Gut Microbiome and Its Impact on Health and Diseases [1st ed.] 9783030473839, 9783030473846

Citation preview

Debabrata Biswas Shaik O. Rahaman  Editors

Gut Microbiome and Its Impact on Health and Diseases

Gut Microbiome and Its Impact on Health and Diseases

Debabrata Biswas  •  Shaik O. Rahaman Editors

Gut Microbiome and Its Impact on Health and Diseases

Editors Debabrata Biswas Department of Animal and Avian Sciences University of Maryland, College Park College Park, MD, USA

Shaik O. Rahaman Department of Nutrition and Food Science University of Maryland, College Park College Park, MD, USA

Center for Food Safety and Security Systems University of Maryland College Park, MD, USA Molecular and Cellular Biology, Biology Program University of Maryland, College Park College Park, MD, USA

ISBN 978-3-030-47383-9    ISBN 978-3-030-47384-6 (eBook) https://doi.org/10.1007/978-3-030-47384-6 © Springer Nature Switzerland AG 2020 This work is subject to copyright. All rights are reserved 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 Switzerland AG The registered company address is: Gewerbestrasse 11, 6330 Cham, Switzerland

Contents

 Contribution of Human and Animal to the Microbial World and Ecological Balance������������������������������������������������������������������������    1 Zajeba Tabashsum, Zabdiel Alvarado-Martinez, Ashely Houser, Joselyn Padilla, Nishi Shah, and Alana Young  Determinants of the Gut Microbiota��������������������������������������������������������������   19 Arunachalam Muthaiyan  Effects of Diet on Human Gut Microbiome and Subsequent Influence on Host Physiology and Metabolism ����������������   63 Bryna Rackerby, Daria Van De Grift, Jang H. Kim, and Si Hong Park  Probiotics and Prebiotics on Intestinal Flora and Gut Health��������������������   85 Mengfei Peng, Nana Frekua Kennedy, Andy Truong, Blair Arriola, and Ahlam Akmel  Role of the Gut Flora in Human Nutrition and Gut Health������������������������  105 Zabdiel Alvarado-Martinez, Stephanie Filho, Megan Mihalik, Rachel Rha, and Michelle Snyder  Gut Microbiome in Inflammation and Chronic Enteric Infections������������  133 Arpita Aditya, Catherine Galleher, Yeal Ad, Mitchell Coburn, and Aaron Zweig Role of Gut Microbiome in Colorectal Cancer ��������������������������������������������  153 Xiaolun Sun  Gut Microbiota and Risk for Atherosclerosis: Current Understanding of the Mechanisms��������������������������������������������������  167 Bidisha Dutta, Chitrine Biswas, Rakesh K. Arya, and Shaik O. Rahaman

v

vi

Contents

 Gut Microbiome and Its Role in Enteric Infections with Microbial Pathogens��������������������������������������������������������������������������������  187 Catherine Galleher, Kyah van Megesen, Audrey Resnicow, Josiah Manning, Lourdes Recalde, Kelly Hurtado, and William Garcia  Antibiotic Therapy and Its Effect on Gut Microbiome in Obesity and Weight Loss����������������������������������������������������������������������������  209 Paola I. Bonilla-Carrero, Hannah Mader, Nathan Meier, Isis Olivas, Bridget Boyle, and P. Bonilla-Carrero  Impact of Gut Microbiota on Host by Exploring Proteomics����������������������  229 Thomas E. Angel and Uma K. Aryal  Modulation of Gut Flora and Its Application in Food Animal Products��������������������������������������������������������������������������������  251 Zajeba Tabashsum, Vinod Nagarajan, and Debabrata Biswas Index������������������������������������������������������������������������������������������������������������������  275

Contribution of Human and Animal to the Microbial World and Ecological Balance Zajeba Tabashsum, Zabdiel Alvarado-Martinez, Ashely Houser, Joselyn Padilla, Nishi Shah, and Alana Young

1  Introduction More than 300 years ago, Antonie van Leeuwenhoek observed morphologically diverse microbes in human plaque, leading to the discovery of a complex microbiota that exists within the environment, as well as in animal and human bodies (Lane 2015). That was the beginning of understanding that microbes are a part of this world, and from then, the idea of microbes playing crucial roles in every sphere of life has become more prominent. The collection of all microbes present in a system is known as the microbiome of that system, which includes beneficial, neutral, and harmful microbes. The various microbes that can be found inhabiting different environments as part of their microbiome, like people, plants, animals, soil, bodies of water, and the atmosphere, have proven to be extremely important for, in turn, shaping and maintaining the health and balance of the microbiome of a host, which is why it has now become the subject of further studies (McFall-Ngai et al. 2013). It has been reported that the microbiome is closely related with various parts of human Zabdiel Alvarado-Martinez, Ashely Houser, Joselyn Padilla, Nishi Shah, and Alana Young have contributed equally with all other contributors. Z. Tabashsum (*) · Z. Alvarado-Martinez Molecular and Cellular Biology, Biology Program, University of Maryland, College Park, MD, USA Department of Animal and Avian Sciences, University of Maryland, College Park, MD, USA e-mail: [email protected] A. Houser Molecular and Cellular Biology, Biology Program, University of Maryland, College Park, MD, USA J. Padilla · N. Shah · A. Young Department of Animal and Avian Sciences, University of Maryland, College Park, MD, USA © Springer Nature Switzerland AG 2020 D. Biswas, S.O. Rahaman (eds.), Gut Microbiome and Its Impact on Health and Diseases, https://doi.org/10.1007/978-3-030-47384-6_1

1

2

Z. Tabashsum et al.

health and disease, such as metabolism, intestinal homeostasis, and immune development (Tasnim et al. 2017). Though each individual’s microbiome is unique, a consistent and diverse gut microbiota is considered to be optimal for maintaining health. The gut microbiota is responsible for producing metabolites that aid physiological and metabolic processes, as well as adjusts local and systemic immune responses that lead to the development of protective immunity against pathogens, while simultaneously maintaining immune lenience toward commensals (Tasnim et al. 2017). On the other hand, imbalance of the gut microbiota (dysbiosis) can disrupt vital health-promoting activities and has been associated with diseases like gastrointestinal, cardiovascular, autoimmune, and metabolic disorders (Jandhyala 2015). Due to such phenomenon, the gut microbiome is considered as a vital organ, and disruption of the balance within the microbial ecosystem can lead to severe chronic diseases and future health consequences. We are still figuring out the ecological processes of a steady and wide-ranging gut microbiome that is comprised of bacteria, archaea, fungi, and viruses, which in themselves include a very diverse bacteriophage community (Tasnim et al. 2017). The microbiota can be permanent (residents), or transient (hitchhikers), but the transmission routes of the microbes are essential for establishing and maintaining the microbial diversity in the human or animal host’s gut; however, the patterns of transmission are not entirely understood. Researches on the influence of environmental factors on the diversity and richness of the human gut microbiota and the process of gut microbiota transmission are still at beginning stages (Hasan and Yang 2019). Many variables outside the host, like geography, weather, and habitat, as well as factors within the host, like personal habits, hygiene, and food, can influence the process of molding the microbiome, which adds many layers of complexity in studies seeking to understand its composition and how it relates to its surroundings. Overall, the microbiome plays a crucial role wherever they inhabit, ultimately forming a big part of that ecosystem. However, researchers are still in the early verge of figuring out the microbiome’s broad role in the health of the host/environmental balance and the extent of problems that can occur from an interruption in the regular interactions between the microbiome and its host/environment.

2  Microbial Ecosystem Microorganisms take up a significant portion of all living beings, exceeding even that of animals, in addition to being highly diverse, which can be seen across multiple ecosystems. The estimated number of prokaryotic cells, which are primary microbe on Earth, is between 4.2 × 1030 and 6.4 × 1030 (Editorial 2011). Eukaryotic microorganisms are also prominent, which leads us to the idea that life on Earth is primarily microbial (Oren 2009). The microbes differ morphologically, metabolically, and phylogenetically. Cell size and shape are far more limited for prokaryotes, with most species being described as rod-shaped or coccoid-shaped with a length of 1–5 μm. However, some giant prokaryotes have been found that dwarf most eukaryotic

Contribution of Human and Animal to the Microbial World and Ecological Balance

3

microorganisms but are not as prevalent. Prokaryotes also differ morphologically by displaying stalks and other appendages as well as spiral shapes (Young 2007). The true diversity of the microbial world becomes apparent when the metabolic potentials of these microbes are compared. Prokaryotic microorganisms can use carbon dioxide, acetate, or organic compounds as their carbon source when performing different metabolic processes, such as photoautotrophy, photoheterotrophy, aerobic heterotrophic metabolism, denitrification, sulfate reduction, dissimilatory metal reduction, chemoautotrophic sulfur oxidation, nitrification, methanogenesis, and fermentation. In the case of some eukaryotic microorganisms, they can use carbon dioxide or organic compounds as their carbon source during photoautotrophy, aerobic heterotrophic metabolism, and fermentation (Oren 2009). The presence of these various types of metabolisms shows how microorganisms have evolved to enable life, even under distinctively different and possibly even adverse conditions. Newly developed molecular technology such as sequencing of the small-unit ribosomal RNA has aided in expanding the current knowledge that is had about the diversity of the microbial world (IOM 2009). The ever-growing database of the living beings on earth has shown that only a few branches in the Eukarya domain contain multicellular organisms, while all other branches in the Eukarya, Archaea, and Bacteria domains are microorganisms (Oren 2009). The human microbiome is also very dynamic and contains a vast array of microbial species, which contribute to the overall health (both positive and negative) of the host (Cho and Blaser 2012). The symbiotic relationship between microorganisms and their host likely originates around the same time animals appeared, about 700 million years ago. Bacteria began to serve as producers of digestible molecules in the animal gut, thus heavily influencing gut evolution and health (Mcfall-Ngai et  al. 2013; Bahrndorff et al. 2016). Microorganisms and their crucial activity in the gut have become an essential part of a healthy life. Diversity of the gut microbiota is an important indicator of a healthy gut and the overall health of the humans or animals. Low diversity of gut microbiota has been closely associated with many diseases specifically chronic diseases, such as inflammatory bowel disease. The microbiome– host association indicates that a species-rich gut ecosystem is stronger against environmental influences because the microbes are functionally related and able to compensate for any missing species (Valdes et al. 2018). Microorganisms reside not only the gut but can also be found in different organs and secretions of the host, such as skin, saliva, stool, and the vagina. Saliva and stool have quite diverse communities of microbes, similar to the gut. However, it was found that other parts are mostly populated by simple communities of microbes, such as in the case of the male urinary tract. On the other hand, an increase in microbial diversity in the vagina leads to health complications, such as bacterial vaginosis (The Human Microbiome Project Consortium 2012). This emphasizes how the microbial communities and their symbiotic relationship with humans have evolved and how microbes have become specific to a certain type of environment; even within a single organism, the structure and function of each microbial community are unique. Due to the dynamic nature of microbial communities, not all microbes will be present in constant ratios; rather, their numbers are unique and can change within a

4

Z. Tabashsum et al.

community and ecosystem at a given time. Some selection pressures must exist in order to isolate the best-suited microbial community. For the gut microbial community, there must be strict requirements for sustaining or gaining membership. Each of these microbes produces a variety of enzymes for utilizing available nutrients and uses their cell-surface molecular paraphernalia to attach to a suitable habitat in which they can colonize and avoid a reaction-ready immune system (Ley et al. 2006). The ability for genetic mutations in order to stay well adapted, ability to grow rapidly to avoid being washed out, and high resistance to stress are some of the mechanisms that have developed and are crucial for surviving the passage, colonization, and prevalence in a new host, even when conditions might be adverse (Ley et  al. 2006). Without such abilities, the microbes would not be able to survive in the gut environment, much less make significant contributions to the community. These factors will be essential, especially at the first stages of microbial discrimination, which begins right after birth. As mentioned before, upsetting the delicate balance of the microbiome can have negative effects on overall health of the host. An example of this is the studies that have shown a possible link between microbiota and cardiovascular disease, based on data about how some microbes metabolize dietary phosphatidylcholine into the proatherosclerotic metabolite trimethylamine-N-oxide (TMAO) (Koeth et al. 2013). In another study, Koeth et al. (2013) observed that a group of healthy people challenged with dietary phosphatidylcholine showed increased plasma levels of TMAO that were suppressed by prior treatment with antibiotics. These increased plasma TMAO levels were found to be associated with increased risk for cardiovascular events in patients with cardiovascular disease risk factors, providing more evidence of a link between the microbiome and cardiovascular disease (Koeth et  al. 2013; Shreiner et al. 2015). A similar link has been found between microbiota and inflammatory bowel disease (IBD). IBD is characterized by inappropriate inflammation in the gut resulting from a combination of environmental and genetic risk factors and is also associated with alterations in the gut microbiota. Studies found that patients with IBD had low-diversity gut microbiomes and that the use of antibiotics amplifies the microbial dysbiosis (Shreiner et al. 2015). The microbiome is clearly important for human health, so its stability and response to disturbances are crucial issues to discuss. Relman (2012) reported that the ecology of human microbiome will be stable as long as the key components of the system remain in equilibrium after a disturbance, and that the system can be resistant to future disturbances if they are experienced for a short period, or as long as it allows enough time for key components to recover to their initial state of equilibrium. As long as the system is robust enough to resist significant change and maintain certain parameters within range, it will still be able to operate and exert its beneficial properties, allowing for some variability without compromising the overall functions. Disturbance can be defined as an event or process (physical or biological) that causes abrupt structural changes to the composition of the community. The most wellknown disturbance is antibiotics. Recently, antibiotics have been used in massive quantities and concentrations relative to their natural occurrence over millions of years in the environment (Relman 2012). This has led to bacteria becoming resistant to antibiotics, thus making them much harder to treat. While this is a widely known

Contribution of Human and Animal to the Microbial World and Ecological Balance

5

problem, very little research has focused on the adverse impact of antibiotics on the composition and structure of the human indigenous microbiota. Longitudinal studies about the human microbiome could result in many important insights. This includes determining the long-term effects of antibiotics on the human microbial ecosystem. In addition to this, more research into symbiotic relationships could also prove useful. Metabolic pathway reconstruction is currently being used to design new growth techniques involving new culture media and better incubation conditions that resemble the microbe’s initial environments, which in turn will lead to a better understanding of the mechanism of organisms involved in symbiosis. With this information, it will be possible to genetically manipulate symbiotic relationships and obtain insight into the mechanisms that regulate them and host colonization (Raina et al. 2018). Another avenue of research is using the human microbiome as an approach for personalized medicine. Currently, individuals have different responses to different therapeutic agents, which has led to an important problem that has proven difficult to solve. Personalized medicine would consider individual variations in genes, environment, and lifestyle for each person. Microbiome sequencing technology would analyze the microbiome of individuals and provide the necessary information to personalize a medication. Potential therapeutic agents that could be used include individualized probiotic and prebiotic supplements, dietary interventions, and fecal microbiota transplantation to modulate the gut microbiome (Ejtahed et al. 2017). The human microbiome is vital for a person to remain healthy, yet so much is still left to learn about the relationship between these microbes and the human host.

3  M  ajor Components of the Microbial World and Their Sources The microbial ecosystems that can be found as part of the environment, animals, and humans are composed of four major types of microorganisms, including fungi, archaea, bacteria, and viruses. The different organisms that make up these groups form crucial components of the microbial ecosystem in addition to being extremely dynamic and interchangeable between each ecosystem in a continuous process. These microbes can originate from many diverse sources, such as plants, soil, animals, other humans, water, air, and even from unusual places like hot springs and hydrothermal vents. All of which can contribute to the exchange of microbes.

3.1  Animal-Contributed Microbes Animals harbor different types of microbes that are found in the gastrointestinal system and external surfaces of animals (Clements 1997). Most of these microbes live in symbiosis with the host. They are able to live inside the host at the expense of providing beneficial help to the host. Animals embrace microbes for their microbiome by the ingestion of food, including plants and animals products and water that

6

Z. Tabashsum et al.

contain microbes. Few animals are coprophagous as they are able to ingest their own feces, and in doing so, they ingest important bacteria like the bacterium Metabacterium polyspora, such as the case of the Guinea pigs (Holtenius and Bjornhag 1985). Another case can be seen when through the ingestion of leaves, bark, stems, shoots, and fruit, gorillas are able to gain firmicutes, actinobacteria, bacteroidetes, lentisphaerae, planctomycetes, spirochetes, and verrucomicrobia, which can be all found later in their excreted feces (Rothman et  al. 2006). In addition to this example, through the ingestion of seawater, animals like the bobtail squid are able to take in bacteria like Vibrio fischeri which aids in providing bio-­luminesce characteristics to marine animals, which are important features needed for survival from predators (Kostic et al. 2013). Although many of the bacteria found in animals, which are later released into the environment, are beneficial or normal flora, there are some bacteria that are capable of causing disease and illness in the animals that serve as reservoirs for these pathogens. Zoonotic pathogens, which are transmitted from one animal to another including humans, can be transmitted within the microbial ecosystem quickly and exponentially. Salmonella enterica, for instance, can contaminate meat coming from animals like poultry, ovine, cattle, and pigs (Tomley and Shirley 2009). These pathogenic bacteria can then be ingested by humans and be able to colonize the gastrointestinal tract of humans, disturbing the normal microbiome (Wiedemann et al. 2015). Through such transmission, pathogenic bacteria like S. enterica can be transmitted throughout the microbial ecosystem. Besides pathogenic bacteria, there are also viruses in the microbial ecosystem that can be transmitted from animals to animals. One such example is that of the blue tongue virus which is transmitted by different species of Culicoides that bite cattle and inject the virus into cows. Once the virus enters the bloodstream, it forms part of the microbiome of the cattle and is capable of causing illness and even death (Reperant et al. 2016). A famous virus that caused an outbreak of illnesses in recent years is that of the H1N1 virus, which was found in pigs and transmitted to humans (Belser et al. 2010). This virus was then able to spread through the microbial system from person to person without the need of its original reservoir.

3.2  Microbes from Plant Sources Plants also contain important microbes, specifically various types of bacteria and fungus that form a symbiotic relationship through which plants get befits, including improvements in their growth and health. Amongst these are arbuscular mycorrhizal (AM) fungi which are found to grow on plants like Lotus japonicus and trigger the plant to undergo hyphal branching, which comes at a benefit for plant growth (Akiyama et al. 2005). Like animals, plants are also susceptible to pathogens that can invade the plant and form part of the plant’s microbiome, which is then a factor in the microbial ecosystem. Such is the case of the fungi Fusarium oxysporum. F. oxysporum is an

Contribution of Human and Animal to the Microbial World and Ecological Balance

7

invasive fungus that is capable of invading banana plants and causing it to wilt and die (Elliott 2011). There are also pathogenic bacteria that exist in the microbial system and can invade the plant. For example, Xanthomonas campestris pv vesicatoria is a bacterium known to act as a pathogen in plants like tomato and pepper, causing spotting disease (Fenselau et al. 1992). Plant microbes are found not only on the leaves and stems but also on the roots and soil in which the plant grows. There are many important microbes that live in the roots of plants that contribute to a chemical output and have a positive impact on the environment and microbial ecosystem. Such is the case of the well-known bacteria called Rhizobium leguminosarum, which is able to convert atmospheric nitrogen to a form of nitrogen that can be used by legume plants as a nutrient source (McNear 2013). Furthermore, in the rhizosphere, or the region of soil on which the roots of a plant grow, there are many bacteria, fungi, and nematodes that are capable of regulating plant health, growth, and budding. Plant growth-promoting rhizobacteria, like Bacillus amyloliquefaciens, are found at the roots of plants and are able to regulate the plant growth, stem size, and disease prevention of crops like chili (Gowtham et al. 2018). There are also fungi like Funneliformis caledonium that are classified to be arbuscular mycorrhizal fungi and help improve soil growth and fertility that regulate the health of plant roots (Khan 2005). However, microscopic eukaryotes called nematodes are pathogenic eukaryotes that are present in plant’s root microbiome. Nematodes like Meloidogyne incognita are capable of preventing the proper degradation of cellulose and the production of plant nutrients like phosphorus (Razavi et al. 2017). Thus, a plant contains different microbiomes with a variety of microorganisms that can either live in symbiosis or be invasive and pathogenic and that form part of a large microbial ecosystem.

3.3  Microbes from Water, Soil, and Air Sources Microbes can also be found in environmental sources like water, air, and soil. Both seawater and freshwater contain naturally occurring microbes, most of which are beneficial to the plants and animals. In seawater, for instance, there exist bacteria that are crucial for nutrient production and regulation of oxygen, sulfur, phosphorus, and other nutrient levels. One of these bacteria is Thiomargarita namibiensis, which is specifically found in the sediments that are present in the ocean water. This bacterium is able to oxidize toxic hydrogen sulfide to sulfide, thus providing an important nutrient for marine life (Schulz and De Beer 2002). Likewise, in freshwater, there are also bacteria that help to regulate the nutrients present and available for consumption by other marine organisms. Specifically, there are ammonia-oxidizing bacteria that are able to oxidize ammonia into forms of nitrogen that serve as nutrients and are not harmful to marine organisms (Lu et al. 2019). Although many of the microorganisms contained in freshwater and seawater are beneficial, there still exist microbes living in these water sources that pose a threat to other marine microorganisms and larger organisms. Such is the case of

8

Z. Tabashsum et al.

cyanobacteria, of which many strains are important for fixing nitrogen, yet some strains are toxic. For instance, Microcystis aeruginosa is a cyanobacterial strain that produces toxins, like microcystins, that deplete oxygen levels in the water and foment algal blooms (Cheung et al. 2013). Microbes can also be found in drinking water and most are harmless, but there are some microbes like pathogenic bacteria that can cause severe illness in animals that drink or come in contact with the water. The most common pathogenic bacteria found in drinking water are Vibrio cholerae, Salmonella enterica, and specific strains of Escherichia coli (Cabral 2010). These pathogenic bacteria become dangerous and harmful to the host that consumes water containing these microbes. Besides water, the air is an environmental component that holds microbes originating from other sources. Such is the case of microbes found the respiratory tracts of humans that are released into the air when they sneeze or cough. Of these microbes, the most prominent ones are Micrococcus spp., Staphylococcus spp., and Streptococcaceae spp. (Prussin and Marr 2015), which are all bacterial strains that are found in the air. Additionally, there are fungi like Cladosporium, Penicillium, and Alternaria that originate from plants and are found as spores in the air (Prussin and Marr 2015). Like this, many other original sources of microbes contribute to environmental microbes found in the air.

3.4  Microbes from Unusual Sources There are also unusual sources in which microbes can survive and multiply. Many of these microbes are labeled as extremophiles as they are able to survive under extreme conditions, including extreme temperature, salinity, acidity, and nonoxygenated environments. For instance, the thermophilic bacteria Streptomyces sp. are found living in hot springs and are able to survive under extremely hot temperatures (Al-Dhabi et al. 2015). Another example can be found in Gallionella ferruginea, are bacteria capable of surviving under acidic conditions and can at the same time reduce iron found in acidic waters (Arce-Rodríguez et al. 2016). There are also microbes like Nesterenkonia lacusekhoensis, which thrive in salt-rich environments and have the best survival under these conditions (Bhattacharya et al. 2007). Finally, hydrothermal vents provide anoxic or oxygen-deficient environments for bacteria to grow. Such is the case of Thiomicrospira crunogena, which is an anaerobic bacterium capable of oxidizing sulfur under extreme conditions (Muyzer et al. 1995).

