiota by promoting the expansion of proteobacteria in C57Bl/6 mice placed on a highfat diet. Ecotoxicol Environ Saf 213:112035. https://doi.org/10.1016/j.ecoenv.2021.112035 Denner DR, Sangwan N, Becker JB et al (2016) Corticosteroid therapy and airflow obstruction influence the bronchial microbiome, which is distinct from that of bronchoalveolar lavage in asthmatic airways. J Allergy Clin Immunol 137:1398–1405. https://doi.org/10.1016/j.jaci.2015. 10.017 Dickson RP, Erb-Downward JR, Freeman CM (2017) Bacterial topography of the healthy human lower respiratory tract. MBio 8:e02287–e02216. https://doi.org/10.1128/mBio.02287-16 Dickson RP, Erb-Downward JR, Huffnagle GB (2013) The role of the bacterial microbiome in lung disease. Expert Rev Respir Med 7:245–257. https://doi.org/10.1586/ers.13.24 Dickson RP, Huffnagle GB (2015) The lung microbiome: new principles for respiratory bacteriology in health and disease. PLoS Pathog 11:e1004923. https://doi.org/10.1371/journal.ppat. 1004923 Durack J, Boushey H, Lynch S (2016) Airway microbiota and the implications of dysbiosis in asthma. Curr Allergy Asthma Rep 16:52–65. https://doi.org/10.1007/s11882-016-0631-8 Durack J, Lynch S, Nariya S et al (2017) Features of the bronchial bacterial microbiome associated with atopy, asthma, and responsiveness to inhaled corticosteroid treatment. J Allergy Clin Immunol 140:63–75. https://doi.org/10.1016/j.jaci.2016.08.055 Earl CS, An SQ, Ryan RP (2015b) The changing face of asthma and its relation with microbes. Trends Microbiol 23:408–418. https://doi.org/10.1016/j.tim.2015.03.005 Earl CS, Keong TW, Murdoch S et al (2015a) Haemophilus influenzae responds to glucocorticoids used in asthma therapy by modulation of biofilm formation and antibiotic resistance. EMBO Mol Med 7(8):1018–1033. https://doi.org/10.15252/emmm.201505088 Ege MJ, Mayer M, Normand AC et al (2011) Exposure to environmental microorganisms and childhood asthma. N Engl J Med 364:701–709. https://doi.org/10.1056/NEJMoa1007302

268

O. Zolnikova and V. Ivashkin

Essilfie AT, Simpson JL, Dunkley ML et al (2012) Combined Haemophilus influenzae respiratory infection and allergic airways disease drives chronic infection and features of neutrophilic asthma. Thorax 67(7):588–599. https://doi.org/10.1136/thoraxjnl-2011-200160 Evsyutina Y, Komkova I, Zolnikova O et al (2017) Lung microbiome in healthy and diseased individuals. World J Respirol 7(2):39–47. https://doi.org/10.5320/wjr.v7.i2.39 Følsgaard NV, Schjørring S, Chawes BL et al (2013) Pathogenic bacteria colonizing the airways in asymptomatic neonates stimulates topical inflammatory mediator release. Am J Respir Crit Care Med 187:589–595. https://doi.org/10.1164/rccm.201207-1297OC Frati F, Salvatori С, Incorvaia С et al (2018) The role of the microbiome in asthma: the gut–lung axis. Int J Mol Sci 20:123–135. https://doi.org/10.3390/ijms20010123 Fujimura KE, Lynch SV (2015) Microbiota in allergy and asthma and the emerging relationship with the gut microbiome. Cell Host Microbe 17:592–602. https://doi.org/10.1016/j.chom.2015. 04.007 Gallaracher DJ, Kotecha S (2016) Respiratory microbiome of new-born infants. Front Pediatr 4:10– 15. https://doi.org/10.3389/fped.2016.00010 Gibbs J, Ince L, Matthews L et al (2014) An epithelial circadian clock controls pulmonary inflammation and glucocorticoid action. Nat Med 20(8):919–926. https://doi.org/10.1038/nm. 3599 Goleva E, Jackson L, Harris J et al (2013) The effects of airway microbiome on corticosteroid responsiveness in asthma. Am J Respir Crit Care Med 188:1193–1201. https://doi.org/10.1164/ rccm.201304-0775OC Green BJ, Wiriyachaiporn S, Grainge C et al (2014) Potentially pathogenic airway bacteria and neutrophilic inflammation in treatment resistant severe asthma. PLoS One 9(6):e100645. https:// doi.org/10.1371/journal.pone.0100645 He Y, We Q, Yao F et al (2017) Gut-lung axis: the microbial contributions and clinical implications. Crit Rev Microbiol 43:81–95. https://doi.org/10.1080/1040841X.2016.1176988 Herbst T, Sichelstiel A, Schear C (2011) Dysregulation of allergic airway inflammation in the absence of microbial colonization. The American Journal of Respiratory and Critical Care Medicine 2:198–205. https://doi.org/10.1164/rccm.201010-1574OC Hill DA, Siracusa MC, Abt MC et al (2012) Commensal bacteria-derived signals regulate basophil hematopoiesis and allergic inflammation. Nat Med 18(4):538–546. https://doi.org/10.1038/nm. 2657 Hilty M, Burke C, Pedro H et al (2010) Disordered microbial communities in asthmatic airways. PLoS One 5(1):e8578. https://doi.org/10.1371/journal.pone.0008578 Hogan DA, Willger SD, Dolben EL et al (2016) Analysis of lung microbiota in bronchoalveolar lavage, protected brush and sputum samples from subjects with mild-to-moderate cystic fibrosis. Lung disease. PLoS One 11(3):e0149998. https://doi.org/10.1371/journal.pone.0149998 Hu B, Kuang Y, Jing Y et al (2021) Pediatric allergic rhinitis with functional gastrointestinal disease: associations with the intestinal microbiota and gastrointestinal peptides and therapeutic effects of interventions. Hum Exp Toxicol 40(11):2012–2021. https://doi.org/10.1177/ 09603271211017325 Huang Y, Marsland B, Bunyavanich S et al (2017) The microbiome in allergic disease: current understanding and future opportunities-2017 PRACTALL document of the American Academy of Allergy, Asthma & Immunology and the European academy of allergy and clinical immunology. J Allergy Clin Immunol 139(4):1099–1110. https://doi.org/10.1016/j.jaci.2017.02.007 Huang YJ, Charlson ES, Collman RG et al (2013) The role of the lung microbiome in health and disease. A National Heart, Lung, and Blood Institute workshop report. Am J Respir Crit Care Med 187:1382–1387. https://doi.org/10.1164/rccm.201303-0488WS Huang YJ, Nariya S, Harris JM et al (2015) The airway microbiome in patients with severe asthma: associations with disease features and severity. J Allergy Clin Immunol 136(4):874–884. https:// doi.org/10.1016/j.jaci.2015.05.044