4  Factors Involved in Shaping the Microbial Ecosystems The diversity of microbial ecosystems in populations of animals and humans, as well as in individuals, is extensively variable depending on age, time, weather, food consumption, life style, and environment. Therefore, it can be said that these factors are

Contribution of Human and Animal to the Microbial World and Ecological Balance

9

involved in shaping the microbial ecology of each individual in a very unique way. The relationship and type of interaction that these microbes will have within its host will be a driving factor in determining how prevalent they will be in the host’s ecosystem, what role they will play, and what potential benefits or disadvantages they will pose for other microbes, and ultimately the host. In human microbial ecosystems, the relationship between the host and the microorganisms can be described as commensal, meaning one organism benefits while the other remains unaffected (either host or microbial counterpart), mutualistic, meaning both organisms benefit, or it could also be pathogenic, which is when host suffers some detrimental consequence because of the microbe’s presence (Ley et al. 2006). An important factor that allows for colonization of various and diverse regions in the host and can determine the nature of the relationship with that microbe and its host is the wide range of metabolic diversity that can be found across all microorganisms. These allow for not only their survival but also their ability to thrive under various nutrient-deficient environments. Further, microorganisms are capable of degrading almost any organic compound found in nature, and they play a key role in decomposing and making available organic materials, some of which can even be found in soil and water (Cho and Blaser 2012). Many microorganisms can perform mixotrophy and, therefore, are capable of degrading not just one but many carbon sources that will serve for generating energy (Shade et al. 2012). Microorganisms also have the ability to respire either aerobically or anaerobically, meaning that they can use molecules other than oxygen as final electron acceptors, allowing them to carry out their metabolic processes and growth in conditions that are low or, in some cases, completely void of oxygen (Oren 2009). Some microorganisms can even perform both anaerobic and aerobic respiration, allowing them to survive under either conditions (Oren 2009). Also, some microorganisms have the ability to survive in extreme environments. The extreme conditions that microorganisms are capable of surviving in include environments of extreme pHs, temperatures, or salinity. This ability of microorganisms to adapt to different environments provides increased resilience of microbial ecosystems (Shade et  al. 2012). These factors will also be important for survival in regions of the host that pose similar challenges, like in the case of microbes that colonize skin, which must overcome high salinity, or also in the case of microbes found in the gastrointestinal tract, which experience highly variable changes in pH, starting from the very acidic stomach, all the way to the mostly neutral colon, in which there is also the added challenge of being a mostly anoxic environment. Host genotype also plays a huge role in determining microbial ecosystems. There is a wide range of variability in microbial ecosystems between different species. For example, it was reported that 85% of the microbial genera found in mice are not found in humans (Cho and Blaser 2012). However, closer interspecies relationships often indicate more similar microbial communities such as in the case of siblings (Chandler et al. 2011). Intraspecies microbial communities also have considerable variation because the genetic background of the host often determines the makeup of microbial ecosystems (Relman 2012). Therefore, individuals with less genetic variation have more similar microbiotas such as in the case of twins. When comparing the

10

Z. Tabashsum et al.

microbiomes of twins to nontwin siblings or parent-offspring microbiomes, twins have greater similarity in their microbiomes (Relman 2012). This demonstrates that even minor genomic alterations have an effect on the microbiome. For instance, studies performed on mice and fruit flies have indicated that even a change in a single gene can alter the composition of microbial ecosystems (Chandler et al. 2011). Another important aspect involved in shaping microbial ecosystem is habitat. The composition of microbial ecosystems differs at varying anatomical sites in humans and animals. The variation in the complexity of microbial communities is determined by the anatomical site in which the microbiota are present. In humans, the microbiome of oral and stool communities is considered complex due to the diversity in microbial membership (The Human Microbiome Project Consortium 2012). On the other hand, the diversity in the vaginal microbial flora is considered to be simple due to less variability in the composition of the microbial ecosystem (The Human Microbiome Project Consortium 2012). The compositions of microbial communities are also considerably affected by time or age, particularly after the formation of a new habitat or after birth (Relman 2012). This effect can be demonstrated by examining microbial ecosystem formation in newborn babies. For instance, the mode of delivery for newborns shapes infant’s microbial ecosystem (Gritz and Bhandari 2015). Intestinal microbial colonization from infants delivered vaginally largely reflects the maternal vaginal flora, while the microbial colonization from delivery via cesarean section is characterized by epidermal microbiota (Gritz and Bhandari 2015). Infants delivered via cesarean section also have lower intestinal microbial diversity as well as delayed or absent colonization of members of Bacteroidetes for up to a year, demonstrating the effects that mode of delivery has on the colonization of intestinal microbiota in infants (Gritz and Bhandari 2015). Overall, over the first 3 years of life for infants, the gut microbiome changes considerably by increasing its diversity as well as stability (Lozupone et al. 2012). Similar to in infants, it is expected that, over time, microbial diversity increases in newly developed environments.

5  P  otential Risks or External Influences on Microbial Ecological Balance A stable microbiome depends upon the resilience of the microbial ecosystem. Resilience can be defined by the amount of stress tolerated by a system before it is unable to maintain equilibrium (Lozupone et al. 2012). The resilience of microbial communities is controlled by the growth rate of the microbiota, the interactions within the microbial community and with the host, environmental parameters, and nutrient availability (Relman 2012). Threats to the stability of microbial ecosystems can be categorized as a type of disturbances. Disturbances are physiological or biological events that cause sudden changes in the composition of microbial ecosystems (Relman 2012). The ability for a disturbance to disrupt a stable microbiome

Contribution of Human and Animal to the Microbial World and Ecological Balance

11

completely depends on the resilience of the microbial community (Lozupone et al. 2012). The effect of disturbances differs depending on which microbial ecosystem is targeted and what types of microbes constitute it. Disturbances to microbial ecosystems can include the use or presence of antibiotics, captivity or housing conditions, health, diet, environmental conditions, etc. With the use of antibiotics becoming more prevalent, questions have been raised about the effect that their constant usage has on microbial ecosystems. It is also known that the use of antibiotics will serve as a drive that will lead to the emergence of resistant species (Relman 2012). Repeated use of antibiotics over time can have considerable effects on the makeup of microbial communities. For example, in studies examining repeated short-term exposures to antibiotics, by the end of the first exposure, there was a sudden decrease in microbial diversity, and after allowing 2 weeks for recovery, the preexposure abundance levels are reached (Relman 2012). However, upon repeated exposure, a similar decrease in microbial diversity is seen, but there is less recovery of microbiota (Relman 2012). Therefore, it can be determined that the long-term use of antibiotics in humans and/or animals can disturb or paralyze microbial ecosystems permanently (Relman 2012). Variances in microbial diversity can be observed in animals, specifically farm animals that are kept in captivity. Compared to wild species, the microbiomes of animals in captivity are shown to be less diverse than their wild counterparts (Bahrndorff et al. 2016). Endangered species being bred in captivity with the goal of repopulating may experience detrimental effects due to changes in the composition of their microbial ecosystems. Changes in the composition of microbiomes in animals bred in captivity may affect the fitness of the animal upon release into the wild (Bahrndorff et al. 2016). Therefore, animals in captivity are not only affected by their captive habitats but are also threatened by their weakened microbial ecosystems (Bahrndorff et al. 2016). The health and diet of the host may also cause significant shifts in diversity at certain anatomical sites. Obesity, for example, plays a role in the composition of the gut microbiome (Bahrndorff et al. 2016). Studies on mice have determined that the abundance of bacterial divisions in the gut is altered in obese animals. A significant change in relative abundance between the lean and obese mice is characterized by a 50% reduction of Bacteroidetes as well as a significant increase in Firmicutes in obese mice (Ley et al. 2005). These differences in obese and lean mice show that the effect of obesity on microbial community structure and abundance is significant (Ley et al. 2005). Host diet also affects microbial ecosystems, specifically in the human and animal intestines. When comparing diets of herbivores, carnivores, and omnivores, it was found that the microbiota of herbivores had the most phyla followed by omnivores and finally carnivores (Ley 2008). Another study on humans found that when humans shift to a low-carbohydrate and low-fat diet, a higher percentage of their intestinal microbiome is Bacteroidetes (Chandler et al. 2011). Changes in the composition of microbial communities due to diet are likely attributed to microbiota being exposed to new substrates (Lozupone et al. 2012). These new substrates may provide a selective advantage for certain microorganisms, allowing them to reproduce more successfully than other community members (Lozupone et al. 2012).

12

Z. Tabashsum et al.

Finally, when host organisms are exposed to unfavorable conditions, the microbial ecosystem may begin to act harmfully. For instance, under unfavorable conditions, microorganisms that usually benefit the host may act as opportunistic pathogens (Bahrndorff et al. 2016). In recent times, with the dramatic effects of climate change, host organisms will not just be impacted by climate change but also will be impacted by the changes in microbial ecosystems as a result of the environmental changes (Bahrndorff et al. 2016). These changes in the microbial composition may affect the hosts’ immune response as well as fitness (Bahrndorff et al. 2016). It can be noted that disturbances to microbial ecosystems can shift the stability of microbial ecosystems. The ability for a disturbance to affect microbial ecosystem varies based on the resilience of the microbiota. Changes in stability due to disturbances can be mitigated in microbial ecosystems with increased resilience. By understanding how antibiotics, captivity, health, diet, and environmental conditions affect microbial ecosystems, disturbances that alter the stability of microbial ecosystems can be prevented.

6  One Health Objective and Future Direction Microbes, specifically bacteria, should not be considered as only pathogens. Instead, it is urgent to view them as a means to positively impact the health of animals and humans across the globe. Understanding the gut microbiome, and knowing how it can be shaped and influenced by the external environment of an organism, has the potential to revolutionize health care. For example, using a combination of probiotics may have the potential to reduce the colonization of microbial pathogens, and therefore preventing them from exerting their virulent properties on the host, which are often the ones responsible for the development of disease and its symptoms. As discussed before, for a long time, medical professionals have been overusing antibiotics for treating patients, which contributes greatly to the rise of antimicrobial resistance, and has recently been found to have damaging effects on the host’s gut microbiome. Instead, utilizing other beneficial microbes can help in developing a balance in the gut, which will aid in preventing the emergence of opportunistic pathogens. While utilizing probiotics has been proven to have tremendous health benefits, it is important that the probiotics that are marketed do not have the potential to disrupt the normal microbial environment in the gut of an individual, which can also lead to disease. The microbiome inside the gut allows for the production of metabolites that facilitate and regulate many crucial aspects of human metabolism, including G-protein-coupled responses, energy homeostasis, glucose uptake, protection against toxins, suppression of pathogenic microbes, prevention of overproduction of free radical species, and regulating DNA replication (Kho and Lal 2018). Therefore, these microbes provide a crucial role in normal digestive health as well as overall health of the consumers. Thus, disruption of normal conditions in the gut and reduction in the numbers of the resident microbes could allow pathogens to occupy an existing niche in the colon that could potentially serve as a footstool for the

Contribution of Human and Animal to the Microbial World and Ecological Balance

13

development of a systemic colonization. This could lead to diseases such as inflammatory bowel disease, irritable bowel syndrome, celiac disease, diabetes, rheumatoid arthritis, and other dangerous conditions (Kho and Lal 2018). Therefore, it is vital that the modulation of the gut microbiome does not disrupt normal and beneficial bacteria that already exist in one’s body (Kho and Lal 2018). Massive strides have recently been taken to develop a better understanding of the complexity of the microbiome and microbial ecosystems, which has been expedited by genome sequencing technology. It has only been in the last decade that researchers have been able to identify a greater range of bacteria in the gut and other microbial ecosystems that were previously unidentifiable because of an inability to be cultured in  vitro, due to their unique nutritional and environmental requirements. This advancement has led to better visualization of bacterial and host interactions, along with the ability to better grasp a more detailed view of the bacterial makeup of the gastrointestinal tract. Additionally, by isolating each bacterial strain, the genome of each bacteria can be determined using 16S RNA sequences, which can be used to gain an insight into each bacterium’s contribution to gut health (Forster et al. 2019). However, complete knowledge of the composition of the microbiome is not entirely insightful on the function of different microbes and how they contribute to health. Metabolomics is a recently emerged technology that is able to measure the number and amount of metabolic end products that are created from an individual’s microbiome. Using this information paired with genomic data, the way that different bacteria contribute to the health of a host can be determined. Still, we are far from having a comprehensive knowledge of the gut and how it can be modulated to improve human health on a broad scale (Zierer et al. 2018). Fecal transplants have been found to be extremely effective at treating colitis caused by Clostridium difficile, which is the transfer of stool from a healthy individual to a diseased person. The introduction of these healthy bacteria allows for the reformation of the diseased individual’s microbiome. The success of this treatment has led to much more interest in better understanding the microbiome and its use in disease control (Brandt 2012). However, there is still so much that is still unknown about how modulation of the gut contributes to disease, which is what a lot of current research in this area is focused on. Recently, many have been looking into how bacteriophages can impact the GI microbiome, and how they can possibly play a role in disease. However, many strides are needed in this area in order to get concrete conclusions, as it is challenging to resolve the origin of the viruses, and novel viral genomes are difficult to characterize (Kho and Lal 2018). Some researchers are looking into using bacteriophages as a method of introducing Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) technology into the gut microbiome as a means to destroy only the disease-causing microbes (Fernandez 2019). Efforts are also currently underway to more accurately cater the probiotic and the prebiotic treatments to the diseased individual and the specific role of dysbiosis on the onset of their disease. It is also vital that when designing probiotic treatments, that there are not any potentially virulent or antimicrobial-resistant factors introduced into the genome, as this could further complicate future infections (Fernandez 2019).

14

Z. Tabashsum et al.

The reality is that every individual’s microbiome is different, and therefore, clinical implementations of modulations to the gut microbiome signify a major component of the future of personalized medicine. A lot of research groups are recently looking into probiotics and gut modulation as a way to prevent and treat cancer. But because of the diversity and variability of microbiomes between individuals, it has been found that the microbiome can act as both an oncogene and a tumor suppressor, depending on the metabolites created by the bacterial population (Vivarelli et  al. 2019). For instance, lipopolysaccharides, which are a normal component of gramnegative bacteria cell walls, are able to activate toll-like receptors on the host cells lining the intestines, which trigger a T-cell-mediated response against cancerous cells (Vivarelli et al. 2019). However, there are many common products produced by bacteria in the gut, including the CagA protein, adhesin A, and the metalloproteinase toxin, which are able to interact with epithelial E-cadherin. This disrupts junctions between the epithelial cells, triggering cell proliferation which may progress to tumor formation. Through monitoring an individual patient’s microbiome, and introducing anti-inflammatory probiotics that are composed of bacteria that the patient lacks, doctors may be able to treat cancer patients better. Lactobacillus rhamnosus, a common gut microbe, has been found to have many anticancer activities both in vitro and in vivo, including the ability to directly modulate cancerous cells by inhibiting proliferation and metastasis, as well as upregulating the immune system (Vivarelli et al. 2019). A future in medicine that involves altering the flora in the gut is slightly challenged, as there is no fixed reference of what a healthy microbiome is. It has been relatively easy to see patterns in different diseased states of the gut, but a normal healthy microbiome can vary greatly from one individual to the next as a result of diet, age, and a variety of different environmental factors (Schmidt et  al. 2018). Therefore, many have termed a healthy microbiome as one that is resilient and can be restored from an altered state to its original state at a relatively fast rate. It is also very difficult to develop models to determine how the gut will respond in different situations due to the complexity and constant changes that occur in the GI tract (Schmidt et al. 2018). However, much is being discovered about the GI microbiome, and researchers are getting closer to developing a complete map of all the different bacteria, and the variety in strains of each, that exist in the gut. “One health” is an initiative to form collaborations between physicians, veterinarians, nurses, dentists, and environmental scientists to interconnect health-related fields. By forming a tighter sense of community between these different groups, a more focused research entity may be established that can go toward finding cures and promoting health around the world (Gyles 2016). Much of the One Health literature that has emerged so far has been related to transfer of bacterial pathogens to humans, either from animals as a zoonotic disease or from the environment (Trinh et al. 2018). Any change in the environment that a human or animal experiences can alter their microbiome, as different bacteria in the environment gain the opportunity to enter the system and have the potential to live either commensally or parasitically in the gut. In a similar way, bacteria can be transferred from animals and humans and

Contribution of Human and Animal to the Microbial World and Ecological Balance

15

introduced into their external environment. As discussed before, long-term changes to the microbiome caused by the environment start as early as birth (Jatzlauk et al. 2017). Many of the “one health” approaches aim to determine how a specific factor in the environment and its respective microbiome alter bacterial communities and human health overall. Studies in this area often involve the alteration of specific factors that are thought to be relevant in microbiome interactions, such as in the case of genetically modified animal models, which aid in determining the potential clinical significance that these alterations have in shaping the health of the organism (Gyles 2016). There are many challenges that arise when it comes to understand microbial transfer across species. For instance, genetic variation within a species and across different ones likely plays a major role in transmission dynamics of bacterial communities. However, because there are millions of different animal species, all of which live in varying environments and have different diets, tracing microbe transfer and the factors that drive it can become very complicated (Gyles 2016). In order to develop more accurate models, it is necessary to perform evolutionary and ecological studies that focus more on the relatedness of hosts, and how phylogenies drive the growth of specific microbial communities (Gyles 2016). Future “one health” research will focus on ways to reduce the spread of pathogenic microbes between animals, humans, and the environment, either by modifying the environmental microbes in a household or by modifying the diet of companion and domestic animals, in addition to supplementing their diet with probiotics so that the potential for transmission is reduced (Gyles 2016).

7  Conclusion The microbial ecosystem is composed of many different microbes, yet the most common and major components are bacteria, fungi, and viruses. These microbes find their home in many diverse ecosystems, with the animal body being a harborer of a myriad of phyla and species that specifically inhabit specific niches across different organs. Plants also provide shelter of these microbes, as do other environmental components like in the cases of water and air, which contain many beneficial microbes, but can also be conduits through which pathogenic microbes can easily enter into contact with a new host. Finally, microbes can also come from unusual sources that include highly saline waters, hot springs, and hydrothermal vents. All these sources together will provide a special array of microbes that form part of a microbial ecosystem that has been named the microbiome, many of which can interact with each other and their environment, which, as we have seen, can often be an animal host. Humans are no exception, as we have learned that the gut comprises one of the richest and most diverse microbial ecosystems.

16

Z. Tabashsum et al.

References Akiyama, K., Matsuzaki, K., & Hayashi, H. (2005). Plant sesquiterpenes induce hyphal branching in arbuscular mycorrhizal fungi. Nature, 435, 824–827. Al-Dhabi, N. A., Esmail, G. A., Duraipandiyan, V., Valan Arasu, M., & Salem-Bekhit, M. M. (2015). Isolation, identification and screening of antimicrobial thermophilic Streptomyces sp. Al-Dhabi-1 isolated from Tharban hot spring, Saudi Arabia. Extremophiles, 20, 79–90. Arce-Rodríguez, A., Puente-Sánchez, F., Avendaño, R., Libby, E., Rojas, L., Cambronero, J. C., Pieper, D. H., Timmis, K. N., & Chavarría, M. (2016). Pristine but metal-rich Río Sucio (Dirty River) is dominated by Gallionella and other iron-sulfur oxidizing microbes. Extremophiles, 21, 235–243. Bahrndorff, S., Alemu, T., Alemneh, T., & Nielsen, J.  L. (2016). The microbiome of animals: Implications for conservation biology. International Journal of Genomics, 2016, 1–7. Belser, J. A., Wadford, D. A., Pappas, C., Gustin, K. M., Maines, T. R., Pearce, M. B., Zeng, H., Swayne, D. E., Pantin-Jackwood, M., Katz, J. M., & Tumpey, T. M. (2010). Pathogenesis of pandemic influenza a (H1N1) and triple-reassortant swine influenza a (H1) viruses in mice. Journal of Virology, 84, 4194–4203. Bhattacharya, A., Goyal, N., & Gupta, A. (2007). Degradation of azo dye methyl red by alkaliphilic, halotolerant Nesterenkonia lacusekhoensis EMLA3: Application in alkaline and salt-rich dyeing effluent treatment. Extremophiles, 21, 479–490. Brandt, L.  J. (2012). Fecal transplantation for the treatment of Clostridium difficile infection. Gastroenterología y Hepatología, 8(3), 191–194. Cabral, J. P. (2010). Water microbiology. Bacterial pathogens and water. IJERPH, 7, 3657–3703. Chandler, J. A., Lang, J. M., Bhatnagar, S., Eisen, J. A., & Kopp, A. (2011). Bacterial communities of diverse Drosophila species: Ecological context of a host-microbe model system. PLoS Genetics, 7, e1002272. Cheung, M. Y., Liang, S., & Lee, J. (2013). Toxin-producing cyanobacteria in freshwater: A review of the problems, impact on drinking water safety, and efforts for protecting public health. Journal of Microbiology, 51, 1–10. Cho, I., & Blaser, M. J. (2012). The human microbiome: At the interface of health and disease. Nature Reviews. Genetics, 13(4), 260–270. Clements, K. D. (1997). Fermentations and gastrointestinal microorganisms in fishes. In R. I. Machie & B. A. White (Eds.), Gastrointestinal microbiology. Boston: Chapman & Hall Microbiology Series. Springer. Editorial. (2011). Microbiology by numbers. Nature Reviews. Microbiology, 9, 628. Ejtahed, H. S., Hasani-Ranjbar, S., & Larijani, B. (2017). Human microbiome as an approach to personalized medicine. Alternative Therapies in Health and Medicine, 23, 8–9. Elliott, M. L. (2011). First report of Fusarium wilt caused by Fusarium oxysporum f. sp. palmarum on Canary Island date palm in Florida. Plant Disease, 95(3), 356–356. Fenselau, S., Balbo, I., & Bonas, U. (1992). Determinants of pathogenicity in Xanthomonas campestris pv. vesicatoria are related to proteins involved in secretion in bacterial pathogens of animals. Molecular Plant-Microbe Interactions, 5, 390–396. Fernandez, C. (2019). No guts, no glory: How microbiome research is changing medicine. Labio Tech. https://labiotech.eu/features/gut-microbiome-research/. Accessed 17 June 2019. Forster, S.  C., Kumar, N., Anonye, B.  O., Almeida, A., Viciani, E., Stares, M.  D., Dunn, M., Mkandawire, T.  T., Zhu, A., Shao, Y., Pike, L.  J., Louie, T., Browne, H.  P., Mitchell, A.  L., Neville, B. A., Finn, R. D., & Lawley, T. D. (2019). A human gut bacterial genome and culture collection for improved metagenomic analyses. Nature Biotechnology, 37, 186–192. Gowtham, H. G., Murali, M., Singh, S. B., Lakshmeesha, T. R., Murthy, K. N., Amruthesh, K. N., & Niranjana, S. R. (2018). Plant growth promoting rhizobacteria- Bacillus amyloliquefaciens improves plant growth and induces resistance in chilli against anthracnose disease. Biological Control, 126, 209–217.

Contribution of Human and Animal to the Microbial World and Ecological Balance

17

Gritz, E. C., & Bhandari, V. (2015). The human neonatal gut microbiome: A brief review. Frontiers in Pediatrics, 3, 17–27. Gyles, C. (2016). One medicine, one health, one world. Canadian Veterinary Journal, 49(11), 1063–1065. Hasan, N., & Yang, H. (2019). Factors affecting the composition of the gut microbiota, and its modulation. PeerJ, 7, e7502. Holtenius, K., & Bjornhag, C. (1985). The colonic separation mechanism in the guinea-pig (Cavia porcellus) and the chinchilla (Chinchilla laniger). Comparative Biochemistry and Physiology. A, Comparative Physiology, 82, 537–542. IOM (Institute of Medicine). (2009). Microbial evolution and co-adaptation: a tribute to the life and scientific legacies of Joshua Lederberg. Washington, DC: The National Academies Press. Jandhyala, S. M. (2015). Role of the normal gut microbiota. World Journal of Gastroenterology, 21(29), 8787–8803. Jatzlauk, G., Bartel, S., Heine, H., Schloter, M., & Krauss-Etschmann, S. (2017). Influences of environmental bacteria and their metabolites on allergies, asthma, and host microbiota. Allergy, 72(12), 1859–1867. Khan, A.  G. (2005). Role of soil microbes in the rhizospheres of plants growing on trace metal contaminated soils in phytoremediation. Journal of Trace Elements in Medicine and Biology, 18, 355–364. Kho, Z., & Lal, S. (2018). The human gut microbiome – a potential controller of wellness and disease. Frontiers in Microbiology, 9, 1835. Kostic, A. D., Howitt, M. R., & Garrett, W. S. (2013). Exploring host-microbiota interactions in animal models and humans. Genes & Development, 27, 701–718. Koeth, R. A., Wang, Z., Levison, B. S., Buffa, J. A., Org, E., Sheehy, B. T., Britt, E. B., Fu, X., Wu, Y., Li, L., Smith, J. D., DiDonato, J. A., Chen, J., Li, H., Wu, G. D., Lewis, J. D., Warrier, M., Brown, J. M., Krauss, R. M., Tang, W. H. W., Bushman, F. D., Lusis, A. J., Hazen, S. L. (2013) Intestinal microbiota metabolism of l-carnitine, a nutrient in red meat, promotes atherosclerosis. Nature Medicine 19(5), 576–585. Lane, N. (2015). The unseen world: reflections on Leeuwenhoek (1677) “Concerning little animals”. Philosophical Transactions of the Royal Society of London. Series B, Biological sciences, 370, 1666. Ley, R. E. (2008). Evolution of mammals and their gut microbes. Science, 320(5883), 1647–1651. Ley, R. E., Bäckhed, F., Turnbaugh, P., Lozupone, C. A., Knight, R. D., & Gordon, J. I. (2005). Obesity alters gut microbial ecology. Proceedings of the National Academy of Sciences of the United States of America, 102, 11070. Ley, R.  E., Peterson, D.  A., & Gordon, J.  I. (2006). Ecological and evolutionary forces shaping microbial diversity in the human intestine. Cell, 124(4), 837–848. Lozupone, C. A., Stombaugh, J. I., Gordon, J. I., Jansson, J. K., & Knight, R. (2012). Diversity, stability and resilience of the human gut microbiota. Nature, 489, 220–230. Lu, S., Liu, X., Liu, C., Wang, X., & Cheng, G. (2019). Review of ammonia-oxidizing bacteria and archaea in freshwater ponds. Reviews in Environmental Science and Biotechnology, 18, 1. McFall-Ngai, M., Hadfield, M.  G., Bosch, T.  C. G., Carey, H.  V., Domazet-Lošo, T., Douglas, A. E., Dubilier, N., Eberl, G., Fukami, T., Gilbert, S. F., Hentschel, U., King, N., Kjelleberg, S., Knoll, A. H., Kremer, N., Mazmanian, S. K., Metcalf, J. L., Nealson, K., Pierce, N. E., Rawls, J. F., Reid, A., Ruby, E. G., Rumpho, M., Sanders, J. G., Tautz, D., & Wernegreen, J. J. (2013). Animals in a bacterial world, a new imperative for the life sciences. Proceedings of the National Academy of Sciences, 110(9), 3229–3236. McNear, D. H., Jr. (2013). The rhizosphere – roots, soil and everything in between. Nature Education Knowledge, 4(3), 1. Muyzer, G., Teske, A., Wirsen, C.  O., & Jannasch, H.  W. (1995). Phylogenetic relationships of Thiomicrospira species and their identification in deep-sea hydrothermal vent samples by denaturing gradient gel electrophoresis of 16S rDNA fragments. Archives of Microbiology, 164, 165–172.

18

Z. Tabashsum et al.

Oren, A. (2009). Microbial diversity. In Encyclopedia of life sciences. Chichester: Wiley. Prussin, A. J., II, & Marr, L. C. (2015). Sources of airborne microorganisms in the built environment. Microbiome, 3, 78. Raina, J.-B., Eme, L., Pollock, F. J., Spang, A., Archibald, J. M., & Williams, T. A. (2018). Symbiosis in the microbial world: from ecology to genome evolution. Biology Open, 7(2), bio032524. Razavi, B. S., Hoang, D. T., Blagodatskaya, E., & Kuzyakov, Y. (2017). Mapping the footprint of nematodes in the rhizosphere: Cluster root formation and spatial distribution of enzyme activities. Soil Biology and Biochemistry, 115, 213–220. Relman, D. A. (2012). The human microbiome: Ecosystem resilience and health. Nutrition Reviews, 70, 2–9. Reperant, L. A., Brown, I. H., Haenen, O. L., de Jong, M. D., Osterhaus, A. D., Papa, A., Rimstad, E., Valarcher, J. F., & Kuiken, T. (2016). Companion animals as a source of viruses for human beings and food production animals. Journal of Comparative Pathology, 155(1 Suppl 1), S41–S53. Rothman, J. M., Dierenfeld, E. S., Molina, D. O., Shaw, A. V., Hintz, H. F., & Pell, A. N. (2006). Nutritional chemistry of the diet of gorillas in the Bwindi Impenetrable National Park, Uganda. American Journal of Primatology, 68, 675–691. Schmidt, T. S., Raes, J., & Bork, P. (2018). The human microbiome: From association to modulation. Cell, 172(6), 1198–1215. Schulz, H.  N., & De Beer, D. (2002). Uptake rates of oxygen and sulfide measured with individual Thiomargarita namibiensis cells by using microelectrodes. Applied and Environmental Microbiology, 68, 5746–5749. Shade, A., Peter, H., Allison, S., Baho, D., Berga, M., Buergmann, H., Huber, D., Langenheder, S., Lennon, J., Martiny, J., Matulich, K., Schmidt, T., & Handelsman, J. (2012). Fundamentals of microbial community resistance and resilience. Frontiers in Microbiology, 3, 417. Shreiner, A. B., Kao, J. Y., & Young, V. B. (2015). The gut microbiome in health and in disease. Current Opinion in Gastroenterology, 31(1), 69–75. Tasnim, N., Abulizi, N., Pither, J., Hart, M. M., & Gibson, D. L. (2017). Linking the gut microbial ecosystem with the environment: Does gut health depend on where we live? Frontiers in Microbiology, 8, 1935. The Human Microbiome Project Consortium. (2012). Structure, function and diversity of the healthy human microbiome. Nature, 486(7402), 207–214. Tomley, F. M., & Shirley, M. W. (2009). Livestock infectious diseases and zoonoses. Philosophical Transactions of the Royal Society B: Biological Sciences, 364, 2637–2642. Trinh, P., Zaneveld, J.  R., Safranek, S., & Rabinowitz, P.  M. (2018). One health relationships between human, animal, and environmental microbiomes: A mini-review. Frontiers in Public Health, 6, 235. Valdes, A. M., Walter, J., Segal, E., & Spector, T. D. (2018). Role of the gut microbiota in nutrition and health. BMJ, 361, k2179. Vivarelli, S., Salemi, R., Candido, S., Falzone, L., Santagati, M., Stefani, S., Torino, F., Banna, G. L., Tonini, G., & Libra, M. (2019). Gut microbiota and cancer: From pathogenesis to therapy. Cancers, 11(1), 38. Wiedemann, A., Virlogeux-Payant, I., Chaussé, A. M., Schikora, A., & Velge, P. (2015). Interactions of Salmonella with animals and plants. Frontiers in Microbiology, 5, 791. Young, K.  D. (2007). Bacterial morphology: Why have different shapes? Current Opinion in Microbiology, 10(6), 596–600. Zierer, J., Jackson, M. A., Kastenmüller, G., Mangino, M., Long, T., Telenti, A., Mohney, R. P., Small, K.  S., Jordana, T., Bell, J.  T., Steves, C.  J., Valdes, A.  M., Spector, T.  D., & Menni, C. (2018). The fecal metabolome as a functional readout of the gut microbiome. Nature Genetics, 50, 790–795.

Determinants of the Gut Microbiota Arunachalam Muthaiyan

1  Introduction In recent decades, the human microbiota is one of the most focused dynamic research areas in the biomedical sciences. In particular, more efforts have been made to study the gastrointestinal (GI) tract, which harbors most of the microbiota of the human body (Huttenhower et al. 2014; Schmidt et al. 2018; Jalili-Firoozinezhad et al. 2019). A human microbiota is the community of microorganisms including bacteria, archaea, eukaryotic microbes, bacteriophages, and eukaryotic viruses living inside and on a human body and influence the host health (Hooper and Gordon 2001; Huttenhower et al. 2012; D’Argenio and Salvatore 2015; Wang et al. 2017; Hugon et  al. 2017; Lederer et  al. 2017). However, interestingly, the study of the healthy human microbiota has been greatly focusing on bacteria, with less attention given to other microbial domains (Lloyd-Price et al. 2016). Genes associated with this microbial community are referred as human microbiome and scientists use the microbiome to describe the composition of microbiota and its function across a number of contexts (Amato 2017). The human microbiome encompasses collection of all the genomic elements of a specific microbiota, which include the microbial genes, gene products, and genomes of the microbiota (Proctor 2011) (Box 1).

A. Muthaiyan (*) Division of Mathematics, Physical and Natural Sciences, University of New Mexico - Gallup, Gallup, NM, USA e-mail: [email protected] © Springer Nature Switzerland AG 2020 D. Biswas, S.O. Rahaman (eds.), Gut Microbiome and Its Impact on Health and Diseases, https://doi.org/10.1007/978-3-030-47384-6_2

19

20

A. Muthaiyan

Box 1 Microbiota or Microbiome? The term “microbiota” refers to all microorganisms including bacteria, archaea, eukaryotic microbes, bacteriophages, and eukaryotic viruses found in a specific environment (e.g., skin and gastrointestinal tract). The “microbiome” refers to the collection of whole genome from the microbiota. These microorganisms, their genes, metabolites, and interactions with one another, as well as with their host collectively, represent our microbiome. Even though these two terms have subtle differences, microbiota and microbiome are often used interchangeably.

The human body carries two genomes, one inherited from the parents and the other acquired from microbiome. This concept is the basis of the definition of humans as “holobiont” or “superorganisms” (Cavalier-Smith 1992; Grice and Segre 2012; Walsh et  al. 2014; van de Guchte et  al. 2018). The National Institutes of Health Common Fund launched the human microbiome project (HMP) in 2007 to understand the human–microbiome interaction, and develop resources for characterizing the microbiome in healthy adults and in people with specific microbiome-­ associated diseases. Now it has been developed into one of the major focuses in the biomedical research. The HMP has provided an extensive resource of data, computational tools, clinical methods, and scientific approaches to study the human microbiome (Proctor 2011, 2016; NIH Common Fund 2019). Data from the HMP have drawn an increasing amount of attention toward gut microbiome research, and emerging evidences from the research studies show the major role of the gut microbiome in the human health and pathogenesis of certain diseases (Richards et  al. 2016; Lagier et al. 2016; Blum 2017; Schmidt et al. 2018; McDonald et al. 2018; Heintz-Buschart and Wilmes 2018; Sitaraman 2018; Pasolli et al. 2019; Nayfach et al. 2019; Khangwal and Shukla 2019; Huang et al. 2019). The term “old friends” has been used for the gut microbes originating from the natural environment such as soil, plants, and domesticated animals. The human gastrointestinal (GI) microbiota also known as gut microbiota is a complex microbial community that lives in the digestive tract of human host and coevolved over thousands of years and has developed a mutually beneficial relationship (Tap et al. 2009; Rajilić-Stojanović and de Vos 2014) (Box 2).

Box 2 The Gastrointestinal Tract The human gastrointestinal tract or GI tract (also known as “human gut”) is a series of joined tubular organs that starts from the mouth, extending through the esophagus, stomach, small intestine, colon, rectum, and ends at the anus. The GI tract and the solid organs such as liver, pancreas, and gallbladder together make up the entire human digestive system.

Determinants of the Gut Microbiota

21

The gut microbiota influence human health by affecting a variety of processes in a host (Kho and Lal 2018). For example, the gut microbes play major roles in the regulation metabolism, breakdown of dietary fiber and access nutrients from the food, production of essential vitamins, and ward off pathogens and infections, development of immune system, influencing postoperative healing, influencing the success of organ transplantation, regulation of brain health and disorders of the central nervous system, maintaining cardiovascular health and diseases, and human behavior, and shaping the personality (Neish 2009; Turnbaugh et al. 2009; Round and Mazmanian 2009; Cerf-Bensussan and Gaboriau-Routhiau 2010; Bercik et al. 2010; LeBlanc et  al. 2013; Belkaid and Hand 2014; Dinan et  al. 2015; Sassone-­ Corsi and Raffatellu 2015; Jiang et al. 2015; Fu et al. 2015; D’Argenio and Salvatore 2015; Wang et al. 2017; Kamo et al. 2017; Rieder et al. 2017; Lederer et al. 2017; Yamashita et  al. 2018; Kim et  al. 2018; Rahim et  al. 2018; Yoshida et  al. 2018; Weber et al. 2019; Abdul Rahim et al. 2019; Lee and Stern 2019). They may also play a major role in human health and disease pathogenesis and have turned out to be biomarkers of health and disease of the host (Richards et  al. 2016; Cani and Knauf 2016) (Fig. 1). The revised estimate of human microbiota number is to be about 3.8  ×  1013 microbial cells, with about 1:1 microbial cells-to-human cells ratio, and the microbial cells total mass is about 0.2 kg (Sender et al. 2016). A dense number of microbes reside in the colon (Walker 2016). In addition, the estimate revealed that the human gut microbiome houses more than 5 million different genes. It is now known that over 1000 different microbial species colonize the human gut (Rosenwald et  al. 2012). The colonization of gut microbes begins at birth and proceeds for several years with complex processes to acquire diverse microbial population throughout the life span of human. The colonization and subsequent establishment of the microbiota in infant are mainly influenced by the mode of delivery (vaginal or cesarean delivery). Other external and internal factors including the feeding method of a neonate, adult diet, drugs used for therapy including antibiotics, host genetics and immune system, and several other factors altogether interact with the human microbiota and influence the composition and function of the microbiome during the life span of the host (Fig. 2) (Ferrer et al. 2014; Goodrich et al. 2014; Moya and Ferrer 2016; Lynch and Pedersen 2016; Thursby and Juge 2017; Blum 2017; Tanaka and Nakayama 2017; Milani et al. 2017; Dong and Gupta 2019; Poole et al. 2019). However, research data show that the human gut microbiota contains a core community of permanent colonizers, and during the adulthood, the external environmental factors primarily affect the abundance of the core community but not the presence of specific microbial species (Rajilić-Stojanović et al. 2013). Therefore, a better understanding of these influential factors that affect our gut microbiome is important, and it will certainly help us to build a beneficial human gut microbial community to improve our health, and design novel microbial interventions to combat diseases in future.

22

A. Muthaiyan

Fig. 1  Role of gut microbiome on human health

2  External Factors Influencing Gut Microbiota 2.1  Mode of Delivery The maternal microbial reservoir plays a crucial role in the process of acquiring the gut microbiota in infants (Mändar and Mikelsaar 1996; Scholtens et al. 2012; Neu 2016; Ferretti et al. 2018). The mode and term of delivery (vaginal vs. cesarean; term vs. preterm) have influence on the microbial community that infants acquire during the birth. Research studies on the initial establishment of microbial communities in infants have revealed that upon delivery, the newborn is exposed for the first time to a wide range of microorganisms from mother as well as from a variety of sources (Fanaro et  al. 2003; Penders et  al. 2006; Dominguez-Bello et  al. 2010; Koenig et al. 2011). The early gut microbial colonization in infant is an important

Determinants of the Gut Microbiota

23

Fig. 2  Factors influencing the composition of gut microbiota

process with an impact on the immunological and metabolic programming of later health of the child (Amato 2017; Vuillermin et al. 2017; Codagnone et al. 2019). Since the birth, human gut serves as a home for myriad microorganisms. These microorganisms are not casual bystanders or invaders during the birth or when the infant is developing its premature immune system (Guarner 2015). It is believed that in infants, the colonization of microbiota usually begins from birth. However, a number of research studies reported the presence of microbes in amniotic fluid and placenta, which may play a role as an initial microbial source for the infant (DiGiulio et al. 2008; Martin et al. 2016; Neu 2016; Gomez-Arango et al. 2017; Younes et al. 2018; Chu et al. 2018). Regardless of these findings, studies show that microbiota is inherited vertically from mothers to infants (Ley et al. 2006), and babies acquire their initial microbiota from the vagina and feces of their mothers (Mändar and Mikelsaar 1996; Rutayisire et al. 2016). Since the infants receive their microbiota during the birth, the mode of delivery plays a key role in the initial microbial colonization. Studies showed that babies delivered by cesarean section (CS) have a different colonization pattern compared to their vaginally delivered counterparts (Penders et al. 2006; Scholtens et al. 2012; Dominguez-Bello et al. 2016; Rutayisire et al. 2016). CS-born infants reportedly had lower numbers of bifidobacteria and

24

A. Muthaiyan

Bacteroides, and more often colonized with C. difficile, compared with vaginally born infants (Penders et al. 2006). Research studies comparing vaginally born and CS-born babies showed that vaginally delivered infants acquired bacterial communities similar to the maternal vaginal and perineal microbiota dominated by Lactobacillus, Prevotella, or Sneathia spp. However, CS-born babies were mostly dominated by Staphylococcus, Corynebacterium, and Propionibacterium spp. from maternal skin, delivery and surgical equipment, air, healthcare workers, and other nosocomial environmental factors (Dominguez-Bello et  al. 2010; Martin et  al. 2016; Blaser and Dominguez-Bello 2016). In addition to the mode of delivery, gestation period (term or preterm) also influences the development of gut microbiota (Mshvildadze et al. 2008). Studies found that, due to the prolonged hospitalization and antibiotic treatment in the preterm deliveries, preterm born infants tend to acquire lower microbial diversity compared to term neonates. Alteration of gut microbiota causes bacterial translocation, inflammation, and oxidative stress, thus contributing to the development of necrotizing enterocolitis, and late-onset sepsis in preterm babies (Collado et al. 2015). Although conflicting reports exist about the role of delivery mode in determining the gut microbe, in summary, research studies indicate that compared to vaginally delivered infants, CS-delivered infants are likely to have reduced anaerobe population and a decreased microbial diversity in their gut (Biasucci et  al. 2008; Jakobsson et  al. 2014; Martin et al. 2016). Also, their gut had delay in colonizing gut microbiota (Wampach et al. 2017), and in their early stages of life, more frequently, they tend to acquire atopic diseases and immune and metabolic disorders (Biasucci et  al. 2008; Dominguez-Bello et al. 2016).

2.2  Diet Dietary habits have a strong influence on the selection of gut microbiota. Diet has a primary role over other factors such as race, age, gender, hygiene, geography, and environment, in shaping the human gut microbiota (Fig.  3). Nutrients from the infant diet and adult diet directly interact with gut microorganisms to promote or inhibit their growth (De Filippo et al. 2010; Kau et al. 2011; Yatsunenko et al. 2012; Moschen et al. 2012; Sheflin et al. 2017; Flint et al. 2017; Singh et al. 2017; Zmora et al. 2019). 2.2.1  Infant Diet Studies found that apart from the mode of delivery, feeding method (breastfeeding or formula feeding) strongly influences the development of the infant gut microbiota. After the birth, breast milk is the first food that is introduced into the GI tract of the infant. The composition of the human milk is believed to have a direct effect on shaping the early GI microbiota (Guaraldi and Salvatori 2012; Scholtens et  al.

Determinants of the Gut Microbiota

25

Fig. 3  Diet and gut microbiota

2012). Human milk plays a major role in providing the substrates and microbial inoculum for the growth and development of the gut microbiota in the early stage of the life. Microbial analysis of breast milk showed the presence of members from Streptococcus and Staphylococcus genera, those being reported as the early colonizers of the gut (Collado et al. 2009). Bifidobacterium and Lactobacillus are also frequently detected in human milk. It suggests that breast milk plays an important role as a delivering system for probiotic bacteria in the early gut. Research reports suggest that the maternal gut could be the source for these live Bifidobacterium and Lactobacillus cells found in breast milk. It is believed that maternal gut microbes would arrive at the mammary gland through an endogenous route, involving maternal dendritic cells and macrophages, and create “breast microbiota” and serve as a source of infant gut microbiota (Fernández et  al. 2013). Besides introducing the bacterial members, breast milk introduces the fungal members as well to the infant gut. A recent study confirmed the presence of fungi in breast milk collected across the continents, and supports the potential role of breast milk in the initial colonization of fungal species in the infant gut (Boix-Amorós et al. 2019). Besides its nutritional values, human milk contains several bioactive components called human milk oligosaccharides (HMOs), a form of prebiotics, that directly influence the developing infant and dictate and support the type of the microbes to colonize the gut (Le Huërou-Luron et al. 2010; Collado et al. 2015; Gomez-Gallego et al. 2016). Results from studies comparing both breast-fed and formula-fed gut microbiota showed that Bifidobacteria were the most-represented species in both breast- and

26

A. Muthaiyan

formula-fed infants (Guaraldi and Salvatori 2012). However, formula-fed infant gut microbiota developed with facultative anaerobes, Bacteroides and Clostridia at higher levels and frequency than in breast-fed infants. Also, breast-fed newborns carried a more stable and uniform microbial population than formula-fed infants (Rastall et  al. 2005; Bezirtzoglou et  al. 2011). Genotyping analysis of microbes presence in the breast milk of mothers and fecal samples of their infants showed the presence of identical strains of Lactobacillus, Staphylococcus, and Bifidobacterium, suggesting the influence of breast-milk in early gut microbial colonization in infants (Martín et al. 2012). 2.2.2  Adult Diet During the early stage of life, weaning, a process of switching an infant’s simple diet (breast milk) to other solid foods, influences the shift of gut microbiota. Reports indicate that the introduction of solid food significantly alters the composition of infant gut microbiota with increased microbial diversity and metabolites produced by gut microbiota (Fuertes et al. 2019). Analysis of the fecal microbial composition of infants after weaning showed a reduced proportions of bifidobacteria, enterobacteria, Clostridium difficile and C. perfringens species, whereas the proportions of the C. coccoides and C. leptum groups were increased (Fallani et al. 2011). The intestinal microbiota of adults is much different from the one of infants. By the end of the first year of life, the baby’s gut microbiota converges toward a profile characteristic of the adult gut (Palmer et  al. 2007). Although the time frame and bacterial species involved in the normal development of the intestinal microbiota of the infant are well understood, the factors affecting the transition of infant gut microbiota to adult gut microbial profile are more difficult to comprehend (Fanaro et  al. 2003; Kumbhare et  al. 2019). It is believed that the rapid response of gut microbiome to altered diet potentially facilitates the diversity of human dietary lifestyles. Generally, the matured adult gut microbiota consists of two main phyla belong to the Firmicutes (Clostridium, Faecalibacterium, Blautia, Ruminococcus, and Lactobacillus) and the Bacteroidetes (Bacteroides and Prevotella) (Tap et al. 2009). More studies have focused on the effect of Firmicutes/Bacteroidetes ratio on human health. Interestingly, this ratio is reportedly linked to obesity and metabolic disorders. The ratio of these two microbial groups originates from the initial development of the microbiota during the early infant stage, and continues throughout the entire life of the individual (Mariat et al. 2009). Besides the common adult nutrients (carbohydrate, protein, and lipid), availability of vitamins also influences the gut microbiota. Research showed that vitamin D regulates the composition of the gut bacterial microflora and that vitamin D deficiency causes dysbiosis (microbial imbalance in the gut), increased inflammation, and more severe experimental colitis in mice model study (Ooi et al. 2013).

Determinants of the Gut Microbiota

27

2.2.3  Carbohydrate, Protein, and Lipid Dietary carbohydrates that are partially digested in the upper gut are known as non-­ digestible carbohydrates. They are the major energy source for the bacterial members that live in human large intestine (Flint et al. 2012, 2015, 2017). Studies have shown that the habitual vegetarian and vegan diets rich in fruit, legumes, whole grains, vegetables, and fibers promote enrichment of fiber-degrading bacteria in the gut and increase the levels of fecal short-chain fatty acids (SCFAs) (Scott et  al. 2008; Martínez et al. 2013; Scott et al. 2013; Matijašić et al. 2014; De Filippis et al. 2016; Kisuse et al. 2018; Jefferson and Adolphus 2019; Tomova et al. 2019). Also the vegan and vegetarian gut microbial profile is unique in several characteristics, including a reduced abundance of disease-related microbes and a greater abundance of protective microbial species (Glick-Bauer and Yeh 2014; Ruengsomwong et al. 2016; Wong et al. 2018; Kisuse et al. 2018). In adults, Firmicutes/Bacteroidetes ratio is influenced by the diet. Research studies have reported that Firmicutes/Bacteroidetes ratio differs between individuals having a rich Western diet or a more rural and vegetable-based Mediterranean diet (Yatsunenko et al. 2012). Studies involving healthy adults exposed to diets restricted to meat or vegetable intake have shown interesting gut microbiota responses. In meat-consuming human subjects, selective enrichment of bile-metabolizing microbiota has been observed, which is associated with inflammatory bowel disease. In vegetable-consuming human subjects, increase of plant polysaccharide-fermenting organisms has been observed (David et al. 2014; Simpson and Campbell 2015). Generally, the diet of Western countries contains higher fat and protein and lower fiber, fruit, and vegetables compared with those of developing countries (De Filippo et al. 2010; Simpson and Campbell 2015; Zinöcker and Lindseth 2018). In general, colonization of specific group of intestinal microbes that degrade polysaccharides from fibers in vegetarian diet is beneficial to the host. This is because they produce various SCFAs, such as butyrate, propionate, and acetate, via fermentation. These SCFAs have beneficial on the host colonic enterocytes. In B cells, SCFAs increase acetyl-CoA and regulate oxidative phosphorylation, glycolysis, and fatty acid synthesis, which produce energy and building blocks supporting antibody production (Kim et al. 2016). On the other hand, consumption of large quantities of meat is associated with the alteration of gut microbiota that processes the excess amount of protein into harmful phenolic compounds, ammonia, and hydrogen disulfide in the colon, which is shown to be harmful to the host health and linked to an increased risk of developing colon cancer. Similar to carbohydrate- and protein-rich diet, fat-exclusive diet also influences the prevalence of specific microbes in the guts of humans and animals (LEE 2013). Such fat-induced changes lead to a substantial decrease in the production of beneficial SCFAs and antioxidants in the colonic region of the gut, and increase the negative health consequences on the host (Scott et al. 2013; Agans et al. 2018). A study found increased abundance of Alistipes, Bilophila, and several genera of the class Gammaproteobacteria on the fats-only medium. In contrast, the presence of glycan and protein-degrading bacterial members, including Bacteroides, Clostridium, and

28

A. Muthaiyan

Table 1  Effect of different types of diet on gut microbiota (Bibbò et al. 2016) Diet type Carbohydrates

Non-digestible starch

High soluble fiber diet Complex carbohydrate Low-fiber diet

Oligosaccharides Fructo-­ oligosaccharides Inulin

Increased gut microbiota Ruminococcus spp., Eubacterium rectale, Bifidobacterium adolescentis, Roseburia spp., Ruminococcus bromii, Parabacteroides diastasonis Bacteroides spp., Clostridium leptum, Eubacterium rectale Bifidobacterium spp., Prevotella spp.