The Human Microbiome and Respiratory Diseases

269

Huang YJ, Nelson CE, Brodie EL et al (2011) Airway microbiota and bronchial hyperresponsiveness in patients with suboptimally controlled asthma. J Allergy Clin Immunol 127:372–381. https://doi.org/10.1016/j.jaci.2010.10.048 Huus KE, Petersen C, Finlay BB (2021) Diversity and dynamism of IgA-microbiota interactions. Nat Rev Immunol 21(8):514–525. https://doi.org/10.1038/s41577-021-00506-1 Ichiohe T, Pang IK, Kumamoto Y (2011) Microbiota regulates immune defense against respiratory tract influenza a virus infection. Proc Natl Acad Sci U S A 108(13):5354–5359. https://doi.org/ 10.1073/pnas.1019378108 Integrative HMP (iHMP) Research Network Consortium (2019) The integrative human microbiome project. Nature 569(7758):641–648. https://doi.org/10.1038/s41586-019-1238-8 Ivashkin V, Zolnikova O, Potskherashvili N et al (2018) A correction of a gut microflora composition for the allergic bronchial asthma complex therapy. Italian J Med 12:260–264. https://doi. org/10.4081/itjm.2018.1040 Ivashkin V, Zolnikova O, Potskherashvili N et al (2019) A metabolic activity of the intestinal microflora in patients with bronchial asthma. Clinics and Practice 9:1126. https://doi.org/10. 4081/cp.2019.1126 Jutel M, Akdis M, Akdis CA (2009) Histamine, histamine receptors and their role in immune pathology. ClinExp Allergy 39:1786–1800. https://doi.org/10.1111/j.1365-2222.2009.03374.x Kåhrström CT, Pariente N, Weiss U (2016) Intestinal microbiota in health and disease. Nature 535(7610):47. https://doi.org/10.1038/535047a Kaiser J (2015) How farm life prevents asthma. Science 349(6252):1034. https://doi.org/10.1126/ science.349.6252.1034 Kim M, Qie Y, Park J et al (2016) Gut microbial metabolites fuel host antibody responses. Cell Host Microbe 20:202–214. https://doi.org/10.1016/j.chom.2016.07.001 Kumar M, Babaei P, Ji B et al (2016) Human gut microbiota and healthy aging: recent developments and future prospective. Nutr Healthy Aging 4:3–16. https://doi.org/10.3233/ NHA-150002 Kuwahara A (2014) Contributions of colonic short-chain fatty acid receptors in energy homeostasis. Front Endocrinol 5:144. https://doi.org/10.3389/fendo.2014.00144 Larsen JM, Steen-Jensen DB, Laursen JM (2012) Divergent pro-inflammatory profile of human dendritic cells in response to commensal and pathogenic bacteria associated with the airway microbiota. PLoS One 7(2):e31976. https://doi.org/10.1371/journal.pone.0031976 Larsen JP, Musavian HS, Butt TM (2015) Chronic obstructive pulmonary disease and asthmaassociated proteobacteria, but not commensal Prevotella spp., promote toll-like receptor 2-independent lung inflammation and pathology. Immunology 144(2):333–342. https://doi. org/10.1111/imm.12376 Liang X, Bushman FD (2015) Rhythmicity of the intestinal microbiota is regulated by gender and the host circadian clock. Proc Natl AcadSci USA 112(33):10479–10484. https://doi.org/10. 1073/pnas.1501305112 Lin L, Zhang J (2017) Role of intestinal microbiota and metabolites on gut homeostasis and human diseases. BMC Immunol 18:2. https://doi.org/10.1186/s12865-016-0187-3 Looft T, Allen HK (2012) Collateral effects of antibiotics on mammalian gut microbiomes. Gut Microbes 3:463–467. https://doi.org/10.4161/gmic.21288 MacGlashan D (2003) Histamine: a mediator of inflammation. J Allergy Clin Immunol 112(4): 53–59. https://doi.org/10.1016/s0091-6749(03)01877-3 Man WH, de Steenhuijsen Piters WA, Bogaert D (2017) The microbiota of the respiratory tract: gatekeeper to respiratory health. Nat Rev Microbiol 15:259–270. https://doi.org/10.1038/ nrmicro.2017.14 McNamee LA, Harmsen AG (2006) Both influenza-induced neutrophil dysfunction and neutrophilindependent mechanisms contribute to increased susceptibility to a secondary Streptococcus pneumoniae infection. Infect Immun 74:6707–6721. https://doi.org/10.1128/IAI.00789-06 Mou Z, Yang Y, Hall AB, Jiang X (2021) The taxonomic distribution of histamine-secreting bacteria in the human gut microbiome. BMC Genomics 22(1):695. https://doi.org/10.1186/ s12864-021-08004-3