Roseburia spp., Eubacterium rectale Bifidobacterium spp., Lactobacillus spp. Bifidobacterium spp., Lactobacillus spp.

Fructans

High-fat diet

Galacto-­ oligosaccharides Arabinoxylan-­ oligosaccharides Safflower oil (containing ω-6 polyunsaturated fatty acids) Polyunsaturated fatty acids (PUFA) ω-6 PUFA Monounsaturated fatty acids (MUFA) High-fat diet

Decreased gut microbiota Eubacterium rectale, Ruminococcus bromii

Bacteroides spp., Clostridium spp. Bifidobacterium spp., F. prausnitzii Bifidobacterium spp. Firmicutes, Actinobacteria, Proteabacteria

Bacteroides spp.

Lactobacillus spp.

Members of Deltaproteobacteria, Bilophila wadsworthia

Bifidobacterium spp. Bifidobacterium spp. Roseburia spp.

Roseburia spp., was decreased in fat-exclusive medium. These dietary changes resulted in lower microbial production of SCFAs and antioxidants (Agans et  al. 2018). Recently, Bibbò et al. have reviewed the literature and emphasized the effect of different types of carbohydrate- and lipid-containing diet on the composition of gut microbiota (Table 1) (Bibbò et al. 2016).

Determinants of the Gut Microbiota

29

2.2.4  Change in the Dietary Pattern In addition to the type of consumed diet (i.e., Western or Mediterranean diet), studies found that the duration of the dietary pattern (i.e., long-term or short-term diet change) also has an influence in determining the type of gut microbial colonization in the host (David et al. 2014; Bibbò et al. 2016; Sonnenburg et al. 2016). David et  al. have shown that in human subjects, short-term (5 days) consumption of entirely animal based- or plant based-diet altered the gut microbial community structure that significantly differed from their microbiota population 4 days before and 6 days after the experimental diet period. In their study, they found that an entirely animal-based short-term diet increased the abundance of bile-tolerant microorganisms such as Alistipes, Bilophila, and Bacteroides and decreased the levels of Firmicutes (Roseburia, Eubacterium rectale, and Ruminococcus bromii) that reportedly metabolize dietary plant polysaccharides. Based on their findings, it has been reported that the gut microbiome can rapidly respond to altered diet pattern and this short-term change may potentially facilitate the ever-changing human dietary lifestyles (David et al. 2014). Unlike the short-term diet change, long-term change in the dietary pattern leads to progressive loss of gut microbial diversity and results in irrecoverable loss of specific group of microbiota. In a human microbiota harboring mouse model study, using MACs (microbiota-accessible carbohydrates, the primary source of carbon and energy for the distal gut microbiota), Sonnenburg et al. have demonstrated the effect of long-term diet change in determining the gut microbiota in mice. They have shown that changes in the microbiota of mice consuming a low-MAC diet over several generations resulted in a progressive loss of gut microbial diversity even in their next generations. Due to the complete disappearance of certain microbial taxa for several generations, the loss of microbial diversity was not recoverable even after the reintroduction of dietary MACs to the mice. Interestingly, to restore the microbiota to its original state required the administration of both missing microbial taxa and dietary MACs in the food (Sonnenburg et al. 2016). It has been observed that when consumption of dietary MACs was inadequate for several generations, the MACs-dependent microbial taxa was driven to low abundance. Therefore, natural transfer of those low-abundant microbial taxa to the next generations was severely affected and eventually those gut microbial taxa became extinct within an isolated population (Sonnenburg et al. 2016). These research findings indicate that the long-term diet-induced loss of microbiota diversity will irrecoverably be prolonged over several generations and have influence on shaping the gut microbiota of the future generations. 2.2.5  Prebiotics and Probiotics Prebiotics are short-chain carbohydrates that influence the composition and metabolism of the gut microorganisms. They provide carbon and energy sources for bacteria residing in the large intestine. Gut microbes ferment the prebiotic carbohydrate

30

A. Muthaiyan

and produce beneficial SCFAs. These SCFAs serve as energy sources for the gut and other body tissues (Macfarlane et al. 2006). Since the past decades, several research studies have been aiming to understand the mechanisms by how prebiotic oligosaccharides selectively allow beneficial gut microbes to metabolize and establish the colonies in gut environment (Rastall et al. 2005). Research studies found that the prebiotic oligofructose, galacto-­oligosaccharides, and lactulose have potential to alter the microbiota in the large intestine by increasing the members of bifidobacteria and Lactobacillus (Macfarlane et  al. 2006; Costalos et al. 2008). These bacterial members are well known for their positive impact on gut health. These gut microbes have an important role in providing increased resistance to gut infections and may have a role in immunomodulatory properties. Even in an infant diet, inclusion of prebiotics influences the gut microbiota of the infants. Reports have shown that an infant formula containing a prebiotic (galacto- and long-chain fructooligosaccharides) reduced the number of clostridia and E. coli, and slightly increased bifidobacteria in infants (Costalos et al. 2008). Probiotics are defined as “live microorganisms which when administered in adequate amounts confer a health benefit on the host” (Food and Agriculture Organization of the United Nations 2006; Hill et al. 2014). In recent decades, growing global interest in understanding the link between the human microbiota and health and a search for effective strategies to shape a healthier microbiota have advanced the field of probiotics (Hill et al. 2014). To improve the health, probiotic supplementation has been one of the approaches commonly used to reshape the host gut microbiota (Kristensen et al. 2016). However, a study of systematic review of literature from clinical trials found lack of evidence for an impact of probiotics on fecal microbiota composition in healthy adults and indicating the minimal influence of probiotics on gut microbiota composition (Kristensen et al. 2016). One possible reason for this minimal effect of probiotics on gut microbiota is believed to be the resistance of innate resident gut microbiota against invading non-resident probiotic intestinal microbes. Unless the incoming probiotics do not metabolically complement the resident gut microbiota, the effect of probiotics supplement on gut microbiota diversity is minimal or none. It has been demonstrated by Buffie et al. in a mouse model study in which the administration of Clostridium scindens was well received by the mice gut microbiota for its metabolic complementation and ability to enhance colonization resistance against pathogenic Clostridium difficile in recipient mice gut (Buffie et al. 2015). Thus, more research studies are required to understand the role and effect of probiotics on shaping the gut microbiota (Schmidt et al. 2018). In summary, diet has a strong influence in deciding diversity and quantity of gut microbiota, which in turn has important effects on a variety of health-related aspects of the host organism. Growing evidences indicate that the type of diet from infancy through adulthood of the life ultimately defines the diversity and colonization of gut microbiota. It is relevant for not only the microbiota colonization but also the host health through a number of physical relations and biochemical signaling between the host and microbiota. Overall, breast milk is an important diet at early infancy

Determinants of the Gut Microbiota

31

and it shows short- and long-term influence on the gut microbiota. During the adulthood, diet rich in fruits, legumes, whole grains, vegetables, and fibers significantly influences greater richness of friendly gut microbiota compared to omnivorous diet (Guaraldi and Salvatori 2012; Losasso et al. 2018; Ercolini and Fogliano 2018).

2.3  Therapeutic Drugs and Fecal Transplantation 2.3.1  Antibiotics Globally, antibiotics are frequently being used for treatments and other agricultural and animal husbandry purposes, and also the prescription of antibiotics is continuing to rise (Ferrer et al. 2017). Gut microbes affect our health by involving in the metabolism of host-targeted drugs and antibiotics. However, the drugs used by the host have been implicated in shaping the gut microbiota and no other external factor has had a faster or more direct effect on gut microbiota than antimicrobial agents. Although antibiotics have a property of selective toxicity, it is a well-known fact that they not only affect the pathogens to which they are directed but may also impact other beneficial commensals of the gut, leading to microbial imbalance (dysbiosis) (Dethlefsen et al. 2008; Dong and Gupta 2019). Antibiotics and host-­targeted drugs rapidly alter the gut microbiome structure, physiology, and gene expression of the active gut microbiome (Maurice et  al. 2013; Gillings et  al. 2015; Bhalodi et al. 2019). Antibiotics are often an unavoidable and sometimes life-saving part of neonatal clinical care. However, the use of antibiotics in neonates influences the initial intestinal colonization pattern and causes major effect on microbial succession (Cotten 2016; Browne 2016). This is also true for infants; if the mother used any type of drug during her pregnancy or during the childbirth, it has a tremendous effect on the infant’s developing microbiota. Also at any time, antibiotic treatment of a feeding mother can indirectly influence the child’s microbiota (Lemas et  al. 2016; Zimmermann and Curtis 2018; Kim et al. 2019). Especially, the effect of antibiotics is more relevant early in life, when the gut microbiota has not yet fully established (Matamoros et al. 2013; Iizumi et al. 2017; Gomez-Arango et al. 2017). The main effects observed in infant gut microbiota include a relevant suppression of all anaerobic bacteria. However, the emergence of antibiotic-resistant gut bacterial strains is fairly common (Jernberg et al. 2007). This is a usual situation in infants cared for in neonatal intensive care units (Fanaro et al. 2003). Since antibiotics are used in all countries in almost all children to inhibit bacterial growth to prevent or treat infections, they may play a strong role in controlling the selection and shaping of gut microbial community at the young age. There have been reports that speculate that the widespread antibiotic usage among young children might have caused alterations in their gut microbial compositions, and the lumenal signals to the host, that are directly contributing to the epidemic of obesity in developed countries (Blaser

32

A. Muthaiyan

and Falkow 2009; Brüssow 2015; Blaser 2016; Ianiro et  al. 2016; Turta and Rautava 2016). Ferrer et al. have reviewed the effect of 68 different antibiotics on human microbiota composition and microbiome function and revealed that antibiotics cause changes in a specific set of bacteria, fungi, archaea, and viruses in human gut. In another study, they have reported that the administration of β-lactam intravenous therapy consisting of ampicillin, sulbactam, and cefazolin significantly affected the distal gut microbial community. Also, their report revealed that the gut microbe metabolic activity is drastically altered as a direct consequence of antibiotic treatments (Ferrer et  al. 2014, 2017). Similarly, it has been reported that in healthy adults, ciprofloxacin (500 mg twice a day for 5 days) reduced the diversity of the intestinal microbiota. About one-third of the bacterial taxa were affected by the ciprofloxacin treatment (Dethlefsen et  al. 2008; Dethlefsen and Relman 2011). Also, in another study, it has been reported that the short-term impact of broad-­ spectrum antibiotics (ciprofloxacin, vancomycin and metronidazole for 7 days) on the gut microbiota was reportedly profound, with a loss of diversity and drastic shifts in gut microbial community composition (Isaac et al. 2017; Haak et al. 2019). In addition, these antibiotics significantly reduced the abundance of bacterial taxa with important metabolic functions, such as the production of butyrate (Haak et al. 2019). However, these studies have reported that despite this disturbance, the members of the microbiota had largely returned to the pretreatment state between 4 weeks to 31 months, but the return was often incomplete and often remained altered from its initial state (Dethlefsen et al. 2008; Dethlefsen and Relman 2011; Haak et al. 2019). In another study, it has been reported that clarithromycin and metronidazole treatment used against H. pylori in the lower intestine dramatically altered the gut microbial composition 1 week after antibiotic treatment with reduced bacterial diversity. Even though the microbial diversity was subsequently recovered to its pretreatment state, in some cases the disrupted microbial diversity was observed for up to 4 years post treatment (Jakobsson et al. 2010). Another popular antibiotic regimen of isoniazid, rifampin, pyrazinamide, ethambutol that was used for tuberculosis (TB) treatment in humans has been reported to disrupt the intestinal microbiome over a long term. During the TB treatment, it has been observed that members of certain gut microbial genera are depleted and these alterations, in terms of both taxonomic and metagenomic function, are extended for more than 1 year after the completion of the therapy (Wipperman et al. 2017). Although it is widely accepted that the resident gut microbiota stabilizes a few weeks after an antibiotic administration, the effect of a short-term clindamycin exposure even for 7 days can have persistent consequences up to 2 years on gut microbiota (Jernberg et  al. 2007; Rashid et  al. 2015). Similarly, amoxicillin and azithromycin treatment for as few as 3 days caused reductions in gut microbial composition. It could have potential implications for the maintenance of human health and disease resistance ability of the body (Abeles et al. 2016). Even single dose of antimicrobial therapy disrupts the gut microbiota and it would take up to several weeks for recovery of the gut microbiota (Bhalodi et al. 2019).

Determinants of the Gut Microbiota

33

Fig. 4  Effect of antibiotics on gut microbiota

In addition to the alteration of the gut microbial population, antibiotics make the gut microbes as a reservoir of resistance genes, which can be transferred to potential pathogens (Ghosh et al. 2013; Modi et al. 2014; Górska et al. 2018; Nogueira et al. 2019). It has been reported that 4 years after clarithromycin and metronidazole treatment, it resulted in high levels of the macrolide resistance gene erm (B) in the human gut microbiome (Jakobsson et al. 2010). A metagenomics study screening for antibiotic resistance genes in human gut microbiome from different geographical regions has discovered the presence of potential antibiotic resistance genes conferring resistance against 53 different antibiotics. Additionally, this study has revealed the presence of mobile multidrug resistance gene in certain gut microbiomes. Besides the daunting report about the presence of resistance genes in gut microbes, the study has revealed an alarmingly high abundance of antibiotic resistance genes in the gut microbiome of two infants (Ghosh et al. 2013). In summary, research studies showed that antibiotics exert a significant impact on the gut microbiota and give a sign of caution for a more restricted use of pharmacological drugs and the use of antibiotics (Fig. 4). The effect of antibiotics is more relevant in the early stage of life when the gut microbiota has not yet fully established (Iizumi et al. 2017). Human gut microbes are continuously exposed to antibiotics because antibiotics are not only used for human treatments but they are also widely utilized in farm animals, and crops to enhance the product. The “friend” or “foe” behavior of antibiotics toward gut microbiota is influenced by their class,

34

A. Muthaiyan

pharmacokinetics, pharmacodynamics, mode of action, as well as their dosage, duration, administration route, host age, lifestyle, and the composition of microbiota (Ianiro et al. 2016; Nogueira et al. 2019; Sun et al. 2019). Recent studies suggest that exposure to antibiotics at early stage of life that alters the gut microbial composition may be a reason for the growing chronic and autoimmune diseases in the population (Keeney et al. 2014; Korpela et al. 2016; Iizumi et al. 2017). However, antibiotics exposure at any stage of human life can rapidly alter the gut microbial composition with potential direct or indirect effects on host health. The change in the gut microbial composition may allow the selection of resistant and opportunistic pathogens that can cause acute disease or can cause long-term diseases by affecting the host immune and metabolic homeostasis. However, besides the harmful effect on gut microbiota, some antibiotics can cause a positive “eubiotic” effect, by increasing the abundance of beneficial bacteria in the gut (Ianiro et al. 2016) (Fig. 4). 2.3.2  Non-antibiotic Drugs Non-antibiotic prescription drugs such as proton pump inhibitors (Imhann et  al. 2016; Jackson et  al. 2016; Reveles et  al. 2018), antipsychotic medications (Bahr et al. 2015; Flowers et al. 2017), non-steroidal anti-inflammatory drugs (NSAIDs) (Rogers and Aronoff 2016), and cytotoxic anticancer drugs (Touchefeu et al. 2014) also have a notable influence on the overall composition of the gut microbiota. A systematic literature review conducted by Le Bastard et al. on studies assessing the gut microbiome alterations associated with proton pump inhibitors (PPIs), metformin, non-steroidal anti-inflammatory drugs (NSAIDs), opioids, statins and antipsychotics found a decrease in diversity in the gut microbiome associated with proton pump inhibitors and antipsychotic medications, whereas an increase in a microbiome diversity has been observed with opioids (Le Bastard et al. 2018). In this study, the authors have found a decrease of Clotridiales and increase of Actinomycetales, Micrococcaceae, and Streptococcaceae by PPI use. Further, they have reported that PPIs, metformin, NSAIDs, opioids, and antipsychotics were either increased the members from class Gammaproteobacteria (Enterobacter, Escherichia, Klebsiella and Citrobacter), or members of family Enterococcaceae (Le Bastard et al. 2018). Research studies that compared the gut microbiome between PPI users and non-­ users showed notable changes in gut microbiome with a significantly lower abundance in gut commensals and lower microbial diversity that altered toward a less healthy gut microbiota in PPI users. However, interestingly, a significant increase in the abundance of oral and upper GI tract commensals was observed in PPI users. These studies have found a higher Streptococcaceae and lower Lachnospiraceae and Erysipelotrichaceae, Bifidobacteriaceae abundance in the gut microbiome of PPI users compared with non-users (Imhann et al. 2016; Jackson et al. 2016; Reveles et al. 2018). Studies on the effect of antipsychotic drugs on the gut microbiome of young patients have shown that the human gut microbiome is altered at the phyla level

Determinants of the Gut Microbiota

35

following both acute and chronic exposure to antipsychotic risperidone (RSP). In young patients, chronic RSP treatment significantly lowered the ratio of Bacteroidetes/Firmicutes as compared with antipsychotic-naïve psychiatric controls (Bahr et  al. 2015). Another study found that in adult human cohort with bipolar disorder (BD) treated with atypical antipsychotic drugs (clozapine, olanzapine, risperidone, quetiapine, asenipine, ziprasodone, lurasidone, aripiprazole, paliperidone, and iloperidone), antidepressant (bupropion, venlafaxine, sertraline, duloxetine, fluoxetine, citalopram, escitalopram), mood stabilizer (topiramate, phenobarbital, lamotrigine, gabapentin, divalproex sodium, carbamazepine), and benzodiazepine (lorazepam, alprazolam, temazepam, clonazepam, diazepam) resulted in a gut dysbiosis with a significant decrease in gut microbial species diversity (Flowers et al. 2017). Fecal specimen analysis from 155 adults who used non-steroidal anti-­ inflammatory drugs (NSAIDs) for 30 days has shown that NSAIDs have an influence on the gut microbiome, and that the gut bacterial composition varied based on the drug type used during the treatment (Rogers and Aronoff 2016). It has been reported that the microbiome profile of Celecoxib users was similar to that of Ibuprofen users, with both showing an increased population of Acidaminococcaceae and Enterobacteriaceae. In Ibuprofen users, Propionibacteriaceae, Pseudomonadaceae, Puniceicoccaceae, and Rikenellaceae were more abundant than in controls or naproxen users. However, species from Prevotella, Bacteroides, Barnesiella, and family Ruminococcaceae distinguished gut microbiome of aspirin users from those non-medicated subjects (Rogers and Aronoff 2016). In cancer chemotherapy, cytotoxic drugs reportedly alter the gut microbiota of the patients. Most frequently, decrease in Bifidobacterium, Clostridium cluster XIVa, and Faecalibacterium prausnitzii and an increase in Enterobacteriaceae and Bacteroides that causes the development of mucositis have been reported in patients receiving cytotoxic drugs (Touchefeu et al. 2014). A recent in vitro systematic drug screen study that used 1000-marketed drugs including 203 human-targeted drugs against 40 representative gut bacterial strains from 38 bacterial species and 21 genera has revealed that 27% of non-antibiotics (24% of human-targeted drugs) have inhibitory effect on at least one human gut bacterial species (Maier et al. 2018). This study has shown that bacterial species associated with healthy status of the gut such as major butyrate producers (E. rectale, R. intestinalis, Coprococcus comes), and propionate producers (B. vulgatus, Prevotella copri, Blautia obeum) were affected by human-targeted non-antibiotic drugs (Maier et al. 2018). In addition, interestingly, this study found a correlation between susceptibility to antibiotics and human-targeted drugs across gut bacterial species, which may confer common resistance mechanisms among commensals and to their closely related pathogens. It warrants the potential risk of non-antibiotics promoting antibiotic resistance in bacteria (Maier et al. 2018). Overall, studies indicate that antibiotics and non-antibiotic drugs disturb the gut microbiota composition and make the gut microbes a significant reservoir of resistance genes and promote bacterial antibiotic resistance, which contributes a serious threat to the treatment of antibiotic resistant-bacterial infections (Francino 2016;

36

A. Muthaiyan

Maier et al. 2018). When it comes to the use of antibiotics or non-antibiotics, one should bear in mind that the old maxim of “prevention is better than cure” is particularly relevant to the gut microbiota. Protecting the gut microbiota from the deleterious effect of antimicrobials initially, rather than seeking to restore it after the damage has been done, seems to be the most effective strategy (Chung et al. 2012). 2.3.3  Fecal Microbiota Transplantation (FMT) In modern medicine, fecal microbiota transplantation (FMT) has been commonly used as an effective method to therapeutically manipulate the disturbed or lost healthy microbiota to treat gastrointestinal diseases such as life-threatening Clostridioides difficile infections (CDI), ulcerative colitis (UC), and irritable bowel syndrome (IBS) and other immunological disorders (Hasan and Yang 2019; Borody et al. 2019). In FMT therapy, gut microbiota containing stool solution from healthy donor is delivered into a patient’s gut via nasogastic, nasojejunal, nasoduodenal, colonoscopy, enema, or oral capsules (Daliri et al. 2018). The success of the FMT treatment is based on a shift in the gut microbiota profile of the recipient toward that of the fecal donor (Wilson et al. 2019). Therefore, FMT is one of the factors that influence the gut microbiota for some individuals. It has been reported that in FMT, members of Ruminococcaceae and Lachnospiraceae families have successfully been transferred from donor to recipient and slowly increased their abundance in recipients’ gut and improved their health condition (Wilson et al. 2019). Growing FMT research studies have shown that the fecal microbiota transplantation effectively alters the gut microbiota of the recipients, leading a promising therapeutic method to positively reprogram the gut microbiota to treat serious gastrointestinal diseases (Kump et al. 2018; Oliphant et al. 2019).

3  Internal Factors Influencing Gut Microbiota 3.1  Host Genetics According to recent report, not many research studies have focused to understand the interactions between host genetics and the microbiome during pregnancy, or focused into offspring during early postnatal development in preclinical models (Codagnone et al. 2019). However, there are conflicting evidences exist regarding the role of host genetics in the colonization and composition of gut microbiota in human, and mouse gut. The composition of the human gut microbiota is determined by many external and internal factors. The gut microbiota is colonized at birth, and develops with its host during the growth. This colonization and diversification are greatly influenced by the diet and other environmental factors. Recently, the role of human genetic

Determinants of the Gut Microbiota

37

variation in the composition of microbiota has emerged as one of the influential factors in accounting for interpersonal differences in microbiota. Thus, human genes may have direct or indirect influence on human health by promoting a beneficial microbiome (Goodrich et al. 2017). Based on a genetically identical germ-free mouse model comparative study using human gut microbiota and mouse gut microbiota, Chung et al. have reported that the prevalence of gut microbiota may vary substantially with the individual and perhaps with age rather than the genetic makeup of the host. Further, the authors have speculated that, instead of host genetic makeup, adaptability between the host and gut microbe relationship influences the gut microbial colonization (Chung et al. 2012). In addition, results from an extensive statistical analysis of the largest metagenomics-­sequenced human cohort so far have revealed that the host genetics has only a minor influence on microbiome variability. This study examined the genotype and microbiome data from 1046 healthy individuals with several distinct ancestral origins, but lived in a relatively common environment. Results of this study have demonstrated that the gut microbiome is not significantly associated with genetic ancestry, and that host genetics have had a minor role in determining microbiome composition. In addition, the study has shown that, by contrast, there are significant similarities in the compositions of the microbiomes of genetically unrelated individuals who share a household. In addition, over 20% of the inter-­ person microbiome variability is associated with factors related to diet, drugs, and anthropometric measurements (Rothschild et al. 2018). In contrast to the above reports, Goodrich et  al. compared microbiota across >1000 fecal samples obtained from the TwinsUK population, which includes 416 twin pairs. They have identified many microbial taxa whose abundances were influenced by host genetics. The members of Christensenellaceae have been reported as the most heritable taxon influenced by host genetics (Goodrich et  al. 2014). Similarly, a human study that analyzed the gut microbiota from a pair of monozygotic twins and a fraternal sibling, with similar pre- and post-natal environmental conditions including similar feeding regime indicated that, initially, host genetics played a major role in determining the composition of microbial community. However, by the beginning of first year of life, environmental factors are the major influential factors in healthy infants (Murphy et  al. 2015). Consequently, these reports have indicated that the human gut microbiota composition is shaped by multiple factors, but the relative contribution of host genetics remains subtle. Other studies showed that abundances of a subset of microbes are partly determined by the host genetics. The notable example has been the presence of more abundant Bifidobacteria among different lactose-intolerant human population who carry the lactase nonpersister genotype. However, it has been reported that the use of genome-wide association studies (GWASs) to identify human genetic variants associated with microbiome phenotypes is a challenging task. This is because studies performed to date are small by GWAS standards, and cross-study comparisons are hampered by differences in analytical methods (Goodrich et al. 2016, 2017).

38

A. Muthaiyan

While studies have been focused on associations between the microbiota and single nucleotide polymorphisms (SNP) in host genes, recently, Poole et al. have reported that the variation in the host gene copy number (CN) can affect the microbiota. In their study, they have shown that variation in the copy number of the human salivary amylase gene AMY1 is associated with the diversity and function of the human oral and gut microbiome. Their findings have demonstrated that the AMY1-CN of the host directly influences the carbohydrate milieu in the GI tract, which in turn influences the gut microbiota, through its dose-dependent effect on salivary amylase production (Poole et al. 2019). In summary, nevertheless, the role of host genetics on gut microbiota has not widely been studied, and the available reports indicate that the associations between microbes and human genes have been emerging in human populations. It is time for the microbiota to be incorporated into studies that quantify interactions among genotype, environment, and the microbiota in order to predict human disease susceptibility (Goodrich et al. 2017).

3.2  Host Immune System Gut microbial colonization in infants begins in utero, as bacteria from the placenta and amniotic fluid colonize the fetal intestine, and subsequently during and after the birth, other external and internal factors influence the gut microbial colonization. The host immune system is one of the factors that plays a significant role in controlling the colonization of gut microbiota. Host and gut microbiota have bidirectional interaction for mutual benefits in which intestinal bacteria shape the development of the host immune system and the host immune system influences the colonization and development of the gut microbiota (Lupp et al. 2007; Belkaid and Hand 2014; Lei et al. 2015). Studies show that the altered host mechanisms of immune regulation have an impact on gut microbiota composition and thus lead to the disease state (Malys et al. 2015). In the initial stage of human gut microbial colonization, breast milk serves as a communication medium between mother’s immune system and the infant. It is an effective system that is actively directing and educating the developing immune, metabolic, and microbiota systems within the infant, while providing protection from pathogens (Field 2005). Several clinical research studies confirm the beneficial effects of breastfeeding on the growth, development, and anti-infective defense from infancy to adulthood. The maternal immunoglobulins (Ig) IgG and IgA are usually passed through the breast milk, and they render passive immunity to the infant and regulate the initial gut microbial colonization and mucosal immune responses, which influence the intestinal homeostasis throughout the life. Especially, it has been observed that the absence of normal IgA leads to a significant shift in anaerobe populations in the small intestine (Suzuki et  al. 2004; Iyengar and Walker 2012; Koch et  al. 2016; Palmeira et al. 2016).

Determinants of the Gut Microbiota

39

The IgA is produced in the intestinal mucosa, where it plays an important role in the maintenance of mucosal homeostasis, and protects the intestine from pathogens. It is believed that IgA prevents bacteria from invading the lamina propria mucosa (LPM) (Malys et  al. 2015). The presence of bacteria-specific IgAs in the gut is related to the habitats of specific bacteria in GI tracts. However, studies show that in the large intestine, most bacteria are not bound to IgA (Suzuki et al. 2004; Bunker et al. 2015). Although, IgAs play an important role in fighting pathogens, they have an influence in controlling gut commensal populations as well. It has been reported that in IgA-knockout mice, segmented filamentous bacteria over colonize the GI tract and strongly induce immunity (Suzuki et  al. 2004). It suggests that the host immune system and immunoglobulins selectively allow certain bacterial members to establish the host-microbiota colonization in the gut (Tanaka and Nakayama 2017). Thus, the production of bacteria-specific IgA in the host may play an important role in shaping the intestinal microbial community composition (Duerkop et al. 2009).

4  Other Factors Influencing the Gut Microbiota As discussed in the previous sections, the mode of delivery, diet, host genetics, and immune system, and use of antibiotics and other drugs play a major role in influencing the colonization and composition of the gut microbiota. However, research studies reveal that several other factors including age, gender, geographical location and culture, and living environment (urban or rural) and pollution, and social factors such as social life, physical exercise, stress and depression, sleep disorders, and smoking habit can also affect the structure and composition of gut microbiota. The following sections present a brief discussion on these factors.

4.1  Aging Studies indicate that the composition of human gut microbiota changes with age. In the aging population, gut microbial resilience to the external factors is generally reduced so that its overall composition is easily affected by the external factors such as lifestyle changes, antibiotics, and disease (Rajilić-Stojanović et al. 2013). The intestinal microbiota is quite stable throughout adult life; however, changes occur in the composition of gut microbiota in elderly individuals (Mariat et  al. 2009). Although the microbiota in adults have has extensively been studied, very limited information is available relating to possible alterations that occur with aging. The human gut microbiota undergoes maturation from birth to adulthood; specifically, the Firmicutes/Bacteroidetes ratio undergoes an increase from birth to adulthood, and upon advanced aging, the ratio is altered. Compared with young adults, elderly people carry high levels of E. coli and Bacteroidetes. In addition, studies have

40

A. Muthaiyan

reported a reduction in the numbers and diversity of many beneficial gut commensals, such as Bacteroides and Bifidobacteria in elderly adults. This change might be due to the influence of a changing digestive physiology that develops during the aging in elderly adults (Mariat et  al. 2009). A research study that analyzed 367 healthy Japanese subjects between the ages of 0 and 104 years has concluded that the gut microbiota of people older than 70 years is changed into the “elderly type.” This study has suggested that nutrients in the gut might be an influential factor that plays an important role in changing the gut microbiota composition with age (Odamaki et al. 2016). Several other factors such as diet, health status, and physical performance have been implicated as influential factors that affect the gut microbiota of elder population (Claesson et al. 2012). In addition, decreased physical activity in the aged population has been speculated as another factor that might contribute to the reduced number and diversity of certain microbial species in the aging gut (Ticinesi et al. 2017). In summary, as an aging population now becomes a general feature of the Western countries and a rising phenomenon among many developing countries, understanding the interaction between the gut microbiota and healthy aging, and the factors affecting the gut microbiota during the aging is the need of the hour for healthy aging for the growing elderly population (Claesson et al. 2012).

4.2  Gender Effect The effect of gender differences on microbiome has been a debated topic. Contradictory reports exist that both support and refute the effect of gender differences on microbiome. This is because the other variables such as diet, age, and genotype may mask a real gender effect on microbiome (Kovacs et  al. 2011). However, when these sources of variability were controlled for in mice, a clear gender effect on the microbiome composition was observed (Lang et  al. 2018). A research study that focused on the influence of gender on gut microbiota that included 56 boys (51.9%) and 52 girls (48.1%) found higher total bacterial count in boys than in girls at birth. In addition, the study found that the girls were six times more frequently colonized by L. ruminis at birth, four times by L. gasseri, and three times by L. reuteri from 2 days to 3 months after birth (Martin et al. 2016). The recent literature review by Taddei et al. found that unique changes occur in the richness and diversity of the gut microbiota of pregnant women. Usually, the hormonal, immunological, and physiological changes that occur during the pregnancy might be the influential factors that alter the gut microbiota in women. However, other factors, such as genetics, BMI, ethnicity, diet, antibiotics, and environmental conditions, may influence the bacterial profile in pregnant women (Taddei et al. 2018). Recently, de la Cuesta-Zuluaga et al. performed a large-scale analysis of the relationship of age and gender with gut bacterial diversity in adult cohorts from the United States, the United Kingdom, Colombia, and China. They found higher gut bacterial diversity in adult women than in men (de la Cuesta-Zuluaga et al. 2019). Studies found that gender-specific microbes might have an important role during

Determinants of the Gut Microbiota

41

fertilization, implantation, and gestation in women. Understanding and identifying the factors that affect the composition of gender specific microbiota will take us a step forward in diagnosing and treating dysbiosis in women’s health (Younes et al. 2018).

4.3  Geography and Culture Research studies found differences between gut microbiome from different countries. However, differences among different races have received less attention. The effect of geography and race on the gut microbiota is again indirectly influenced by the traditional diet used in the region (Ruengsomwong et al. 2016; Jain et al. 2018). Many countries have their own cultural customs and traditional food habits, and are practicing these customs for a long time. Yatsunenko et al. examined gut bacteria species and gene content of 531 individuals from the Amazonas of Venezuela, rural Malawi, and US metropolitan areas. In their study, they found prominent differences in bacterial assemblages and functional gene repertoires between US residents and those in the other two countries (Yatsunenko et al. 2012). A study that compared the diversity, composition, and stability of the gut microbiota of healthy children living in an urban slum in Bangladesh with that of children of the same age range in an upper middle-class suburban community in the United States found that the Bangladeshi and US children had distinct gut bacterial community and structure. In addition, Bangladeshi children harbored significantly greater bacterial diversity than that of US children and the diversity and structure in Bangladeshi children were significantly less stable month to month than in the US children. However, this study speculates that the differing environmental or genetic factors might be the influential factors behind this geographical difference among the gut microbiota (Lin et  al. 2013). Analyses of the expression levels of 9,879,896 gut microbial genes from 1267 samples of three different races, which included 139 Americans, 368 Chinese, and 760 Europeans revealed the differences in the gut microbiome among these races (Chen et al. 2016). Similar to this report, differing gut microbiota has been reported from studies that compared the gut microbial population from Europe and rural Africa (De Filippo et  al. 2010), and Indian and Chinese population (Jain et al. 2018). These study reports indicate that the eating habits and living environments are the major factors that influence the composition of the gut microbiome among population from different countries and races. Recently, a large-scale metagenomic assembly analysis covering body sites, ages, countries, and lifestyles identified thousands of microbial genomes from yet-to-be-­ named species from different geographical regions. This analysis found a significant difference in microbiome between different geographical regions and found that non-Westernized populations harbor a large fraction of the newly discovered species (Pasolli et  al. 2019). Overall, the culture-based diet, genetics, and the hygienic procedures followed in different countries play an important role in shaping the gut microbiota in different geographical regions. The effect of geography

42

A. Muthaiyan

and culture on gut microbiota suggests that while making global policies about sustainable agriculture and improved nutrition, the policy-makers should not only consider the varying cultural traditions but also should consider the varied gut microbiomes specific to the geographical regions (Yatsunenko et al. 2012).

4.4  Environment and Pollution 4.4.1  Living Environment A person’s living environment has been reportedly influencing the gut microbial colonization. Studies show that growing in microbe-rich environments, such as traditional farms, provides opportunity for early-life exposure to environmental microbes, and increases gut microbiota diversity and it might have protective health effects on children (Tasnim et  al. 2017). Importantly, the type of environment in which the child takes birth and grows in its early stage of life affects the child’s gut microbial population. However, few studies have focused to understand the role of the external environment in the gut microbiome and immune development. Reports indicate that the colonization pattern of newborn infants varies among the infants born at home or at hospital environments, and different wards and hospitals (Fanaro et al. 2003; Martin et al. 2016). These reports show the influence of microbial load available in the immediate environment in the early-stage microbiota. In the developed countries, routine hygienic procedures practiced to reduce the spread of bacterial infections in neonatal wards further influence the colonization pattern of gut microbiota in infants (Fanaro et al. 2003). Similarly, in an elderly population, the individual microbiota of people living in long-stay care was significantly less diverse than that of people living in community. In addition, the loss of community-­ associated microbiota has been reportedly correlated with increased frailty. The data support a relationship between diet and environment-driven microbiota alterations that directly affect the health condition in the aged group (Claesson et al. 2012). Interestingly, Martin et al. reported that the presence of pets, siblings, and even the number of siblings in the household environment influence the type of gut microbial colonization in infants (Martin et al. 2016). 4.4.2  Environmental Pollution Due to industrialized lifestyle, in the last several decades, environmental pollutants have not only become a common health hazard but they have a profound influence on our gut microbiota as well. Several research studies have found that the diversity of gut microbiota is affected by pollutants and toxicants present in the environment and they have reportedly been involved in influencing a person’s gut microbiota (Kish et al. 2013; Salim et al. 2014; Jin et al. 2017; Chi et al. 2017; Mutlu et al. 2018). According to the World Health Organization, air pollution is a major environmental risk to health and was estimated that in both cities and rural areas, it caused

Determinants of the Gut Microbiota

43

4.2 million premature deaths worldwide in 2016. This mortality is due to exposure to small particulate matter of 2.5 microns or less in diameter (PM2.5), which causes cardiovascular and respiratory disease, and cancers (WHO 2018). In an IL-10−/− mice (whose colitis development depends on the gut microbiota) model study, it has been shown that particulate matter (PM) added in their feed significantly changed the relative amounts of gut Bacteroidetes, Firmicutes, and Verrucomicrobia (Kish et al. 2013). Thus, the urban airborne particulate matter ingested via contaminated food can alter the gut microbiome and immune function under both normal and inflammatory conditions (Salim et al. 2014). Recently, Mutlu et al. have shown that the exposure to inhaled PM at clinically relevant doses significantly altered the diversity of gut microbiome in the small bowel, colon, and the feces, and altered the bacterial composition throughout the GI tract in mice (Mutlu et al. 2018). These PM-induced alterations in the composition of bacteria increased from the proximal to distal parts of the GI tract with a significant reduction in Firmicutes. In addition to specific changes in the gut microbial diversity, blooming of some distinct bacterial groups throughout the GI tract has been observed with PM exposure (Mutlu et al. 2018). Besides air pollution, other contaminants such as arsenic also affect the diversity of gut microbiota. Arsenic enters both humans and animals primarily through the contaminated drinking water and food, and affects the health of millions of people around the world (Chakraborti et al. 2016). The GI tract is the first location at where the arsenic enters into the body, and perturbs the gut microbiota (Chi et al. 2017). A recent mouse model study that used an environmentally relevant level of arsenic (100 ppb) to expose the mice for 13 weeks found a change in the composition of gut microbiome and subsequent alteration in a variety of important bacterial functional pathways (Chi et al. 2017). Similarly, effects of other environmental pollutants such as heavy metals (cadmium, lead), persistent organic pollutants (polychloro biphenyls, dioxins), pesticides, nanomaterials (Permethrin, Pentachlorophenol, Epoxiconazole, Chlorpyrifos, Carbendazim, and Imazalil), and food additives (non-­ caloric artificial sweeteners, and emulsifiers) on gut microbiota composition and their subsequent effects on health have been reported by other studies (Jin et al. 2017).

4.5  Urbanization Reports indicate that urbanization is another factor that strongly influences the composition and structure of the gut microbiota. Studies show that children who grew up in microbe-rich rural environments, such as traditional farms, have positive and protective health conditions. Because of the growing urbanization, these positive health effects exerted by the microbe-rich rural environment are usually overlooked due to changes in the lifestyle, diet, living condition, and environmental biodiversity. Interestingly, early-life exposure to environmental microbes, which is rich in rural environment, increases gut microbiota diversity by influencing patterns of gut microbial assembly (Tasnim et al. 2017). A research study that evaluated the effect of urbanization on gut microbiota among traditional and urbanized Tibetan

44

A. Muthaiyan

herdsmen found that fiber-degrading bacteria, such as Prevotella, are abundant in the traditional Tibetan herdsmen, whereas bacteria associated with diets rich in animal protein, such as Bacteroides, are dominant in the urbanized herdsmen (Li et al. 2018). In urbanized herdsmen, different types of selective pressures create diverse gut community compositions in response to urban lifestyles. However, compared with traditional herdsmen, the microbial interaction of urbanized herdsmen was weak. These findings suggest that urban lifestyles not only affect the composition and structure of human gut microbiota, but also influence the microbial interaction and community assembly patterns (Li et al. 2018). Due to the changes in the land-­ use pattern by the rapid urbanization, the soil biodiversity is rapidly altered and diminished. Such drastic changes to the human environment may interrupt the healthy development of the microbiota and increase the risk of inflammatory diseases. Further studies are required to evaluate the alteration of gut microbiota and their effect on human health during urbanization (Tasnim et al. 2017).

4.6  Social Factors Social activities such as smoking, physical exercise, duration of active screen time, and social gathering also influence the gut microbial composition (Fig. 5). Recently, research studies have been interested to understand the influence of these social

Fig. 5  Social factors that influence the gut microbiota

Determinants of the Gut Microbiota

45

factors on gut microbiota. To provide a starting point to the readers, this section briefly discusses the social factors that influence the gut microbiota. 4.6.1  Social Interaction Studies have been reporting that social relationships such as healthy marriage, cohabiting with family members, having siblings, and socializing with friends and relatives exert a sustained influence on human microbiota and a positive effect on health and mortality than being in social isolation (Umberson et al. 2010; Song et al. 2013; Zimmermann and Curtis 2018). A recent study on the close relationship and its effect on microbiota revealed interesting findings that social interactions with relatives and friends have a strong influence on the gut microbial diversity in individuals. Individuals who were cohabitating with a spouse or partner had more similar microbiota composition with their cohabitating spouse or partner as well as higher diversity and richness than unmarried, non-cohabitating or living alone individuals (Dill-McFarland et al. 2019). Thus, this study indicated that it is possible that relationships with others have an influence on an individual’s gut microbiota and consequently confer positive health outcomes (Lozupone et al. 2012), through either direct microbial transfer or reinforcement of healthy microbiota behaviors. Among all types of social relationship, close healthy marriage relationships are found to have a stronger influence on the microbiota than the other factors such as shared genetic factors, and early-life environments among siblings (Dill-McFarland et al. 2019). Thus, high-quality marriage has a strong influence on shaping the gut microbiota of spouses. 4.6.2  Physical Exercise As discussed in the earlier section, during the aging, lack of enough physical activity has been identified as one of the factors that affects the gut microbial composition in seniors. However, only a few studies have demonstrated exercise-induced changes on gut microbiota in humans. An observation study has reported a significant increase of some health-promoting bacterial species such as Akkermansia, Faecalibacterium, and Roseburia, in the fecal samples of adult women with active lifestyles compared with sedentary age-matched women (Bressa et al. 2017). Barton et al. showed the differences in gut microbiome composition between professional rugby players and non-athlete controls. In addition, these two groups significantly differed in the fecal metabolome as well by representing a higher number of SCFA-­ producing bacteria and bacterial genes involved in carbohydrate and amino acid metabolism in athlete group samples. Also, in fecal samples, higher concentrations of acetate, butyrate, and propionate were observed in the athlete group compared to the non-athlete controls (Barton et  al. 2017). In another study, physical activity influenced the population of Prevotella, Akkermansia, and SCFA producers, which has also been confirmed by analyses carried out on the fecal microbiota of

46

A. Muthaiyan

professional cyclists (Petersen et al. 2017). Overall, these study reports indicate that the physical exercise is one of the influential factors that shapes the composition of gut microbiota. 4.6.3  Stress and Depression Depression is a common mental disorder that globally affects around 300 million people and every year, this number keeps growing. It causes the affected person to suffer greatly and function poorly in their day-to-day activities such as at work, at school, and in the family (WHO 2017). Generally, a complex interaction of social, psychological, and biological factors is considered as a cause of depression. However, interestingly, Winter et al. have proposed that the alterations in the gut microbiota populations of specific species might contribute to depression. In addition, the authors have speculated that depressive states might trigger a modification of specific gut microbiota species and eventually contribute to more severe depression (Winter et al. 2018). In a research study on gut microbiota of depressed human subjects, Jiang et al. have reported a strong increase of Bacteroidetes, Proteobacteria, and Actinobacteria, and a significant decrease of Firmicutes in the active-major depressive disorder and responded major depressive disorder groups compared with the healthy controls group. Even though the subjects showed interindividual variability, several predominant genera were significantly different between the major depressive disorder and healthy control groups. Notably, increased levels of Enterobacteriaceae and Alistipes but reduced levels of Faecalibacterium in the gut microbial population were observed in depressive disorder subjects (Jiang et  al. 2015). In support of earlier research, a recent literature analysis study has concluded that stress and depression may indirectly lead to alterations of gut microbiota. The mechanism behind these depression-driven gut microbiota alternations has been reported as the depressive state may affect hypothalamus-pituitary-adrenal axis and cortisol secretion, which alters cytokine production and immune activity in the gut. These physiological changes then affect the gut microbiota habitat, which in turn lead to altered microbial population (Winter et al. 2018; Dong and Gupta 2019). 4.6.4  Sleep Disorders Sleep disorders are changes in sleeping patterns or habits, and one of the common health issues that negatively affects the health of human population. Now, research studies have found a link between sleep disorders and its role on the composition of gut microbiota of the host, and consequently, overall health of the host (Thaiss et al. 2014; Poroyko et al. 2016; Benedict et al. 2016; Smith et al. 2019). Evidences from both animal and human model studies indicate that any ablation of host molecular circadian components or induced jet lag leads to fluctuations in the composition of gut microbiota and even dysbiosis (Thaiss et al. 2014). Chronic sleep fragmentation (SF) or Fragmented sleep is a type of sleep disorder that is associated with many

Determinants of the Gut Microbiota

47

highly prevalent disorders in human population. However, instead of affecting the circadian rhythm, SF significantly alters feeding behaviors that ultimately promote obesity and insulin resistance. Apparently, these symptoms have been related to the imbalance of host gut microbiota (Poroyko et al. 2016). In a mouse model study, Poroyko et  al. have subjected the mice to SF for 4 weeks, then allowed them to recover for 2 weeks, and then evaluated the effect of SF on gut microbiota. Interestingly, they have found increased food intake and reversible change in a gut microbiota characterized by the preferential growth of highly fermentative members of Lachnospiraceae and Ruminococcaceae and a decrease of Lactobacillaceae families in chronic SF-induced mice (Poroyko et al. 2016). A gut microbiota analysis study by Benedict et al. using nine normal-weight men at two different sleep patterns viz. two nights of partial sleep deprivation (PSD), and two nights of normal sleep (NS) provides evidence for sleep deprivation-induced changes in bacterial families found in the gut microbial population with an increased Firmicutes/ Bacteroidetes ratio. Also in this study, following two nights of PSD compared with two nights of NS, increased levels of the families Coriobacteriaceae from phylum Actinobacteria and Erysipelotrichaceae from phylum Firmicutes, and a lower abundance of the phylum Tenericutes have been reported in fecal sample analysis (Benedict et al. 2016). In another human subjects study, it has been reported that better sleep quality has increased the gut microbial phyla Verrucomicrobia and Lentisphaerae, and improved neurocognitive outcomes in adult humans (Anderson et al. 2017). A long-term study that collected data from adult human subjects for 30 days of sleep pattern and associated microbiota change has found a positive correlation between the sleep efficiency, total sleep time, and microbiome diversity, and negative correlation with wake after sleep onset (Smith et  al. 2019). In this study, microbiota analysis revealed the richness of phyla Bacteroidetes and Firmicutes that positively correlated with sleep efficiency, interleukin-6 concentrations, and abstract thinking. Several other taxa including Lachnospiraceae, Corynebacterium, and Blautia were negatively correlated with sleep measures (Smith et al. 2019). 4.6.5  Smoking Reports from observational and interventional studies suggest that smoking alters the composition of gut microbiome (Savin et al. 2018; Dong and Gupta 2019). A study found that the microbial profile of saliva in individuals is influenced by smoking (Belstrøm et al. 2014), and there is an evidence that the salivary microbiome influences the gut microbiome (Cao 2017). However, very few reports are available on the effect of smoking on gut microbiota. Savin et  al. surveyed the published reports on the effect of smoking on gut microbiota between the years 2000 and 2016 and concluded that overall smoking habit decreased the diversity of the intestinal microbiome (Savin et al. 2018). Specifically, members from the phyla Proteobacteria and Bacteroidetes, and the members from genera Clostridium, Bacteroides and Prevotella were increased in the gut microbial population. Conversely, Actinobacteria

48

A. Muthaiyan

and Firmicutes phyla and the members belonging to the genera Bifidobacteria and Lactococcus were decreased. Interestingly, the reported smoking-induced gut microbial alterations reportedly resemble those demonstrated in conditions such as inflammatory bowel disease and obesity (Savin et  al. 2018). However, the exact mechanism of how smoking affects the microbiome remains an active area of research (Dong and Gupta 2019).