270

O. Zolnikova and V. Ivashkin

Mukhopadhya I, Hansen R, El-Omar EM (2012) IBD-what role do proteobacteria play? Nat Rev Gastroenterol Hepatol 9:219–230. https://doi.org/10.1038/nrgastro.2012.14 O’Dwyer D, Dickson R, Moore B (2016) The lung microbiome, immunity, and the pathogenesis of chronic lung disease. J Immunol 196(12):4839–4847. https://doi.org/10.4049/jimmunol. 1600279 Olszak T, An D, Zeissig S et al (2012) Microbial exposure during early life has persistent effects on natural killer T cell function. Science 336:485–489. https://doi.org/10.1126/science.1219328 Ownby DR, Johnson CC, Peterson EL (2002) Exposure to dogs and cats in the first year of life and risk of allergic sensitization at 6 to 7 years of age. JAMA 288:963–972. https://doi.org/10.1001/ jama.288.8.963 Ozdemir O (2018) Microbial dysbiosis in allergic lower airway disease (asthma). MOJ Immunol 6(4):129–132. https://doi.org/10.15406/moji.2018.06.00207 Pabst O, Slack E (2020) IgA and the intestinal microbiota: the importance of being specific. Mucosal Immunol 13(1):12–21. https://doi.org/10.1038/s41385-019-0227-4 Park H, Shin JW, Park S-G et al (2014) Microbial communities in the upper respiratory tract of patients with asthma and chronic obstructive pulmonary disease. PLoS One 9(10):e109710. https://doi.org/10.1371/journal.pone.0109710 Parker D, Ahn D, Cohen T et al (2016) Innate immune signaling activated by MDR bacteria in the airway. Physiol Rev 96:19–53. https://doi.org/10.1152/physrev.00009.2015 Potskhverashvili ND, Zolnikova ОY, Kokina NI et al (2018) Small bowel bacterial overgrowth syndrome in patients with bronchial asthma. Russian journal of gastroenterology, hepatology. Coloproctology 28(4):47–54. https://doi.org/10.22416/1382-4376-2018-28-4-47-54 Rabe H, Lundell AC, Sjöberg F et al (2020) Neonatal gut colonization by Bifidobacterium is associated with higher childhood cytokine responses Gut Microbes 12(1):1–14. https://doi.org/ 10.1080/19490976.2020.1847628 Riedler J, Braun-Fahrlander C, Eder W et al (2001) Exposure to farming in early life and development of asthma and allergy: a cross-sectional survey. Lancet 358:1129–1133. https:// doi.org/10.1016/S0140-6736(01)06252-3 Russel SL, Gold MJ, Willing BP (2013) Perinatal antibiotic treatment affects murine microbiota, immune responses and allergic asthma. Gut Microbes 4(2):158–164. https://doi.org/10.4161/ gmic.23567 Russell SL, Gold MJ, Hartmann M et al (2012) Early life antibiotic-driven changes in microbiota enhance susceptibility to allergic asthma. EMBO Rep 13(5):440–447. https://doi.org/10.1038/ embor.2012.32 Sánchez-Pérez S, Comas-Basté O, Duelo A et al (2022) Intestinal dysbiosis in patients with histamine intolerance. Nutrients 14(9):1774. https://doi.org/10.3390/nu14091774 Schmidt LA (2011) Analysis of the lung microbiome in the “healthy” smoker and in COPD. PLoS One 6:e16384. https://doi.org/10.1371/journal.pone.0016384 Schmidt LA, Belaaouaj A, Bissinger R (2014) Neutrophil elastase-mediated increase in airway temperature during inflammation. J Cyst Fibros 13(6):623–631. https://doi.org/10.1016/j.jcf. 2014.03.004 Segal LN, Blaser MJ (2014) A brave new world: the lung microbiota in an era of change. Ann Am Thorac Soc 11(1):s21–s27. https://doi.org/10.1513/AnnalsATS.201306-189MG Simpson JL, Daly J, Baines KJ et al (2016) Airway dysbiosis: Haemophilus influenzae and Tropheryma in poorly controlled asthma. Eur Respir J 47(3):792–800. https://doi.org/10. 1183/13993003.00405-2015 Sivan A, Corrales L, Hubert N et al (2015) Commensal Bifidobacterium promotes antitumor immunity and facilitates anti-PD-L1 efficacy. Science 350:1084–1089. https://doi.org/10. 1126/science.aac4255 Slater M, Rivett DW, Williams L et al (2014) The impact of azithromycin therapy on the airway microbiota in asthma. Thorax 69(7):673–674. https://doi.org/10.1136/thoraxjnl-2013-204517 Small CL, Shaler CR, McCormick S (2010) Influenza infection leads to increased susceptibility to subsequent bacterial superinfection by impairing NK cell responses in the lung. J Immunol 184: 2048–2056. https://doi.org/10.4049/jimmunol.0902772

The Human Microbiome and Respiratory Diseases

271

Smolinska S, Jutel M, Crameri R, O’Mahony L (2014) Histamine and gut mucosal immune regulation. Allergy 69(3):273–281. https://doi.org/10.1111/all.12330 Stiemsma L, Turvey S (2017) Asthma and the microbiome: defining the critical window in early life. Allergy Asthma Clin Immunol 13:3–12. https://doi.org/10.1186/s13223-016-0173-6 Stokholm J, Blaser MJ, Thorsen J et al (2018) Maturation of the gut microbiome and risk of asthma in childhood. Nat Commun 9:141. https://doi.org/10.1038/s41467-017-02573-2 Sullivan А, Hunt Е, MacSharry J et al (2016) The microbiome and the pathophysiology of asthma. Respir Res 17:163–174. https://doi.org/10.1186/s12931-016-0479-4 Sun K, Metzger DW (2008) Inhibition of pulmonary antibacterial defense by interferon-γ during recovery from influenza infection. Nat Med 14:558–564. https://doi.org/10.1038/nm1765 Sze MA, Tsuruta M, Yang SW et al (2014) Changes in the bacterial microbiota in gut, blood, and lungs following acute LPS instillation into mice lungs. PLoS One 9:e111228. https://doi.org/10. 1371/journal.pone.0111228 Tanoue T, Atarashi K, Honda K (2016) Development and maintenance of intestinal regulatory T cells. Nat Rev Immunol 16:295–309. https://doi.org/10.1038/nri.2016.36 Theiler A, Bärnthaler T, Platzer W et al (2019) Butyrate ameliorates allergic airway inflammation by limiting eosinophil trafficking and survival. J Allergy Clin Immunol 144:764–776. https:// doi.org/10.1016/j.jaci.2019.05.002 Thursby E, Juge N (2017) Introduction to the human gut microbiota. Biochem J 474:1823–1836. https://doi.org/10.1042/BCJ20160510 Trompette A, Gollwitzer ES, Yadava K (2014) Gut microbiota metabolism of dietary fiber influences allergic airway disease and hematopoiesis. Nat Med 2:159–166. https://doi.org/10. 1038/nm.3444 Van de Flier M, Chunn N, Wizemann TM (1995) Adherence of Streptococcus pneumoniae to immobilized fibronectin. Infect Immun 63:4317–4322. https://doi.org/10.1128/iai.63.11. 4317-4322.1995 Van De Pol M, Lutter R, Smids B et al (2010) Synbiotics reduce allergen-induced T-helper 2 response and improve peak expiratory flow in allergic asthmatics. Allergy 66:39–47. https:// doi.org/10.1111/j.1398-9995.2010.02454.x van Tilburg BE, Arrieta M (2017) Hygiene hypothesis in asthma development: is hygiene to blame? Arch Med Res 48(8):717–726. https://doi.org/10.1016/j.arcmed.2017.11.009 Venkataraman A, Bassis C, Beck J et al (2015) Application of a neutral community model to assess structuring of the human lung microbiome. mBio 6:e02284-14. https://doi.org/10.1128/mBio. 02284-14 Wu H, Kuzmenko A, Wan S (2003) Surfactant proteins a and D inhibit the growth of gram-negative bacteria by increasing membrane permeability. J Clin Invest 111:1589–1602. https://doi.org/10. 1172/JCI16889 Yaung SJ, Church GM, Wang HH (2014) Recent Progress in engineering human-associated microbiomes. Methods Mol Biol 1151:3–25. https://doi.org/10.1007/978-1-4939-0554-6_1 Zhang Q, Cox M, Liang Z et al (2016) Airway microbiota in severe asthma and relationship to asthma severity and phenotypes. PLoS One 11(4):e0152724. https://doi.org/10.1371/journal. pone.0152724 Zolnikova O, Komkova I, Potskherashvili N et al (2018) Application of probiotics for acute respiratory tract infections. Italian J Med 12:32–38. https://doi.org/10.4081/itjm.2018.931 Zolnikova O, Potskhverashvili N, Kokina N et al (2020b) A change in the gut microbiota as a risk factor for asthma. Vrach 31(1):3–7. https://doi.org/10.29296/25877305-2020-01-01 Zolnikova O, Potskhverashvili N, Kokina N et al (2020c) The oropharyngeal microbiome change under bronchial asthma disease. Vrach 31(2):37–41. https://doi.org/10.29296/25877305-202002-08 Zolnikova ОY, Potskherashvili ND, Kudryavtseva AV et al (2020a) Changes in gut microbiota with bronchial asthma. Therap Arch 92(4):56–60. https://doi.org/10.26442/00403660.2020.03. 000554

Part III

Manipulation of the Human Microbiome for Better Health

Probiotics: An Emerging Strategy for Oral Health Care Subramani Parasuraman , Venkata Kanthi Vaishnavi Vedam, and Gokul Shankar Sabesan

Abstract The mouth (Synonym: Oral cavity) comprises a complex habitat with an abundant diversity of multifaceted and multivariate microbial species. More than 700 species of bacteria exist in the oral cavity. Microbial species residing in the oral cavity are termed as “oral microflora” and this resident microflora blocks the primary colonization of pathogens and provides protection to the host by a strong immune system, modulates the balance in the release of inflammatory cytokines, cell adhesion molecules, and growth factors, thereby aiding in maintaining the homeostasis of host tissues. It is scientifically evident that around hundreds of species of microorganisms inhabit the oral cavity; thereby, the oral microflora is invariably a major component of the oral ecosystem. The most common oral diseases include dental caries, odontogenic infections, periodontitis, and halitosis. The treatment methods for oral diseases include scaling, antimicrobial therapy, and probiotic therapy. In that probiotic therapy has been an emerging strategy in preventive therapy for oral health. Probiotics are live microorganisms and are considered generally safe to consume and used to treat various systemic disorders including inflammatory disorders. Lactobacillus, Bifidobacterium, and Streptococcus genera have been commonly used as probiotics. In this chapter, the effect of probiotics on various oral diseases is discussed. Keywords Bifidobacterium · Dysbiosis · Lactobacillus · Microflora · Streptococcus