5  Concluding Remarks The gut microbiota is now considered an important versatile “organ” of human body (Rajilić-Stojanović and de Vos 2014). In recent years, the study of the gut microbiota has received new interest due to the development of molecular and multi“omics” methods for more accurately assessing its composition and diversity (Browne et al. 2016; Sung et al. 2016; Lagier et al. 2016; Park et al. 2017; Lyu and Hsu 2018; Kho and Lal 2018; Almeida et al. 2019). Report shows that in the year 2017 alone, approximately 4000 papers focusing on the gut microbiota were published, and between the years 2013 and 2017, more than 12,900 publications were dedicated to the study of the gut microbiota (Cani 2018). The increasing number of publications emphasizes the fact that the gut microbiome research is not only emerging but also strongly suggests the need for advancement in gut microbiome research (Huttenhower et al. 2014; Lieberman 2018; Huang et al. 2019). So far, the research studies are helping us to identify the factors that influence our gut microbiota. Notable factors such as industrialization, exposure to pollutants, cesarean section, formula feeding, modern agriculture, changes in diet, consumption of increasingly hygienic and processed food, increasing use of antimicrobials, modern lifestyle, stressful urban life, more screen time and less social interaction even among family members, growing isolated elder care centers, and reduced microbial transmission between individuals due to sanitation are influencing the composition and colonization of the gut microbiota, continuously leading to the loss of gene functions in gut microbial populations (Gillings et al. 2015). Due to these factors, since the origin of the first human gut microbial colonization, the microbial diversity has been gradually declining in each generation and reduces the diversity available for transmission to the next generations. Because developments in medicine and technology now provide alternative ways to fight diseases, humans are becoming less dependent on their coevolved inborn friend “gut microbiota” for their health and survival. More and more research evidences indicate that the increasing weakness of the coevolved human–microbe relationship is the reason for the current prevalence of autoimmune diseases, whose frequency has shown a dramatic increase over the last half century (Chung et al. 2012; Gillings et al. 2015; Park et al. 2017; Kho and Lal 2018). However, there is a good news! To improve human health, now scientists have started to utilize the combination of genomics, metabolomics, genetic engineering, and bio-mathematical and computational modeling to manipulate human microbes

Determinants of the Gut Microbiota

49

to create personalized human–microbe relationships (Rojo et al. 2017; Xia and Sun 2017; Lyu and Hsu 2018; Whiteson 2018; Magnúsdóttir and Thiele 2018; Khangwal and Shukla 2019). The research community is currently focusing on “resetting” the microbiota of individuals with disease, and developing personalized diets supplemented with next-generation probiotics (Derrien and Veiga 2017). Recently, the “intestine-on-a-chip” consisting of over 200 unique operational taxonomic units from 11 different genera and an abundance of obligate anaerobic bacteria, with ratios of Firmicutes and Bacteroidetes similar to those observed in human feces has been introduced as a new discovery tool for the development of microbiome-related therapeutics, probiotics, and nutraceuticals (Jalili-Firoozinezhad et  al. 2019). In addition, further efforts have been made to develop “Disease-on-a-chip,” “Patient-­ on-­a-chip,” and personalized “human organs-on-chips” with physiologically relevant host–gut microbiome interactions to replace the costly inefficient germ-free or conventional animal models and accelerate the drug development process (Park et  al. 2017). Recent research studies have been leading toward the directions to shape infant microbiomes and healthy immune development, and specifically target bacterial strains to combat infection and engineer microbiomes (Whiteson 2018), and to understand how “gut microbiome-metabolomic-human health axis” affects human health (Lyu and Hsu 2018). Thus, the growing advancement in the gut microbiome research suggests that the next 5 years will be an exciting period for human microbiome research and a wealth of data associated with myriad factors that influence gut microbiota will become available for evolutionary and ecological study (Lieberman 2018). These valuable data will help scientists to understand the important role of human microbiome in health and disease, with a focus on “personalized medicine” or “P4-preventive medicine” (personalized, predictive, preventive, participatory medicine) (Gurwitz 2013; Peñalver Bernabé et al. 2018). More and more human trials will begin to test the therapeutic efficacy of designed probiotics even for non-infectious diseases. Gut microbiome-based therapies may one day improve drug metabolism, supply vital nutrients and other microbiome-targeted manipulations, and modulate the immune system (Grady et  al. 2016; Lieberman 2018).

References Abdul Rahim, M.  B. H., Chilloux, J., Martinez-Gili, L., et  al. (2019). Diet-induced metabolic changes of the human gut microbiome: Importance of short-chain fatty acids, methylamines and indoles. Acta Diabetologica, 56, 493–500. https://doi.org/10.1007/s00592-019-01312-x. Abeles, S. R., Jones, M. B., Santiago-Rodriguez, T. M., et al. (2016). Microbial diversity in individuals and their household contacts following typical antibiotic courses. Microbiome, 4, 39. https://doi.org/10.1186/s40168-016-0187-9. Agans, R., Gordon, A., Kramer, D. L., et al. (2018). Dietary fatty acids sustain the growth of the human gut microbiota. Applied and Environmental Microbiology, 84, e01525-18. https://doi. org/10.1128/AEM.01525-18.

50

A. Muthaiyan

Almeida, A., Mitchell, A. L., Boland, M., et al. (2019). A new genomic blueprint of the human gut microbiota. Nature, 568, 499–504. https://doi.org/10.1038/s41586-019-0965-1. Amato, K.  R. (2017). An introduction to microbiome analysis for human biology applications. American Journal of Human Biology, 29, e22931. https://doi.org/10.1002/ajhb.22931. Anderson, J.  R., Carroll, I., Azcarate-Peril, M.  A., et  al. (2017). A preliminary examination of gut microbiota, sleep, and cognitive flexibility in healthy older adults. Sleep Medicine, 38, 104–107. https://doi.org/10.1016/j.sleep.2017.07.018. Bahr, S. M., Tyler, B. C., Wooldridge, N., et al. (2015). Use of the second-generation antipsychotic, risperidone, and secondary weight gain are associated with an altered gut microbiota in children. Translational Psychiatry, 5, e652. https://doi.org/10.1038/tp.2015.135. Barton, W., Penney, N.  C., Cronin, O., et  al. (2017). The microbiome of professional athletes differs from that of more sedentary subjects in composition and particularly at the functional metabolic level. Gut, 67, 625–633. https://doi.org/10.1136/gutjnl-2016-313627. Belkaid, Y., & Hand, T. W. (2014). Role of the microbiota in immunity and inflammation. Cell, 157, 121–141. https://doi.org/10.1016/J.CELL.2014.03.011. Belstrøm, D., Holmstrup, P., Nielsen, C. H., et al. (2014). Bacterial profiles of saliva in relation to diet, lifestyle factors, and socioeconomic status. Journal of Oral Microbiology, 6, 23609. https://doi.org/10.3402/jom.v6.23609. Benedict, C., Vogel, H., Jonas, W., et al. (2016). Gut microbiota and glucometabolic alterations in response to recurrent partial sleep deprivation in normal-weight young individuals. Molecular Metabolism, 5, 1175–1186. https://doi.org/10.1016/j.molmet.2016.10.003. Bercik, P., Verdu, E. F., Foster, J. A., et al. (2010). Chronic gastrointestinal inflammation induces anxiety-like behavior and alters central nervous system biochemistry in mice. Gastroenterology, 139, 2102–2112.e1. https://doi.org/10.1053/J.GASTRO.2010.06.063. Bezirtzoglou, E., Tsiotsias, A., & Welling, G.  W. (2011). Microbiota profile in feces of breastand formula-fed newborns by using fluorescence in situ hybridization (FISH). Anaerobe, 17, 478–482. https://doi.org/10.1016/j.anaerobe.2011.03.009. Bhalodi, A. A., van Engelen, T. S. R., Virk, H. S., & Wiersinga, W. J. (2019). Impact of antimicrobial therapy on the gut microbiome. The Journal of Antimicrobial Chemotherapy, 74, i6–i15. https://doi.org/10.1093/jac/dky530. Biasucci, G., Benenati, B., Morelli, L., et  al. (2008). Cesarean delivery may affect the early biodiversity of intestinal bacteria. The Journal of Nutrition, 138, 1796S–1800S. https://doi. org/10.1093/jn/138.9.1796S. Bibbò, S., Ianiro, G., Giorgio, V., et al. (2016). The role of diet on gut microbiota composition. European Review for Medical and Pharmacological Sciences, 20, 4742–4749. Blaser, M. J. (2016). Antibiotic use and its consequences for the normal microbiome. Science, 352, 544–545. https://doi.org/10.1126/science.aad9358. Blaser, M. J., & Dominguez-Bello, M. G. (2016). The human microbiome before birth. Cell Host & Microbe, 20, 558–560. https://doi.org/10.1016/j.chom.2016.10.014. Blaser, M. J., & Falkow, S. (2009). What are the consequences of the disappearing human microbiota? Nature Reviews. Microbiology, 7, 887–894. https://doi.org/10.1038/nrmicro2245. Blum, H. E. (2017). The human microbiome. Advances in Medical Sciences, 62, 414–420. https:// doi.org/10.1016/J.ADVMS.2017.04.005. Boix-Amorós, A., Puente-Sánchez, F., du Toit, E., et al. (2019). Mycobiome profiles in breast milk from healthy women depend on mode of delivery, geographic location, and interaction with bacteria. Applied and Environmental Microbiology, 85, e02994-18. https://doi.org/10.1128/ aem.02994-18. Borody, T. J., Eslick, G. D., & Clancy, R. L. (2019). Fecal microbiota transplantation as a new therapy: From Clostridioides difficile infection to inflammatory bowel disease, irritable bowel syndrome, and colon cancer. Current Opinion in Pharmacology, 49, 43–51. Bressa, C., Bailén-Andrino, M., Pérez-Santiago, J., et al. (2017). Differences in gut microbiota profile between women with active lifestyle and sedentary women. PLoS One, 12, e0171352. https://doi.org/10.1371/journal.pone.0171352.

Determinants of the Gut Microbiota

51

Browne, H. (2016). Antibiotics, gut bugs and the young. Nature Reviews. Microbiology, 14, 336. https://doi.org/10.1038/nrmicro.2016.73. Browne, H.  P., Forster, S.  C., Anonye, B.  O., et  al. (2016). Culturing of “unculturable” human microbiota reveals novel taxa and extensive sporulation. Nature, 533, 543–546. https://doi. org/10.1038/nature17645. Brüssow, H. (2015). Growth promotion and gut microbiota: Insights from antibiotic use. Environmental Microbiology, 17, 2216–2227. https://doi.org/10.1111/1462-2920.12786. Buffie, C. G., Bucci, V., Stein, R. R., et al. (2015). Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile. Nature, 517, 205–208. https://doi. org/10.1038/nature13828. Bunker, J.  J., Flynn, T.  M., Koval, J.  C., et  al. (2015). Innate and adaptive humoral responses coat distinct commensal bacteria with immunoglobulin A. Immunity, 43, 541–553. https://doi. org/10.1016/J.IMMUNI.2015.08.007. Cani, P. D. (2018). Human gut microbiome: Hopes, threats and promises. Gut, 67, 1716–1725. https://doi.org/10.1136/gutjnl-2018-316723. Cani, P. D., & Knauf, C. (2016). How gut microbes talk to organs: The role of endocrine and nervous routes. Molecular Metabolism, 5, 743–752. https://doi.org/10.1016/j.molmet.2016.05.011. Cao, X. (2017). Intestinal inflammation induced by oral bacteria. Science, 358, 308–309. https:// doi.org/10.1126/science.aap9298. Cavalier-Smith, T. (1992). Symbiosis as a source of evolutionary innovation: Speciation and morphogenesis. Trends in Ecology & Evolution, 7, 422–423. https://doi. org/10.1016/0169-5347(92)90028-A. Cerf-Bensussan, N., & Gaboriau-Routhiau, V. (2010). The immune system and the gut microbiota: Friends or foes? Nature Reviews. Immunology, 10, 735–744. https://doi.org/10.1038/nri2850. Chakraborti, D., Rahman, M. M., Chatterjee, A., et al. (2016). Fate of over 480 million inhabitants living in arsenic and fluoride endemic Indian districts: Magnitude, health, socio-­economic effects and mitigation approaches. Journal of Trace Elements in Medicine and Biology, 38, 33–45. Chen, L., Zhang, Y.-H., Huang, T., & Cai, Y.-D. (2016). Gene expression profiling gut microbiota in different races of humans. Scientific Reports, 6, 23075. https://doi.org/10.1038/srep23075. Chi, L., Bian, X., Gao, B., et al. (2017). The effects of an environmentally relevant level of arsenic on the gut microbiome and its functional metagenome. Toxicological Sciences, 160, 193–204. https://doi.org/10.1093/toxsci/kfx174. Chu, D. M., Seferovic, M., Pace, R. M., & Aagaard, K. M. (2018). The microbiome in preterm birth. Best Practice & Research. Clinical Obstetrics & Gynaecology, 52, 103–113. Chung, H., Pamp, S.  J., Hill, J.  A., et  al. (2012). Gut immune maturation depends on colonization with a host-specific microbiota. Cell, 149, 1578–1593. https://doi.org/10.1016/J. CELL.2012.04.037. Claesson, M. J., Jeffery, I. B., Conde, S., et al. (2012). Gut microbiota composition correlates with diet and health in the elderly. Nature, 488, 178–184. https://doi.org/10.1038/nature11319. Codagnone, M. G., Spichak, S., O’Mahony, S. M., et al. (2019). Programming bugs: Microbiota and the developmental origins of brain health and disease. Biological Psychiatry, 85, 150–163. https://doi.org/10.1016/j.biopsych.2018.06.014. Collado, M. C., Cernada, M., Neu, J., et al. (2015). Factors influencing gastrointestinal tract and microbiota immune interaction in preterm infants. Pediatric Research, 77, 726–731. https://doi. org/10.1038/pr.2015.54. Collado, M. C., Delgado, S., Maldonado, A., & Rodríguez, J. M. (2009). Assessment of the bacterial diversity of breast milk of healthy women by quantitative real-time PCR. Letters in Applied Microbiology, 48, 523–528. https://doi.org/10.1111/j.1472-765X.2009.02567.x. Costalos, C., Kapiki, A., Apostolou, M., & Papathoma, E. (2008). The effect of a prebiotic supplemented formula on growth and stool microbiology of term infants. Early Human Development, 84, 45–49. https://doi.org/10.1016/j.earlhumdev.2007.03.001.

52

A. Muthaiyan

Cotten, C. M. (2016). Adverse consequences of neonatal antibiotic exposure. Current Opinion in Pediatrics, 28, 141–149. https://doi.org/10.1097/MOP.0000000000000338. de la Cuesta-Zuluaga, J., Kelley, S. T., Chen, Y., et al. (2019). Age- and sex-dependent patterns of gut microbial diversity in human adults. mSystems, 4, e00261-19. https://doi.org/10.1128/ mSystems.00261-19. D’Argenio, V., & Salvatore, F. (2015). The role of the gut microbiome in the healthy adult status. Clinica Chimica Acta, 451, 97–102. https://doi.org/10.1016/J.CCA.2015.01.003. Daliri, E. B. M., Tango, C. N., Lee, B. H., & Oh, D. H. (2018). Human microbiome restoration and safety. International Journal of Medical Microbiology, 308, 487–497. David, L. A., Maurice, C. F., Carmody, R. N., et al. (2014). Diet rapidly and reproducibly alters the human gut microbiome. Nature, 505, 559–563. https://doi.org/10.1038/nature12820. De Filippis, F., Pellegrini, N., Vannini, L., et al. (2016). High-level adherence to a Mediterranean diet beneficially impacts the gut microbiota and associated metabolome. Gut, 65, 1812–1821. https://doi.org/10.1136/gutjnl-2015-309957. De Filippo, C., Cavalieri, D., Di Paola, M., et al. (2010). Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proceedings of the National Academy of Sciences, 107, 14691–14696. https://doi.org/10.1073/pnas.1005963107. Derrien, M., & Veiga, P. (2017). Rethinking diet to aid human–microbe symbiosis. Trends in Microbiology, 25, 100–112. https://doi.org/10.1016/j.tim.2016.09.011. Dethlefsen, L., Huse, S., Sogin, M. L., & Relman, D. A. (2008). The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biology, 6, e280. https://doi.org/10.1371/journal.pbio.0060280. Dethlefsen, L., & Relman, D. A. (2011). Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. Proceedings of the National Academy of Sciences, 108, 4554–4561. https://doi.org/10.1073/pnas.1000087107. DiGiulio, D. B., Romero, R., Amogan, H. P., et al. (2008). Microbial prevalence, diversity and abundance in amniotic fluid during preterm labor: A molecular and culture-based investigation. PLoS One, 3, e3056. https://doi.org/10.1371/journal.pone.0003056. Dill-McFarland, K. A., Tang, Z.-Z., Kemis, J. H., et al. (2019). Close social relationships correlate with human gut microbiota composition. Scientific Reports, 9, 703. https://doi.org/10.1038/ s41598-018-37298-9. Dinan, T. G., Stilling, R. M., Stanton, C., & Cryan, J. F. (2015). Collective unconscious: How gut microbes shape human behavior. Journal of Psychiatric Research, 63, 1–9. Dominguez-Bello, M.  G., Costello, E.  K., Contreras, M., et  al. (2010). Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proceedings of the National Academy of Sciences of the United States of America, 107, 11971–11975. https://doi.org/10.1073/pnas.1002601107. Dominguez-Bello, M. G., De Jesus-Laboy, K. M., Shen, N., et al. (2016). Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transfer. Nature Medicine, 22, 250–253. https://doi.org/10.1038/nm.4039. Dong, T. S., & Gupta, A. (2019). Influence of early life, diet, and the environment on the microbiome. Clinical Gastroenterology and Hepatology, 17, 231–242. Duerkop, B.  A., Vaishnava, S., & Hooper, L.  V. (2009). Immune responses to the microbiota at the intestinal mucosal surface. Immunity, 31, 368–376. https://doi.org/10.1016/J. IMMUNI.2009.08.009. Ercolini, D., & Fogliano, V. (2018). Food design to feed the human gut microbiota. Journal of Agricultural and Food Chemistry, 66, 3754–3758. https://doi.org/10.1021/acs.jafc.8b00456. Fallani, M., Amarri, S., Uusijarvi, A., et al. (2011). Determinants of the human infant intestinal microbiota after the introduction of first complementary foods in infant samples from five European centres. Microbiology, 157, 1385–1392. https://doi.org/10.1099/mic.0.042143-0. Fanaro, S., Chierici, R., Guerrini, P., & Vigi, V. (2003). Intestinal microflora in early infancy: Composition and development. Acta Paediatrica. Supplement, 91, 48–55. https://doi. org/10.1111/j.1651-2227.2003.tb00646.x.

Determinants of the Gut Microbiota

53

Fernández, L., Langa, S., Martín, V., et al. (2013). The human milk microbiota: Origin and potential roles in health and disease. Pharmacological Research, 69, 1–10. https://doi.org/10.1016/j. phrs.2012.09.001. Ferrer, M., Martins dos Santos, V.  A. P., Ott, S.  J., & Moya, A. (2014). Gut microbiota disturbance during antibiotic therapy: A multi-omic approach. Gut Microbes, 5, 64–70. https://doi. org/10.4161/gmic.27128. Ferrer, M., Méndez-García, C., Rojo, D., et al. (2017). Antibiotic use and microbiome function. Biochemical Pharmacology, 134, 114–126. https://doi.org/10.1016/j.bcp.2016.09.007. Ferretti, P., Pasolli, E., Tett, A., et al. (2018). Mother-to-infant microbial transmission from different body sites shapes the developing infant gut microbiome. Cell Host & Microbe, 24, 133–145.e5. https://doi.org/10.1016/j.chom.2018.06.005. Field, C. J. (2005). The immunological components of human milk and their effect on immune development in infants. The Journal of Nutrition, 135, 1–4. https://doi.org/10.1093/jn/135.1.1. Flint, H.  J., Duncan, S.  H., & Louis, P. (2017). The impact of nutrition on intestinal bacterial communities. Current Opinion in Microbiology, 38, 59–65. https://doi.org/10.1016/j. mib.2017.04.005. Flint, H. J., Duncan, S. H., Scott, K. P., & Louis, P. (2015). Links between diet, gut microbiota composition and gut metabolism. The Proceedings of the Nutrition Society, 74, 13–22. https:// doi.org/10.1017/S0029665114001463. Flint, H.  J., Scott, K.  P., Louis, P., & Duncan, S.  H. (2012). The role of the gut microbiota in nutrition and health. Nature Reviews. Gastroenterology & Hepatology, 9, 577–589. https://doi. org/10.1038/nrgastro.2012.156. Flowers, S. A., Evans, S. J., Ward, K. M., et al. (2017). Interaction between atypical antipsychotics and the gut microbiome in a bipolar disease cohort. Pharmacotherapy: The Journal of Human Pharmacology and Drug Therapy, 37, 261–267. https://doi.org/10.1002/phar.1890. Food and Agriculture Organization of the United Nations WHO. (2006). Probiotics in food: health and nutritional properties and guidelines for evaluation. NLM Catalog – NCBI. https://www. ncbi.nlm.nih.gov/nlmcatalog/101617803. Accessed 22 Dec 2019. Francino, M. P. (2016). Antibiotics and the human gut microbiome: Dysbioses and accumulation of resistances. Frontiers in Microbiology, 6, 1543. https://doi.org/10.3389/fmicb.2015.01543. Fu, J., Bonder, M. J., Cenit, M. C., et al. (2015). The gut microbiome contributes to a substantial proportion of the variation in blood lipids. Circulation Research, 117, 817–824. https://doi. org/10.1161/CIRCRESAHA.115.306807. Fuertes, A., Pérez-Burillo, S., Apaolaza, I., et al. (2019). Adaptation of the human gut microbiota metabolic network during the first year after birth. Frontiers in Microbiology, 10, 848. https:// doi.org/10.3389/fmicb.2019.00848. Ghosh, T.  S., Gupta, S.  S., Nair, G.  B., & Mande, S.  S. (2013). In silico analysis of antibiotic resistance genes in the gut microflora of individuals from diverse geographies and age-groups. PLoS One, 8, e83823. https://doi.org/10.1371/journal.pone.0083823. Gillings, M., Paulsen, I., Tetu, S., et al. (2015). Ecology and evolution of the human microbiota: Fire, farming and antibiotics. Genes (Basel), 6, 841–857. https://doi.org/10.3390/genes6030841. Glick-Bauer, M., & Yeh, M.-C. (2014). The health advantage of a vegan diet: Exploring the gut microbiota connection. Nutrients, 6, 4822–4838. https://doi.org/10.3390/nu6114822. Gomez-Arango, L. F., Barrett, H. L., McIntyre, H. D., et al. (2017). Antibiotic treatment at delivery shapes the initial oral microbiome in neonates. Scientific Reports, 7, 43481. https://doi. org/10.1038/srep43481. Gomez-Gallego, C., Garcia-Mantrana, I., Salminen, S., & Collado, M. C. (2016). The human milk microbiome and factors influencing its composition and activity. Seminars in Fetal & Neonatal Medicine, 21, 400–405. https://doi.org/10.1016/J.SINY.2016.05.003. Goodrich, J.  K., Davenport, E.  R., Beaumont, M., et  al. (2016). Genetic determinants of the gut microbiome in UK twins. Cell Host & Microbe, 19, 731–743. https://doi.org/10.1016/J. CHOM.2016.04.017.