Subramani Parasuraman and Venkata Kanthi Vaishnavi Vedam contributed equally with all other contributors. S. Parasuraman (✉) Department of Pharmacology, Faculty of Pharmacy, AIMST University, Bedong, Malaysia e-mail: [email protected] V. K. V. Vedam Department of Oral Pathology, Faculty of Dentistry, AIMST University, Bedong, Malaysia G. S. Sabesan Faulty of Medicine, Manipal University College Malaysia (MUCM), Melaka, Malaysia © The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd. 2023 V. Kothari et al. (eds.), Probiotics, Prebiotics, Synbiotics, and Postbiotics, https://doi.org/10.1007/978-981-99-1463-0_15

275

276

S. Parasuraman et al.

1 Introduction The mouth (Synonym: Oral cavity) comprises a complex habitat with an abundant diversity of multifaceted and multivariate microbial species (Reddy et al. 2011). More than 700 species of bacteria (predominantly facultative and obligate anaerobic bacteria) exist in the oral cavity (Faran Ali and Tanwir 2012). Microbial species residing in the oral cavity are termed as “oral microflora” or “oral microbiome” or “oral microbiota.” They present as “commensal” or “resident” microflora or “planktonic” or “harmless” bacteria in host oral mucosal tissues. This resident microflora blocks the primary colonization of pathogens and provides protection to the host by a strong immune system, modulates the balance in the release of inflammatory cytokines, cell adhesion molecules, and growth factors, thereby aiding in maintaining the homeostasis of host tissues (Jain and Sharma 2012). It is scientifically evident that around hundreds of species of microorganisms inhabit the oral cavity; thereby, oral microflora is invariably a major component of the oral ecosystem. There are several microorganisms which predominantly include the prokaryotes and to a small extent eukaryotic microorganism like yeasts, protozoa, etc. (Table 1) (Chugh et al. 2020; Gulabivala and Ng 2015; Deo and Deshmukh 2019). There are several oral conditions such as halitosis, gingivitis periodontitis, and dental caries, which hamper the social and healthy life of humankind. Oral diseases have commercial implications as they cause emotional stress due to social taboo or embarrassment. It is therefore important to maintain proper oral health and hygiene. Many oral conditions are known to occur due to the dysbiosis of microorganisms in the oral environment. The present and future of oral health rely not only on the concept of antimicrobial activity to inhibit the overgrowth of harmful organisms but focus more on creating and maintaining an ecologically sound oral equilibrium. There is intensive research on the normalization process of oral health with the help of probiotics. There is a need for a multifactorial approach using probiotics (Fig. 1).

2 Dental Plaque Biofilm Biofilm is a microbial-derived sessile community characterized by cells that are irreversibly attached to a substratum or interface to each other, embedded in a matrix of extracellular polymeric substances that they have produced and show a changed aggregate concerning development rate and genetic makeup (Saini 2011). Biofilms are composed of exopolysaccharides and enable microorganisms to resist antimicrobial agents and host immune systems (Kalia et al. 2014; Kumar et al. 2020). Biofilm formation occurs in the following stages (Tahmourespour 2012): • Stage 1: Inactive or least metabolically active state. • Stage 2: Significant genetic upregulation.

Probiotics: An Emerging Strategy for Oral Health Care Table 1 Common microorganisms found in oral cavity

Microorganism Gram-negative bacteria

Gram-positive bacteria

Fungi

Protozoa

277 Common Genera Actinobacillus, Bacteroides, Campylobacter, Capnocytophaga, Eikenella, Fusobacterium, Haemophilus, Leptotrichia, Neisseria, Porphyromonas, Prevotella, Simonsiella, Veillonella, Wolinella Actinomyces, Arachnia, Bacillus, Bifidobacterium, Clostridium, Corynebacterium, Enterococcus, Eubacterium, Lactobacillus, Micrococcus, Peptococcus, Peptostreptococcus, Propionibacterium, Rothia, Streptococcus Aspergillus, Aureobasidium, Candida, Cladosporium, Cryptococcus, Fusarium, Gibberella, Malassezia, Penicillium, Rhodotorula, Saccharomyces, Schizophyllum Entamoeba gingivalis, Trichomonas tenax

• Stage 3: Maturation of biomass with an increase in concentration of 1 × 1011 or 12 colony-forming units (CFU) per milliliter (CFU/ml). Expression of new antigens, genetic exchange, and membrane transport may be maximized. This phase results in increased virulence potential, metabolic stresses, and environmental stresses (primary colonizers: pioneer bacteria results in microcolonies formation

278

S. Parasuraman et al.

Fig. 1 Pivotal role of probiotics in oral health

implanted in a suitable extracellular material; secondary colonizers: co-aggregation and co-adhesion of secondary bacterial species to dental plaque occurs in a bacterially altered environment by primary colonizers resulting in a complex diversified multispecies biofilm). • Stage 4: Detachment of oral biofilm due to physical shear forces by an enzymatic breakdown that results in apoptosis or cell death. The ecological plaque hypothesis states that oral biofilm always exhibits symbiosis between bacteria and the host. Switch of particular genes in oral microflora with constant changes in the host environment results in the rapid shift from “planktonic state” to “dental plaque biofilm” formation. This dental plaque exists in two forms, namely supragingival plaque (microbial interactions located over the teeth above gingival margins [tooth fissures] and interdental surfaces) and subgingival plaques (microbial interactions in the gingival crevice) (McBain et al. 2009). Dental plaque biofilm constitutes a network of microbial species with a predominance of strict Gram-negative pathogens over facultative pathogens, resulting in an imbalance leading toward oral diseases. Redox potential and nutrient availability at various tooth/tissue surfaces play a major role in the transformation of Gram-positive bacteria to Gram-negative anaerobic species. These pathogenic microflora presents as a favorable niche in “plaque” either associated with a tooth or epithelial surfaces in our mouth. Sustained growth and molecular interactions of microorganisms in “dental plaque biofilm” help them in evasion of antimicrobial activity and host protective systems (Seminario-Amez et al. 2017). As time progresses, plaque biofilm matures and undergoes calcification due to the deposition of minerals from host saliva to form a yellowish substance termed “calculus” or “tartar” formation around the teeth. An increase in the thickness and complexity of this dental plaque biofilm results in damage to the teeth and surrounding tissues causing oral diseases,

Probiotics: An Emerging Strategy for Oral Health Care

279

including dental caries and periodontitis (Chugh et al. 2020). The type and composition of the bacterium in dental plaque biofilm thus vary from person to person, between various oral diseases and are completely distinct from healthy oral sites. Human Microbiome Project as designed by the National Institutes of Health (NIH) has demonstrated at least nine biological niches of dental biofilm at specific sites with distinct characteristics in the oral cavity. They include mucosa of the mouth, hard palate, keratinized gingiva, palatine tonsils, supragingival and subgingival plaque, saliva, throat, and dorsal surface of the tongue (Pujia et al. 2017). One-third of these oral bacterial species reside on the dorsum surface of the tongue due to the highly papillated surface that provides a larger surface area for attachment and growth (Palmer Jr 2014). As a result, resident consortia differ in composition and metabolic activity on various sites colonized. Microbes are constantly affected by host environmental factors for the permanency of the establishment of bacteria in the mouth. Saliva and gingival crevicular fluid (GCF) with various substances (lysozyme, lactoferrin, salivary peroxidase, cystatins, secretory immunoglobulin A [IgA]) affect the colonization and bacterial interactions, viability, and cell morphology of bacteria in the human oral biofilm. In addition, the rate of salivary flow in turn results in the elimination of few microbes from the host surface, thereby altering microbial colonization (Stamatova and Meurman 2009).

3 Paradigm Shift of Treatment Strategy in Oral Diseases As stated above, mature oral biofilm occurs after a series of stepwise processes from adhesion of planktonic cells to single or mixed bacterial communities. Management for oral diseases must be targeted either to attack biofilm directly or the target molecules/processes involved in the adhesion mechanism of biofilm over the host surface. Restorative therapy (restorative materials and fluorides, surgical and non-surgical procedures, reconstructive and regenerative procedures) and other modes (chemoprophylactic therapy, caries vaccine, antimicrobial mouthwashes, sugar substitutes like xylitol, calcium phosphate remineralizing agents, and casein phosphopeptides) are available for management of these oral diseases (Krishnappa et al. 2013; Shenbagam et al. 2021). However, these modes of treatment target both disease producing and normal oral microflora of the oral cavity and causing undesirable adverse effects. To overcome this problem, it is time to switch from a therapeutic approach to preventive treatment that favors selective inhibition of oral pathogens by restoring normal microbial ecological balance in the oral cavity. Several preventive strategies shed light on the alteration of causative factors like dental plaque (bacterial composition), saliva and GCF composition, diet, host (tooth mineral density), and other microbial interactions. Search for preventive strategies in overcoming the traditional mode of management should also take into consideration

280

S. Parasuraman et al.

the biotherapeutic effect, cost, and physical and chemical properties of products, which remain a challenge to humankind. Considering this, bacteria replacement therapy (BRT) utilizing natural bacteria, effector strain, or secondary metabolites from these bacteria targeted on the oral pathogens is under investigation. Overall, “ecological plaque hypotheses” have been emphasized to inhibit the activity of oral pathogens and their interference with host environmental factors that are primarily involved in the adhesion and enrichment of bacteria (Rosier et al. 2014). Several types of interaction have been described which include (i) battle for nutrient supply, (ii) bacterial synergism and antagonism, (iii) nullification of virulence, and (iv) intervention with the bacterial signaling systems (quorum sensing) in bacteria-host pathophysiology (Miller and Bassler 2001; Tsigarida et al. 2003). In BRT, the persistence of the effector strain of bacteria, the ability to colonize the susceptible host tissues and competing with host nutrients are essential to improve the host’s oral health.

4 Probiotics: Emerging Treatment Strategy in Oral Health Probiotics are live microorganisms and are considered generally safe to consume. Organic acids such as lactic and acetic acid, hydrogen peroxide, and bacteriocins are all produced by probiotics. Bacteriocin is a type of ribosomal synthesized antimicrobial peptides substances produced by the bacteria that inhibits the growth of similar or closely related bacterial strains (Ke et al. 2021; Yang et al. 2014). In recent years, probiotics are used to treat various systemic disorders including inflammatory disorders. Probiotics have an impact on oral health, and they contribute to healthy microbial balance. The microbiome including bacteria, fungi, and viruses is more than ten times to the number of cells in the human body (Mahasneh and Mahasneh 2017). Probiotics have been an emerging strategy in preventive therapy for oral health (Kumar et al. 2018). Bacteriotherapy/BRT using probiotics in oral well-being is the promising and cost-effective method for evasion of pathology (Revathi et al. 2012). In this method, beneficial bacteria occurring naturally in the human system can be administered to the host in restoring a balance between pathogenic and beneficial bacteria, the patient’s oral and general well-being (Laleman and Teughels 2015). However, preclinical studies and clinical trials are needed to establish a definite link between probiotic uses with oral diseases. With the available literature, probiotics have been showing remarkable results in reducing the onset of pathology with a probable action broadly on the alteration of only pathogenic microbial flora and host–microbial interactions (Malathi et al. 2015). It is also hypothesized that once pathogenic microflora is removed by probiotics, microbes find themselves difficult to re-grow due to competitive inhibition situations. Probiotics are divided into four major groups based on their physical and chemical reactions viz. (i) Lactic acid producing bacteria (LAB) (Lactobacillus, Bifidobacterium, Streptococcus); (ii) Non-lactic acid producing bacterial species