54

A. Muthaiyan

Goodrich, J. K., Davenport, E. R., Clark, A. G., & Ley, R. E. (2017). The relationship between the human genome and microbiome comes into view. Annual Review of Genetics, 51, 413–433. https://doi.org/10.1146/annurev-genet-110711-155532. Goodrich, J. K., Waters, J. L., Poole, A. C., et al. (2014). Human genetics shape the gut microbiome. Cell, 159, 789–799. https://doi.org/10.1016/j.cell.2014.09.053. Górska, A., Peter, S., Willmann, M., et  al. (2018). Dynamics of the human gut phageome during antibiotic treatment. Computational Biology and Chemistry, 74, 420–427. https://doi. org/10.1016/j.compbiolchem.2018.03.011. Grady, N. G., Petrof, E. O., & Claud, E. C. (2016). Microbial therapeutic interventions. Seminars in Fetal & Neonatal Medicine, 21, 418–423. https://doi.org/10.1016/J.SINY.2016.04.005. Grice, E.  A., & Segre, J.  A. (2012). The human microbiome: Our second genome. Annual Review of Genomics and Human Genetics, 13, 151–170. https://doi.org/10.1146/ annurev-genom-090711-163814. Guaraldi, F., & Salvatori, G. (2012). Effect of breast and formula feeding on gut microbiota shaping in newborns. Frontiers in Cellular and Infection Microbiology, 2, 94. https://doi.org/10.3389/ fcimb.2012.00094. Guarner, F. (2015). The gut microbiome: What do we know? Clinics in Liver Disease, 5, 86–90. https://doi.org/10.1002/cld.454. Gurwitz, D. (2013). The gut microbiome: Insights for personalized medicine. Drug Development Research, 74, 341–343. https://doi.org/10.1002/ddr.21095. Haak, B. W., Lankelma, J. M., Hugenholtz, F., et al. (2019). Long-term impact of oral vancomycin, ciprofloxacin and metronidazole on the gut microbiota in healthy humans. The Journal of Antimicrobial Chemotherapy, 74, 782–786. https://doi.org/10.1093/jac/dky471. Hasan, N., & Yang, H. (2019). Factors affecting the composition of the gut microbiota, and its modulation. PeerJ, 7, e7502. https://doi.org/10.7717/peerj.7502. Heintz-Buschart, A., & Wilmes, P. (2018). Human gut microbiome: Function matters. Trends in Microbiology, 26, 563–574. https://doi.org/10.1016/J.TIM.2017.11.002. Hill, C., Guarner, F., Reid, G., et al. (2014). Expert consensus document: The international scientific association for probiotics and prebiotics consensus statement on the scope and appropriate use of the term probiotic. Nature Reviews. Gastroenterology & Hepatology, 11, 506–514. https://doi.org/10.1038/nrgastro.2014.66. Hooper, L. V., & Gordon, J. I. (2001). Commensal host-bacterial relationships in the gut. Science, 292, 1115–1118. https://doi.org/10.1126/SCIENCE.1058709. Huang, X., Fan, X., Ying, J., & Chen, S. (2019). Emerging trends and research foci in gastrointestinal microbiome. Journal of Translational Medicine, 17, 67. https://doi.org/10.1186/ s12967-019-1810-x. Hugon, P., Lagier, J.-C., Colson, P., et al. (2017). Repertoire of human gut microbes. Microbial Pathogenesis, 106, 103–112. https://doi.org/10.1016/j.micpath.2016.06.020. Huttenhower, C., Gevers, D., Knight, R., et  al. (2012). Structure, function and diversity of the healthy human microbiome. Nature, 486, 207–214. https://doi.org/10.1038/nature11234. Huttenhower, C., Knight, R., Brown, C. T., et al. (2014). Advancing the microbiome research community. Cell, 159, 227–230. https://doi.org/10.1016/J.CELL.2014.09.022. Ianiro, G., Tilg, H., & Gasbarrini, A. (2016). Antibiotics as deep modulators of gut microbiota: Between good and evil. Gut, 65, 1906–1915. https://doi.org/10.1136/gutjnl-2016-312297. Iizumi, T., Battaglia, T., Ruiz, V., & Perez Perez, G. I. (2017). Gut microbiome and antibiotics. Archives of Medical Research, 48, 727–734. https://doi.org/10.1016/j.arcmed.2017.11.004. Imhann, F., Bonder, M. J., Vila, A. V., et al. (2016). Proton pump inhibitors affect the gut microbiome. Gut, 65, 740–748. https://doi.org/10.1136/gutjnl-2015-310376. Isaac, S., Scher, J. U., Djukovic, A., et al. (2017). Short- and long-term effects of oral vancomycin on the human intestinal microbiota. The Journal of Antimicrobial Chemotherapy, 72, 128–136. https://doi.org/10.1093/jac/dkw383.

Determinants of the Gut Microbiota

55

Iyengar, S. R., & Walker, W. A. (2012). Immune factors in breast milk and the development of atopic disease. Journal of Pediatric Gastroenterology and Nutrition, 55, 641–647. https://doi. org/10.1097/MPG.0b013e3182617a9d. Jackson, M. A., Goodrich, J. K., Maxan, M. E., et al. (2016). Proton pump inhibitors alter the composition of the gut microbiota. Gut, 65, 749–756. https://doi.org/10.1136/gutjnl-2015-310861. Jain, A., Li, X. H., & Chen, W. N. (2018). Similarities and differences in gut microbiome composition correlate with dietary patterns of Indian and Chinese adults. AMB Express, 8, 104. https:// doi.org/10.1186/s13568-018-0632-1. Jakobsson, H. E., Abrahamsson, T. R., Jenmalm, M. C., et al. (2014). Decreased gut microbiota diversity, delayed Bacteroidetes colonisation and reduced Th1 responses in infants delivered by Caesarean section. Gut, 63, 559–566. https://doi.org/10.1136/gutjnl-2012-303249. Jakobsson, H. E., Jernberg, C., Andersson, A. F., 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. Jalili-Firoozinezhad, S., Gazzaniga, F. S., Calamari, E. L., et al. (2019). A complex human gut microbiome cultured in an anaerobic intestine-on-a-chip. Nature Biomedical Engineering, 3(7), 520–531. https://doi.org/10.1038/s41551-019-0397-0. Jefferson, A., & Adolphus, K. (2019). The effects of intact cereal grain fibers, including wheat bran on the gut microbiota composition of healthy adults: A systematic review. Frontiers in Nutrition, 6, 33. https://doi.org/10.3389/fnut.2019.00033. Jernberg, C., Löfmark, S., Edlund, C., & Jansson, J. K. (2007). Long-term ecological impacts of antibiotic administration on the human intestinal microbiota. The ISME Journal, 1, 56–66. https://doi.org/10.1038/ismej.2007.3. Jiang, H., Ling, Z., Zhang, Y., et  al. (2015). Altered fecal microbiota composition in patients with major depressive disorder. Brain, Behavior, and Immunity, 48, 186–194. https://doi. org/10.1016/j.bbi.2015.03.016. Jin, Y., Wu, S., Zeng, Z., & Fu, Z. (2017). Effects of environmental pollutants on gut microbiota. Environmental Pollution, 222, 1–9. Kamo, T., Akazawa, H., Suda, W., et  al. (2017). Dysbiosis and compositional alterations with aging in the gut microbiota of patients with heart failure. PLoS One, 12, e0174099. https://doi. org/10.1371/journal.pone.0174099. Kau, A. L., Ahern, P. P., Griffin, N. W., et al. (2011). Human nutrition, the gut microbiome and the immune system. Nature, 474, 327–336. https://doi.org/10.1038/nature10213. Keeney, K. M., Yurist-Doutsch, S., Arrieta, M.-C., & Finlay, B. B. (2014). Effects of antibiotics on human microbiota and subsequent disease. Annual Review of Microbiology, 68, 217–235. https://doi.org/10.1146/annurev-micro-091313-103456. Khangwal, I., & Shukla, P. (2019). Combinatory biotechnological intervention for gut microbiota. Applied Microbiology and Biotechnology, 103, 3615–3625. https://doi.org/10.1007/ s00253-019-09727-w. Kho, Z. Y., & Lal, S. K. (2018). The human gut microbiome – a potential controller of wellness and disease. Frontiers in Microbiology, 9, 1835. https://doi.org/10.3389/fmicb.2018.01835. Kim, H., Sitarik, A. R., Woodcroft, K., et al. (2019). Birth mode, breastfeeding, pet exposure, and antibiotic use: Associations with the gut microbiome and sensitization in children. Current Allergy and Asthma Reports, 19, 22. https://doi.org/10.1007/s11882-019-0851-9. Kim, H. N., Yun, Y., Ryu, S., et al. (2018). Correlation between gut microbiota and personality in adults: A cross-sectional study. Brain, Behavior, and Immunity, 69, 374–385. https://doi. org/10.1016/j.bbi.2017.12.012. Kim, M., Qie, Y., Park, J., & Kim, C.  H. (2016). Gut microbial metabolites fuel host antibody responses. Cell Host & Microbe, 20, 202–214. https://doi.org/10.1016/j.chom.2016.07.001. Kish, L., Hotte, N., Kaplan, G. G., et al. (2013). Environmental particulate matter induces murine intestinal inflammatory responses and alters the gut microbiome. PLoS One, 8, e62220. https:// doi.org/10.1371/journal.pone.0062220.

56

A. Muthaiyan

Kisuse, J., La-ongkham, O., Nakphaichit, M., et  al. (2018). Urban diets linked to gut microbiome and metabolome alterations in children: A comparative cross-sectional study in Thailand. Frontiers in Microbiology, 9, 1345. https://doi.org/10.3389/fmicb.2018.01345. Koch, M. A., Reiner, G. L., Lugo, K. A., et al. (2016). Maternal IgG and IgA antibodies dampen mucosal T helper cell responses in early life. Cell, 165, 827–841. https://doi.org/10.1016/J. CELL.2016.04.055. Koenig, J. E., Spor, A., Scalfone, N., et al. (2011). Succession of microbial consortia in the developing infant gut microbiome. Proceedings of the National Academy of Sciences, 108, 4578–4585. https://doi.org/10.1073/pnas.1000081107. Korpela, K., Salonen, A., Virta, L.  J., et  al. (2016). Intestinal microbiome is related to lifetime antibiotic use in Finnish pre-school children. Nature Communications, 7, 10410. https://doi. org/10.1038/ncomms10410. Kovacs, A., Ben-Jacob, N., Tayem, H., et  al. (2011). Genotype is a stronger determinant than sex of the mouse gut microbiota. Microbial Ecology, 61, 423–428. https://doi.org/10.1007/ s00248-010-9787-2. Kristensen, N. B., Bryrup, T., Allin, K. H., et al. (2016). Alterations in fecal microbiota composition by probiotic supplementation in healthy adults: A systematic review of randomized controlled trials. Genome Medicine, 8, 52. https://doi.org/10.1186/s13073-016-0300-5. Kumbhare, S. V., Patangia, D. V., Patil, R. H., et al. (2019). Factors influencing the gut microbiome in children: From infancy to childhood. Journal of Biosciences, 44, 49. https://doi.org/10.1007/ s12038-019-9860-z. Kump, P., Wurm, P., Gröchenig, H. P., et al. (2018). The taxonomic composition of the donor intestinal microbiota is a major factor influencing the efficacy of faecal microbiota transplantation in therapy refractory ulcerative colitis. Alimentary Pharmacology & Therapeutics, 47, 67–77. https://doi.org/10.1111/apt.14387. Lagier, J.  C., Khelaifia, S., Alou, M.  T., et  al. (2016). Culture of previously uncultured members of the human gut microbiota by culturomics. Nature Microbiology, 1, 16203. https://doi. org/10.1038/nmicrobiol.2016.203. Lang, J. M., Pan, C., Cantor, R. M., et al. (2018). Impact of individual traits, saturated fat, and protein source on the gut microbiome. MBio, 9, e01604–e01618. https://doi.org/10.1128/ MBIO.01604-18. Le Bastard, Q., Al-Ghalith, G.  A., Grégoire, M., et  al. (2018). Systematic review: Human gut dysbiosis induced by non-antibiotic prescription medications. Alimentary Pharmacology & Therapeutics, 47, 332–345. https://doi.org/10.1111/apt.14451. Le Huërou-Luron, I., Blat, S., & Boudry, G. (2010). Breast- v. formula-feeding: Impacts on the digestive tract and immediate and long-term health effects. Nutrition Research Reviews, 23, 23–36. https://doi.org/10.1017/S0954422410000065. LeBlanc, J.  G., Milani, C., de Giori, G.  S., et  al. (2013). Bacteria as vitamin suppliers to their host: A gut microbiota perspective. Current Opinion in Biotechnology, 24, 160–168. https:// doi.org/10.1016/j.copbio.2012.08.005. Lederer, A.-K., Pisarski, P., Kousoulas, L., et al. (2017). Postoperative changes of the microbiome: Are surgical complications related to the gut flora? A systematic review. BMC Surgery, 17, 125. https://doi.org/10.1186/s12893-017-0325-8. Lee, J. A., & Stern, J. M. (2019). Understanding the link between gut microbiome and urinary stone disease. Current Urology Reports, 20, 19. https://doi.org/10.1007/s11934-019-0882-8. Lee, Y.-K. (2013). Effects of diet on gut microbiota profile and the implications for health and disease. Bioscience of Microbiota, Food and Health, 32, 1–12. https://doi.org/10.12938/ bmfh.32.1. Lei, Y. M. K., Nair, L., & Alegre, M.-L. (2015). The interplay between the intestinal microbiota and the immune system. Clinics and Research in Hepatology and Gastroenterology, 39, 9–19. https://doi.org/10.1016/J.CLINRE.2014.10.008.

Determinants of the Gut Microbiota

57

Lemas, D. J., Yee, S., Cacho, N., et al. (2016). Exploring the contribution of maternal antibiotics and breastfeeding to development of the infant microbiome and pediatric obesity. Seminars in Fetal & Neonatal Medicine, 21, 406–409. https://doi.org/10.1016/J.SINY.2016.04.013. Ley, R.  E., Peterson, D.  A., & Gordon, J.  I. (2006). Ecological and evolutionary forces shaping microbial diversity in the human intestine. Cell, 124, 837–848. https://doi.org/10.1016/j. cell.2006.02.017. Li, H., Li, T., Li, X., et  al. (2018). Gut microbiota in Tibetan herdsmen reflects the degree of urbanization. Frontiers in Microbiology, 9, 1745. https://doi.org/10.3389/fmicb.2018.01745. Lieberman, T. D. (2018). Seven billion microcosms: Evolution within human microbiomes. mSystems, 3, e00171-17. https://doi.org/10.1128/msystems.00171-17. Lin, A., Bik, E.  M., Costello, E.  K., 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. Lloyd-Price, J., Abu-Ali, G., & Huttenhower, C. (2016). The healthy human microbiome. Genome Medicine, 8, 51. https://doi.org/10.1186/s13073-016-0307-y. Losasso, C., Eckert, E. M., Mastrorilli, E., et al. (2018). Assessing the influence of vegan, vegetarian and omnivore oriented westernized dietary styles on human gut microbiota: A cross sectional study. Frontiers in Microbiology, 9, 317. https://doi.org/10.3389/fmicb.2018.00317. Lozupone, C. A., Stombaugh, J. I., Gordon, J. I., et al. (2012). Diversity, stability and resilience of the human gut microbiota. Nature, 489, 220–230. https://doi.org/10.1038/nature11550. Lupp, C., Robertson, M. L., Wickham, M. E., et al. (2007). Host-mediated inflammation disrupts the intestinal microbiota and promotes the overgrowth of Enterobacteriaceae. Cell Host & Microbe, 2, 119–129. https://doi.org/10.1016/j.chom.2007.06.010. Lynch, S. V., & Pedersen, O. (2016). The human intestinal microbiome in health and disease. The New England Journal of Medicine, 375, 2369–2379. https://doi.org/10.1056/NEJMra1600266. Lyu, Q., & Hsu, C.-C. (2018). Can diet influence our health by altering intestinal microbiota-derived fecal metabolites? mSystems, 3, e00187-17. https://doi.org/10.1128/mSystems.00187-17. Macfarlane, S., Macfarlane, G. T., & Cummings, J. H. (2006). Review article: Prebiotics in the gastrointestinal tract. Alimentary Pharmacology & Therapeutics, 24, 701–714. Magnúsdóttir, S., & Thiele, I. (2018). Modeling metabolism of the human gut microbiome. Current Opinion in Biotechnology, 51, 90–96. https://doi.org/10.1016/J.COPBIO.2017.12.005. Maier, L., Pruteanu, M., Kuhn, M., et  al. (2018). Extensive impact of non-antibiotic drugs on human gut bacteria. Nature, 555, 623–628. https://doi.org/10.1038/nature25979. Malys, M. K., Campbell, L., & Malys, N. (2015). Symbiotic and antibiotic interactions between gut commensal microbiota and host immune system. Medicina (Kaunas), 51, 69–75. Mändar, R., & Mikelsaar, M. (1996). Transmission of mother’s microflora to the newborn at birth. Neonatology, 69, 30–35. https://doi.org/10.1159/000244275. Mariat, D., Firmesse, O., Levenez, F., et  al. (2009). The Firmicutes/Bacteroidetes ratio of the human microbiota changes with age. BMC Microbiology, 9, 123. https://doi. org/10.1186/1471-2180-9-123. Martin, R., Makino, H., Yavuz, A. C., et al. (2016). Early-life events, including mode of delivery and type of feeding, siblings and gender, shape the developing gut microbiota. PLoS One, 11, e0158498. https://doi.org/10.1371/journal.pone.0158498. Martín, V., Maldonado-Barragán, A., Moles, L., et  al. (2012). Sharing of bacterial strains between breast milk and infant feces. Journal of Human Lactation, 28, 36–44. https://doi. org/10.1177/0890334411424729. Martínez, I., Lattimer, J. M., Hubach, K. L., et al. (2013). Gut microbiome composition is linked to whole grain-induced immunological improvements. The ISME Journal, 7, 269–280. https:// doi.org/10.1038/ismej.2012.104. Matamoros, S., Gras-Leguen, C., Le Vacon, F., et al. (2013). Development of intestinal microbiota in infants and its impact on health. Trends in Microbiology, 21, 167–173.

58

A. Muthaiyan

Matijašić, B. B., Obermajer, T., Lipoglavšek, L., et al. (2014). Association of dietary type with fecal microbiota in vegetarians and omnivores in Slovenia. European Journal of Nutrition, 53, 1051–1064. https://doi.org/10.1007/s00394-013-0607-6. Maurice, C. F., Haiser, H. J., & Turnbaugh, P. J. (2013). Xenobiotics shape the physiology and gene expression of the active human gut microbiome. Cell, 152, 39–50. https://doi.org/10.1016/J. CELL.2012.10.052. McDonald, D., Hyde, E., Debelius, J.  W., et  al. (2018). American gut: An open platform for citizen science microbiome research. mSystems, 3, e00031-18. https://doi.org/10.1128/ mSystems.00031-18. Milani, C., Duranti, S., Bottacini, F., et al. (2017). The first microbial colonizers of the human gut: Composition, activities, and health implications of the infant gut microbiota. Microbiology and Molecular Biology Reviews, 81, e00036-17. https://doi.org/10.1128/MMBR.00036-17. Modi, S. R., Collins, J. J., & Relman, D. A. (2014). Antibiotics and the gut microbiota. The Journal of Clinical Investigation, 124, 4212–4218. Moschen, A. R., Wieser, V., & Tilg, H. (2012). Dietary factors: Major regulators of the gut’s microbiota. Gut and Liver, 6, 411–416. https://doi.org/10.5009/gnl.2012.6.4.411. Moya, A., & Ferrer, M. (2016). Functional redundancy-induced stability of gut microbiota subjected to disturbance. Trends in Microbiology, 24, 402–413. Mshvildadze, M., Neu, J., & Mai, V. (2008). Intestinal microbiota development in the premature neonate: Establishment of a lasting commensal relationship? Nutrition Reviews, 66, 658–663. https://doi.org/10.1111/j.1753-4887.2008.00119.x. Murphy, K., O’Shea, C. A., Ryan, C. A., et al. (2015). The gut microbiota composition in dichorionic triplet sets suggests a role for host genetic factors. PLoS One, 10, e0122561. https://doi. org/10.1371/journal.pone.0122561. Mutlu, E.  A., Comba, I.  Y., Cho, T., et  al. (2018). Inhalational exposure to particulate matter air pollution alters the composition of the gut microbiome. Environmental Pollution, 240, 817–830. https://doi.org/10.1016/j.envpol.2018.04.130. Nayfach, S., Shi, Z.  J., Seshadri, R., et  al. (2019). New insights from uncultivated genomes of the global human gut microbiome. Nature, 568, 505–510. https://doi.org/10.1038/ s41586-019-1058-x. Neish, A. S. (2009). Microbes in gastrointestinal health and disease. Gastroenterology, 136, 65–80. https://doi.org/10.1053/j.gastro.2008.10.080. Neu, J. (2016). The microbiome during pregnancy and early postnatal life. Seminars in Fetal & Neonatal Medicine, 21, 373–379. https://doi.org/10.1016/j.siny.2016.05.001. NIH Common Fund. (2019, May 29). The Human Microbiome Project expands the toolbox for studying host and microbiome interactions. National Institutes of Health (NIH). News Releases. https://www.nih.gov/news-events/news-releases/human-microbiome-project-expands-toolbox-studying-host-microbiome-interactions. Accessed 29 May 2019. Nogueira, T., David, P.  H. C., & Pothier, J. (2019). Antibiotics as both friends and foes of the human gut microbiome: The microbial community approach. Drug Development Research, 80, 86–97. Odamaki, T., Kato, K., Sugahara, H., et al. (2016). Age-related changes in gut microbiota composition from newborn to centenarian: A cross-sectional study. BMC Microbiology, 16, 90. https:// doi.org/10.1186/s12866-016-0708-5. Oliphant, K., Parreira, V.  R., Cochrane, K., & Allen-Vercoe, E. (2019). Drivers of human gut microbial community assembly: Coadaptation, determinism and stochasticity. The ISME Journal, 13, 3080–3092. https://doi.org/10.1038/s41396-019-0498-5. Ooi, J. H., Li, Y., Rogers, C. J., & Cantorna, M. T. (2013). Vitamin D regulates the gut microbiome and protects mice from dextran sodium sulfate–induced colitis. The Journal of Nutrition, 143, 1679–1686. https://doi.org/10.3945/jn.113.180794. Palmeira, P., Carneiro-Sampaio, M., Palmeira, P., & Carneiro-Sampaio, M. (2016). Immunology of breast milk. Revista da Associação Médica Brasileira, 62, 584–593. https://doi. org/10.1590/1806-9282.62.06.584.