Probiotics: An Emerging Strategy for Oral Health Care

281

Table 2 Lactic acid producing bacteria (LAB) probiotics used for oral health LAB probiotics Lactobacillus [L.] • L. acidophilus • L. rhamnosus • L. reuteri • L. brevis • L. jhonsonii • L. salivarius • L. plantarum • L. gasseri • L. casei • L. paracasei • L. fermentum • L. delbreuckii • L. crispatus • L. lactis • L. helveticus • L. gallinarum

Bifidobacterium [B.] • B. longum • B. bifidum • B. lactis • B. infantis • B. adolescentis • B. breve • B. animalis • B. thermophilum

Streptococcus [S.] • S. salivarius • S. thermophilus • S. sanguinis • S. mitis

(Bacillus, Propionibacterium); (iii) Nonpathogenic yeasts (Saccharomyces), and (iv) Non-spore forming and non-flagellated rod or coccobacillus (Sareen et al. 2012). As LAB are good colonizers of the gastrointestinal tract and oral cavity, it has a greater significance in biotherapy (Mahasneh and Mahasneh 2017). Among all the probiotics that have been accepted by Food and Agriculture Organization/World Health Organization (FAO/WHO) and are considered “Generally recognized as safe” (GRAS), strains specific to Lactobacillus, Bifidobacterium, and Streptococcus genera have been commonly used for experimental and clinical studies. Lactobacillus (1% cultivable bacteria in the oral cavity) are Gram-positive, rod-shaped, facultative anaerobes that produce enzymes for digestion, metabolism of proteins/carbohydrates and synthesizing vitamin K and B that facilitate the breakdown of bile salts (Dash et al. 2015; Saraf et al. 2010). Bifidobacterium is Grampositive anaerobic bacteria that especially cause the metabolism of lactose, generate lactic acid ions from lactate and ferment indigestible carbohydrates producing fatty acids when administered. The first probiotic used for research purposes was Lactobacillus acidophilus (LA) and Bifidobacterium bifidum (BB) (Holcomb et al. 1991; Tandon et al. 2015). From the current literature, all the certified LAB probiotics used for oral health are listed under Table 2 (Holcomb et al. 1991; Tandon et al. 2015; Alok et al. 2017; Masood et al. 2011). Probiotic strains of special interest that are cultivable are Lactobacilli (L. paracasei, L. plantarum, L. rhamnosus, L. salivarius) and Bifidobacterium (B. bifidum, B. dentium, and B. longum) have been associated with better colonization in oral mucosal tissues. Probiotic adhesion has shown better results by pretreatment of host tissue surface with lysozymes without affecting the survival of the cells. The individual strain-specific properties, adhesion properties, molecular interactions, and probiotic species/strains with increased synergistic activity must be considered for an effective role against oral diseases.

282

S. Parasuraman et al.

5 Mechanism of Action of Probiotics (in Oral Health) Probiotics possibly act by two routes (direct and indirect action) in the oral cavity (Fig. 2). This section gives an overview on the compilation of predominantly in vitro results, clinical studies, and few in vivo studies to date on oral health (Chalas et al. 2016).

5.1

Direct Action

Antimicrobial Mechanism Probiotics produce a wide range of antimicrobial metabolites, i.e., bacteriocins (cationic peptides), salivaricin (L. salivarius and S. salivarius), plantaricin (L. plantarum), nisin (L. lactis), reuterin (L. reuteri), pediocin, bacteriocin like substances (BLIS), organic acid, diacetyl, hydrogen peroxide, and carbon peroxide which exhibit antimicrobial activity. Probiotics may be able to adhere to epithelial cells causing toxicological degradation of oral pathogens. Probiotics also modulate microbial cell cycle (proliferation and apoptosis) via alteration of cellular responses, fatty acid production, and cytokine-mediated apoptosis (Yan and Polk 2020). Probiotics target pathogen quorum sensing systems (is a communication process by which bacteria monitor their population in a cell-density dependent manner) rather than their fundamental structures, which is an attractive approach to control conventional and emerging illnesses (Ghanei-Motlagh et al. 2019).

Fig. 2 Mechanism of action: probiotics and oral health

Probiotics: An Emerging Strategy for Oral Health Care

283

Antiplaque Mechanism Probiotics contribute to ecological equilibrium by the integrity of the protective epithelial lining from oral biofilm formation (attachment of microorganisms with proteins) (Flichy Fernández et al. 2010). Probiotics also interferes with bacterial attachment, colonization, and biofilm formation (Rastogi et al. 2011). Interspecies crosstalk is another important characteristic of the composition and stability of dental plaque. Probiotics thus compete/intervene with the inter- and intrabacterial interactions. Adhesive mechanism of probiotics increases the retention period between the microbe or probiotics and host surfaces, thereby facilitating the probiotic activity. Probiotics with the increased ability of adhesion (first phase: negatively charged bacterial cell surfaces with positively charged tooth surfaces [weak interactions]; second phase: attachment of bacteria via bacterial adhesins and receptors with saliva coated tooth surface [irreversible interactions]) compete with the pathogens for binding to cell adhesion sites and host substrates (Gruner et al. 2016; Singh et al. 2013). Secretion of biosurfactants and anti-adhesion molecules by the probiotics decreases interbacterial and bacterial plaque/tooth surfaces (Amargianitakis et al. 2021). Probiotics also modify salivary pellicle and increase intestinal mucin production (Allaker and Stephen 2017; Javanshir et al. 2021). In generally, antimicrobial and antiplaque mechanisms result in the modification of composition and metabolic activity of the host microbial activity at a specific location, thereby reducing the pathological load in the biofilm and directly preventing oral diseases.

5.2

Indirect Action

Antioxidant Mechanism Antioxidants properties of probiotics helps to prevent plaque formation by neutralizing the free radicals needed for the mineralization of plaque (Nanavati et al. 2021).

Anti-Inflammatory Mechanism Probiotics decreases proinflammatory cytokines (prostaglandin E2 [PGE2]), lytic enzymes (collagenases), and other inflammatory molecules. Probiotics also boost anti-inflammatory cytokines, host defense peptides, and beta-defensins, thereby preventing the cytokine-mediated apoptosis (Haukioja 2010; Youssef et al. 2021).

284

5.3

S. Parasuraman et al.

Immune Modulation

Specific Immune Response on Oral Mucosal Immune System Probiotics enhances IgA production in the mouth, activates oral mucosal tissues for bacterial recognition and stimulation of T-cell responses (Th1 responses in intracellular microbes and Th2 cells in extracellular pathogens) (Reddy et al. 2010).

Non-specific Immune Response Probiotics enhances innate immunity against plaque-induced inflammation via expression of toll-like receptors (TLRs) on immune cells (humoral immune response) and enhances phagocytosis either directly by neutrophils (PMNs) or macrophages or natural killer cells (N-K cells) or indirectly by modification of the Th1/Th2 proportion of cells in the mucosal tissues (cell-mediated immune response) (Allaker and Stephen 2017). In general, the indirect action of probiotics helps to maintain oral epithelium, strengthen the epithelial barrier, and modulate the immune system.

5.4

Miscellaneous

Probiotics may modify enzyme activity (glucosyltransferase’s enzyme inhibition) and having capability to improve the human defense mechanism of the gastrointestinal system (Gomes et al. 2015; Mahasneh and Mahasneh 2017).

6 Oral Probiotics: Methods of Delivery Delivery of the probiotics to the consumer in a suitable dosage form is very important. Probiotics are live microorganisms that need to be administered in sufficient amounts to achieve the health effect (Fenster et al. 2019). The oral probiotics can be administered in the following forms: – Culture concentration added to beverage or food (e.g.: fresh juice). – Probiotics inoculated prebiotic fibers (e.g.: onions or legumes). – Probiotics inoculated into dairy products (e.g.: milk, yoghurt, cheese, ice cream, biodrink). – Concentrated and dried cells packed into dietary supplements (e.g.: capsules, liquid, powder, chewing gum, gelatin tablets, chewing gums, lozenges, mouthwash, and toothpaste) (Reddy et al. 2010; Sareen et al. 2012).

Probiotics: An Emerging Strategy for Oral Health Care

285

In probiotics formulation development, stability is very import parameter that affected various biological and physicochemical factors. These factors significantly affect the viability of probiotics in environmental stress (temperature, humidity, oxidation, reduction, pH change), stability in biological fluids, and susceptibility to enzymatic degradation (Baral et al. 2021). Commercially available probiotics for oral health are toothpaste, mouthwash, lozenges, and chewing gums. When formulating the probiotics for oral health, major attention is paid on type of formulation, vehicles for probiotics administration, concentration of a probiotic in a formulation, pH, and stability of the formulation. Vehicles for probiotics administration and concentration to be administered are also important for improving the biological activity of the probiotics. Among all the available vehicles for probiotics administration, in view of lowering acidic pH effect in the oral cavity, oral probiotics are given in yogurt form for neutralization of acidic pH and cheese to prevent demineralization and aid in remineralization of tooth. The minimum concentration of a probiotic should be at least 1 × 106–107 live organisms per g/mL of product with a frequency of consumption of probiotics five billion to 10 billion CFU/day to yield maximum advantage to the human (Nanavati et al. 2021). The adjuvant used in the probiotic formation also pay a major role in the bioavailability of the formulation after systemic administration. For example, LAB causes acidification of pH by fermentation of carbohydrates, vehicles like milk and milk products (colloid) are beneficial to oral health in view of buffering capacity (enamel protective) and presence of high content of calcium that help protect the tooth surfaces and prevent the growth of oral pathogens. The same effect is seen when administered with calcium lactate (another form of dairy formulation). As probiotics work well for the adults on the daily administration, research can be focused in including probiotics as a constituent in toothpaste in future in addition to all other general modes of administration.

7 Probiotics and Dental Caries Dental caries (tooth decay) is an irreversible infectious disease of the calcified tissues of the teeth resulting in tooth cavitation. This disease occurs as an interaction between cariogenic microorganisms, diet rich in fermentable carbohydrates (quality and quantity), time, and host factors like saliva and GCF. In addition, salivary composition/secretion rate, buffering capacity, and protective factors at the tooth– biofilm interface play a key role in the oral cavity (Chugh et al. 2020). The teeth mineralization process is sensitive to alterations in oral cavity pH. Fermentation of the carbohydrates by cariogenic microorganisms produces lactic acid and extracellular polysaccharides like glucan and fructan, resulting in acidification of host pH (