Determinants of the Gut Microbiota

59

Palmer, C., Bik, E. M., DiGiulio, D. B., et al. (2007). Development of the human infant intestinal microbiota. PLoS Biology, 5, e177. https://doi.org/10.1371/journal.pbio.0050177. Park, G.-S., Park, M.  H., Shin, W., et  al. (2017). Emulating host-microbiome ecosystem of human gastrointestinal tract in vitro. Stem Cell Reviews and Reports, 13, 321–334. https://doi. org/10.1007/s12015-017-9739-z. Pasolli, E., Asnicar, F., Manara, S., et al. (2019). Extensive unexplored human microbiome diversity revealed by over 150,000 genomes from metagenomes spanning age, geography, and lifestyle. Cell, 176, 649–662.e20. https://doi.org/10.1016/j.cell.2019.01.001. Peñalver Bernabé, B., Cralle, L., & Gilbert, J. A. (2018). Systems biology of the human microbiome. Current Opinion in Biotechnology, 51, 146–153. Penders, J., Thijs, C., Vink, C., et al. (2006). Factors influencing the composition of the intestinal microbiota in early infancy. Pediatrics, 118, 511–521. https://doi.org/10.1542/peds.2005-2824. Petersen, L.  M., Bautista, E.  J., Nguyen, H., et  al. (2017). Community characteristics of the gut microbiomes of competitive cyclists. Microbiome, 5, 98. https://doi.org/10.1186/ s40168-017-0320-4. Poole, A. C., Goodrich, J. K., Youngblut, N. D., et al. (2019). Human salivary amylase gene copy number impacts oral and gut microbiomes. Cell Host & Microbe, 25, 553–564.e7. https://doi. org/10.1016/j.chom.2019.03.001. Poroyko, V. A., Carreras, A., Khalyfa, A., et al. (2016). Chronic sleep disruption alters gut microbiota, induces systemic and adipose tissue inflammation and insulin resistance in mice. Scientific Reports, 6, 35405. https://doi.org/10.1038/srep35405. Proctor, L. M. (2011). The human microbiome project in 2011 and beyond. Cell Host & Microbe, 10, 287–291. https://doi.org/10.1016/J.CHOM.2011.10.001. Proctor, L. M. (2016). The National Institutes of Health human microbiome project. Seminars in Fetal & Neonatal Medicine, 21, 368–372. https://doi.org/10.1016/J.SINY.2016.05.002. Rahim, H., Taylor, M. R., Hirota, S. A., & Greenway, S. C. (2018). Microbiome alterations following solid-organ transplantation: Consequences, solutions, and prevention. Transplant Research and Risk Management, 10, 1–11. https://doi.org/10.2147/TRRM.S143063. Rajilić-Stojanović, M., & de Vos, W.  M. (2014). The first 1000 cultured species of the human gastrointestinal microbiota. FEMS Microbiology Reviews, 38, 996–1047. https://doi. org/10.1111/1574-6976.12075. Rajilić-Stojanović, M., Heilig, H. G. H. J., Tims, S., et al. (2013). Long-term monitoring of the human intestinal microbiota composition. Environmental Microbiology, 15, 1146–1159. https://doi.org/10.1111/1462-2920.12023. Rashid, M.-U., Zaura, E., Buijs, M. J., et al. (2015). Determining the long-term effect of antibiotic administration on the human normal intestinal microbiota using culture and pyrosequencing methods. Clinical Infectious Diseases, 60, S77–S84. https://doi.org/10.1093/cid/civ137. Rastall, R. A., Gibson, G. R., Gill, H. S., et al. (2005). Modulation of the microbial ecology of the human colon by probiotics, prebiotics and synbiotics to enhance human health: An overview of enabling science and potential applications. FEMS Microbiology Ecology, 52, 145–152. Reveles, K. R., Ryan, C. N., Chan, L., et al. (2018). Proton pump inhibitor use associated with changes in gut microbiota composition. Gut, 67, 1369–1370. Richards, A.  L., Burns, M.  B., Alazizi, A., et  al. (2016). Genetic and transcriptional analysis of human host response to healthy gut microbiota. mSystems, 1, e00067-16. https://doi. org/10.1128/mSystems.00067-16. Rieder, R., Wisniewski, P.  J., Alderman, B.  L., & Campbell, S.  C. (2017). Microbes and mental health: A review. Brain, Behavior, and Immunity, 66, 9–17. https://doi.org/10.1016/j. bbi.2017.01.016. Rogers, M.  A. M., & Aronoff, D.  M. (2016). The influence of non-steroidal anti-inflammatory drugs on the gut microbiome. Clinical Microbiology and Infection, 22, 178.e1–178.e9. https:// doi.org/10.1016/j.cmi.2015.10.003.

60

A. Muthaiyan

Rojo, D., Méndez-García, C., Raczkowska, B. A., et al. (2017). Exploring the human microbiome from multiple perspectives: Factors altering its composition and function. FEMS Microbiology Reviews, 41, 453–478. https://doi.org/10.1093/femsre/fuw046. Rosenwald, A. G., Arora, G. S., Madupu, R., et al. (2012). The human microbiome project: An opportunity to engage undergraduates in research. Procedia Computer Science, 9, 540–549. https://doi.org/10.1016/J.PROCS.2012.04.058. 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. Round, J. L., & Mazmanian, S. K. (2009). The gut microbiota shapes intestinal immune responses during health and disease. Nature Reviews. Immunology, 9, 313–323. https://doi.org/10.1038/ nri2515. Ruengsomwong, S., La-ongkham, O., Jiang, J., et  al. (2016). Microbial community of healthy Thai vegetarians and non-vegetarians, their Core gut microbiota, and pathogen risk. Journal of Microbiology and Biotechnology, 26, 1723–1735. https://doi.org/10.4014/jmb.1603.03057. Rutayisire, E., Huang, K., Liu, Y., & Tao, F. (2016). The mode of delivery affects the diversity and colonization pattern of the gut microbiota during the first year of infants’ life: A systematic review. BMC Gastroenterology, 16, 86. https://doi.org/10.1186/s12876-016-0498-0. Salim, S. Y., Kaplan, G. G., & Madsen, K. L. (2014). Air pollution effects on the gut microbiota. Gut Microbes, 5, 215–219. https://doi.org/10.4161/gmic.27251. Sassone-Corsi, M., & Raffatellu, M. (2015). No vacancy: How beneficial microbes cooperate with immunity to provide colonization resistance to pathogens. Journal of Immunology, 194, 4081–4087. https://doi.org/10.4049/jimmunol.1403169. Savin, Z., Kivity, S., Yonath, H., & Yehuda, S. (2018). Smoking and the intestinal microbiome. Archives of Microbiology, 200, 677–684. https://doi.org/10.1007/s00203-018-1506-2. Schmidt, T. S. B., Raes, J., & Bork, P. (2018). The human gut microbiome: From association to modulation. Cell, 172, 1198–1215. https://doi.org/10.1016/J.CELL.2018.02.044. Scholtens, P. A. M. J., Oozeer, R., Martin, R., et al. (2012). The early settlers: Intestinal microbiology in early life. Annual Review of Food Science and Technology, 3, 425–447. https://doi. org/10.1146/annurev-food-022811-101120. Scott, K. P., Duncan, S. H., & Flint, H. J. (2008). Dietary fibre and the gut microbiota. Nutrition Bulletin, 33, 201–211. https://doi.org/10.1111/j.1467-3010.2008.00706.x. Scott, K. P., Gratz, S. W., Sheridan, P. O., et al. (2013). The influence of diet on the gut microbiota. Pharmacological Research, 69, 52–60. https://doi.org/10.1016/j.phrs.2012.10.020. Sender, R., Fuchs, S., & Milo, R. (2016). Revised estimates for the number of human and bacteria cells in the body. PLoS Biology, 14(8), e1002533. https://doi.org/10.1371/journal. pbio.1002533. Sheflin, A. M., Melby, C. L., Carbonero, F., & Weir, T. L. (2017). Linking dietary patterns with gut microbial composition and function. Gut Microbes, 8, 113–129. https://doi.org/10.108 0/19490976.2016.1270809. Simpson, H. L., & Campbell, B. J. (2015). Review article: Dietary fibre-microbiota interactions. Alimentary Pharmacology & Therapeutics, 42, 158–179. https://doi.org/10.1111/apt.13248. Singh, R.  K., Chang, H.-W., Yan, D., et  al. (2017). Influence of diet on the gut microbiome and implications for human health. Journal of Translational Medicine, 15, 73. https://doi. org/10.1186/s12967-017-1175-y. Sitaraman, R. (2018). Prokaryotic horizontal gene transfer within the human holobiont: Ecological-evolutionary inferences, implications and possibilities. Microbiome, 6, 163. https:// doi.org/10.1186/s40168-018-0551-z. Smith, R. P., Easson, C., Lyle, S. M., et al. (2019). Gut microbiome diversity is associated with sleep physiology in humans. PLoS One, 14, e0222394. https://doi.org/10.1371/journal. pone.0222394. Song, S. J., Lauber, C., Costello, E. K., et al. (2013). Cohabiting family members share microbiota with one another and with their dogs. eLife, 2, e00458. https://doi.org/10.7554/eLife.00458.

Determinants of the Gut Microbiota

61

Sonnenburg, E.  D., Smits, S.  A., Tikhonov, M., et  al. (2016). Diet-induced extinctions in the gut microbiota compound over generations. Nature, 529, 212–215. https://doi.org/10.1038/ nature16504. Sun, L., Zhang, X., Zhang, Y., et al. (2019). Antibiotic-induced disruption of gut microbiota alters local metabolomes and immune responses. Frontiers in Cellular and Infection Microbiology, 9, 99. https://doi.org/10.3389/fcimb.2019.00099. Sung, J., Hale, V., Merkel, A. C., et al. (2016). Metabolic modeling with Big Data and the gut microbiome. Applied & Translational Genomics, 10, 10–15. https://doi.org/10.1016/J. ATG.2016.02.001. Suzuki, K., Meek, B., Doi, Y., et al. (2004). Aberrant expansion of segmented filamentous bacteria in IgA-deficient gut. Proceedings of the National Academy of Sciences of the United States of America, 101, 1981–1986. https://doi.org/10.1073/pnas.0307317101. Taddei, C. R., Cortez, R. V., Mattar, R., et al. (2018). Microbiome in normal and pathological pregnancies: A literature overview. American Journal of Reproductive Immunology, 80, e12993. https://doi.org/10.1111/aji.12993. Tanaka, M., & Nakayama, J. (2017). Development of the gut microbiota in infancy and its impact on health in later life. Allergology International, 66, 515–522. Tap, J., Mondot, S., Levenez, F., et  al. (2009). Towards the human intestinal microbiota phylogenetic core. Environmental Microbiology, 11, 2574–2584. https://doi. org/10.1111/j.1462-2920.2009.01982.x. Tasnim, N., Abulizi, N., Pither, J., et al. (2017). Linking the gut microbial ecosystem with the environment: Does gut health depend on where we live? Frontiers in Microbiology, 8, 1935. https:// doi.org/10.3389/fmicb.2017.01935. Thaiss, C.  A., Zeevi, D., Levy, M., et  al. (2014). Transkingdom control of microbiota diurnal oscillations promotes metabolic homeostasis. Cell, 159, 514–529. https://doi.org/10.1016/j. cell.2014.09.048. Thursby, E., & Juge, N. (2017). Introduction to the human gut microbiota. The Biochemical Journal, 474, 1823–1836. https://doi.org/10.1042/BCJ20160510. Ticinesi, A., Lauretani, F., Milani, C., et al. (2017). Aging gut microbiota at the cross-road between nutrition, physical frailty, and sarcopenia: Is there a gut–muscle axis? Nutrients, 9, 1303. https://doi.org/10.3390/nu9121303. Tomova, A., Bukovsky, I., Rembert, E., et al. (2019). The effects of vegetarian and vegan diets on gut microbiota. Frontiers in Nutrition, 6, 47. https://doi.org/10.3389/fnut.2019.00047. Touchefeu, Y., Montassier, E., Nieman, K., et al. (2014). Systematic review: The role of the gut microbiota in chemotherapy- or radiation-induced gastrointestinal mucositis – current evidence and potential clinical applications. Alimentary Pharmacology & Therapeutics, 40, 409–421. Turnbaugh, P. J., Hamady, M., Yatsunenko, T., et al. (2009). A core gut microbiome in obese and lean twins. Nature, 457, 480–484. https://doi.org/10.1038/nature07540. Turta, O., & Rautava, S. (2016). Antibiotics, obesity and the link to microbes – what are we doing to our children? BMC Medicine, 14, 57. https://doi.org/10.1186/s12916-016-0605-7. Umberson, D., Crosnoe, R., & Reczek, C. (2010). Social relationships and health behavior across the life course. Annual Review of Sociology, 36, 139–157. https://doi.org/10.1146/ annurev-soc-070308-120011. van de Guchte, M., Blottière, H. M., & Doré, J. (2018). Humans as holobionts: Implications for prevention and therapy. Microbiome, 6, 81. https://doi.org/10.1186/s40168-018-0466-8. Vuillermin, P. J., Macia, L., Nanan, R., et al. (2017). The maternal microbiome during pregnancy and allergic disease in the offspring. Seminars in Immunopathology, 39, 669–675. https://doi. org/10.1007/s00281-017-0652-y. Walker, A. W. (2016). Studying the human microbiota. Advances in Experimental Medicine and Biology, 902, 5–32. https://doi.org/10.1007/978-3-319-31248-4_2. Walsh, C. J., Guinane, C. M., O’Toole, P. W., & Cotter, P. D. (2014). Beneficial modulation of the gut microbiota. FEBS Letters, 588, 4120–4130. https://doi.org/10.1016/j.febslet.2014.03.035.

62

A. Muthaiyan

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. Frontiers in Microbiology, 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. Weber, D., Hiergeist, A., Weber, M., et al. (2019). Detrimental effect of broad-spectrum antibiotics on intestinal microbiome diversity in patients after allogeneic stem cell transplantation: Lack of commensal sparing antibiotics. Clinical Infectious Diseases, 68, 1303–1310. https://doi. org/10.1093/cid/ciy711. Whiteson, K. L. (2018). Vive la persistence: engineering human microbiomes in the 21st century. mSystems, 3, e00166-17. https://doi.org/10.1128/mSystems.00166-17. WHO. (2017). Depression. World Health Organization. https://www.who.int/mental_health/management/depression/en/. Accessed 18 Jun 2019. WHO. (2018). Ambient (outdoor) air pollution. World Health Organization. https://www.who. int/news-room/fact-sheets/detail/ambient-(outdoor)-air-quality-and-health. Accessed 18 Dec 2019. Wilson, B. C., Vatanen, T., Cutfield, W. S., & O’Sullivan, J. M. (2019). The super-donor phenomenon in fecal microbiota transplantation. Frontiers in Cellular and Infection Microbiology, 9, 2. Winter, G., Hart, R. A., Charlesworth, R. P. G., & Sharpley, C. F. (2018). Gut microbiome and depression: What we know and what we need to know. Reviews in the Neurosciences, 29, 629–643. https://doi.org/10.1515/revneuro-2017-0072. Wipperman, M. F., Fitzgerald, D. W., Juste, M. A. J., et al. (2017). Antibiotic treatment for tuberculosis induces a profound dysbiosis of the microbiome that persists long after therapy is completed. Scientific Reports, 7, 10767. https://doi.org/10.1038/s41598-017-10346-6. Wong, M.-W., Yi, C.-H., Liu, T.-T., et  al. (2018). Impact of vegan diets on gut microbiota: An update on the clinical implications. Tzu Chi Medical Journal, 30, 200. https://doi.org/10.4103/ tcmj.tcmj_21_18. Xia, Y., & Sun, J. (2017). Hypothesis testing and statistical analysis of microbiome. Genes & Diseases, 4, 138–148. https://doi.org/10.1016/J.GENDIS.2017.06.001. Yamashita, T., Hayashi, T., Yoshida, N., & Hirata, K. I. (2018). Gut microbial dysbiosis in heart failure – is it a future therapeutic target or not? Circulation Journal, 82, 1507–1509. Yatsunenko, T., Rey, F. E., Manary, M. J., et al. (2012). Human gut microbiome viewed across age and geography. Nature, 486, 222–227. https://doi.org/10.1038/nature11053. Yoshida, N., Yamashita, T., & Hirata, K. (2018). Gut microbiome and cardiovascular diseases. Diseases, 6, 56. https://doi.org/10.3390/diseases6030056. Younes, J. A., Lievens, E., Hummelen, R., et al. (2018). Women and their microbes: The unexpected friendship the impact of microbes on the vaginal niche. Trends in Microbiology, 26, 16–32. https://doi.org/10.1016/j.tim.2017.07.008. Zimmermann, P., & Curtis, N. (2018). Factors influencing the intestinal microbiome during the first year of life. The Pediatric Infectious Disease Journal, 37, e315–e335. https://doi.org/10.1097/ INF.0000000000002103. Zinöcker, M., & Lindseth, I. (2018). The western diet–microbiome-host interaction and its role in metabolic disease. Nutrients, 10, 365. https://doi.org/10.3390/nu10030365. Zmora, N., Suez, J., & Elinav, E. (2019). You are what you eat: Diet, health and the gut microbiota. Nature Reviews. Gastroenterology & Hepatology, 16, 35–56. https://doi.org/10.1038/ s41575-018-0061-2.

Effects of Diet on Human Gut Microbiome and Subsequent Influence on Host Physiology and Metabolism Bryna Rackerby, Daria Van De Grift, Jang H. Kim, and Si Hong Park

1  Introduction The gut microbiome is the microbial ecosystem composed primarily of bacteria that inhabits the gastrointestinal tract of humans and animals. It is thought to be influenced by a variety of factors, including host genetics, diet, and environment (Zoetendal et al. 2001). The gut microbiome performs many functions vital to the host, including immune regulation, organ development, host metabolism (Sommer and Bäckhed 2013), and maintenance of the structural integrity of the intestinal mucosa (Jandhyala et al. 2015). Recently, it has been found that the gut microbiome can even alter behavior (Sommer and Bäckhed 2013). The metabolic power of the intestinal microbiota equals that of the liver, and its genetic potential is two orders of magnitude beyond that of the human body alone (Sommer and Bäckhed 2013); for this reason, the human gut microbiome is often considered as an additional organ (Sommer and Bäckhed 2013; O’Hara and Shanahan 2006; Quigley 2013; Clarke et al. 2014). It is thought that the gut microbiome plays a role in human diseases such as inflammatory bowel disease (IBD), asthma, obesity, diabetes (Shen and Wong 2016), and cardiovascular disease (Sandoval and Seeley 2010). Through studies on germ-free animals, it has been determined that the gut microbiome does indeed play a role in immunity (O’Hara and Shanahan 2006; Shen and Wong 2016). The normal gut microbiome consists primarily of the phyla Firmicutes and Bacteroidetes (Sommer and Bäckhed 2013; Jandhyala et al. 2015), though members of Proteobacteria, Verrucomicrobia, Actinobacteria, Fusobacteria, and Cyanobacteria are also present (Sommer and Bäckhed 2013). B. Rackerby · D. Van De Grift · S. H. Park (*) Department of Food Science and Technology, Oregon State University, Corvallis, OR, USA e-mail: [email protected] J. H. Kim School of Family and Consumer Sciences, College of Agricultural and Life Sciences, University of Idaho, Moscow, ID, USA © Springer Nature Switzerland AG 2020 D. Biswas, S.O. Rahaman (eds.), Gut Microbiome and Its Impact on Health and Diseases, https://doi.org/10.1007/978-3-030-47384-6_3

63

64

B. Rackerby et al.

Though it is known that the gut microbiome is heavily involved in host metabolism (Sommer and Bäckhed 2013; Quigley 2013; Clarke et al. 2014; Faderl et al. 2015), the mechanism is not fully understood (Sommer and Bäckhed 2013). The gut microbiota aids in the metabolism of compounds including nutrients, xenobiotics, and bile acids, as well as the production of short-chain fatty acids, vitamin K, components of vitamin B, and other important products (Jandhyala et al. 2015; Quigley 2013; Clarke et al. 2014). It is important to note that, as with the human genome, the human gut microbiome is unique to each individual, with a core microbiome established through extensive research (Sommer and Bäckhed 2013). The presence, absence, or dysbiosis of this core microbiome influences host physiology and metabolism. Though it is apparent that diet is an influencing factor in the composition of the gut microbiome, it is harder to determine whether a particular gut microbiota is causative of, contributing to, or a consequence of a given disease state (Sommer and Bäckhed 2013; Clarke et al. 2014; Faderl et al. 2015). A study in which germ-free mice adopted the phenotype of their microbiome donor (Clarke et al. 2014) demonstrated that the gut microbiome does affect host physiology, and some studies indicate that the gut microbiome is indeed a causal factor of obesity (Clarke et al. 2014). From this data, we can infer that causal relationships with the gut microbiome may exist in other physiological or metabolic states as well; however, it is important to remember that most conditions are multifactorial. The influence of diet over health may be due largely to the impact that diet has on the richness and diversity of organisms living in our gastrointestinal tract. Research has found that the gut microbiome begins to change soon after dietary changes. These dietary alterations impact the environmental conditions and nutrient availability inside the intestinal tract, which is enough to shift the microbial population. The ways in which specific dietary changes impact the host microbiome is inconsistent across papers, though some of the discrepancy may be explained by the  concept of enterotypes, in which either Prevotella, Ruminococcus, or Bacteroidetes are found to dominate (Quigley 2013; Clarke et  al. 2014). While alterations in diet induce the compositional changes in the gut microbiome, these changes are not sufficient to cause a change in enterotype (De Filippis et al. 2016). Efforts to change the gut microbiome later in life may be occluded by the lasting effects of early life diet. The initial colonizers of the gut appear to have an impact on the host’s gene expression, manipulating it to create an environment that favors the initial inhabitants (O’Hara and Shanahan 2006; Guarner and Malagelada 2003). One study found that identical twins had similar gut microbiota while marital partners did not (Zoetendal et al. 2001). The paper concluded that this association was due to genetic relatedness; however, a possible nongenetic explanation for these results lies in the finding that the infant gut microbiome matches the mother’s milk microbiome (Quigley et al. 2013a). Therefore, the importance of the initial colonizers in the lifelong broad makeup of the gut microbiome may be understated, and early-life diet may influence an individual’s core gut microbiome more than diet later in life. A study in obese children and parents found that 10 years after an 8-month dietary change treatment, children were able to maintain weight loss while

Effects of Diet on Human Gut Microbiome and Subsequent Influence on Host…

65

parents gained it back. The level of malleability seen in children may be related to an increased microbial richness (Heiman and Greenway 2016), though there are likely other factors involved as well, as the ability to permanently alter the preadolescent gut microbiota has been repeatedly demonstrated (Sommer and Bäckhed 2013; Quigley 2013; Heiman and Greenway 2016; Mao et al. 2018).

2  Fermented Foods In the past, people encountered a higher level and wider range of microorganisms via their diets and environments than they do today (ISAPP 2016). Where fermentation used to be a primary form of food preservation, it declined with the advent and spread of canning and artificial refrigeration (Saxe 2019). The industrial revolution also led a switch from spontaneous fermentation to inoculation with specific starter strains, increasing product consistency but decreasing microbial diversity (Paul Ross et al. 2002). Comparison of the gut microbiomes of people living in unindustrialized areas with those living modernized lifestyles demonstrates a correlation between decreased microbial diversity and industrialization (Deehan and Walter 2016). Recently, many medical conditions have been associated with gut dysbiosis, which has been linked to many factors including diet. Due to widespread awareness of the gut microbiome, many people have been turning to fermented foods, as well as prebiotics and probiotics, to fortify their gut microbiota. Foods such as sourdough bread or soy sauce that are baked or pasteurized after fermentation contain the metabolites produced during fermentation, but no longer contain live microorganisms. This section will focus on products that still contain live organisms. Fermentation can increase the concentration of vitamins or bioactive compounds in foods to inhibit the growth of spoilage organisms or foodborne pathogens and eliminate toxic compounds (ISAPP 2016; Paul Ross et al. 2002). One of the main factors of interest in fermented foods is the presence of live beneficial microorganisms, called probiotics. Probiotics are live microorganisms that can confer health benefits when delivered in adequate doses (Jandhyala et al. 2015). Common examples of probiotics include strains of Lactobacillus species (spp.), Streptococcus thermophilus, and bifidobacteria, particularly Bifidobacterium infantis (Jandhyala et al. 2015; Quigley 2013). For foods to be considered probiotic, they need to contain high enough levels of probiotic organisms, though many fermented foods naturally contain beneficial organisms at lower levels (ISAPP 2016). As with probiotics, many foods also contain prebiotic compounds, which have been concentrated into dietary supplements as well. Prebiotics consist primarily of nondigestible oligosaccharides that intestinal microorganisms can break down into SCFAs through fermentation (Jandhyala et al. 2015; Pandey et al. 2015). They are chosen to selectively stimulate the growth of beneficial organisms, particularly lactobacilli and bifidobacteria (Pandey et  al. 2015). Some bifidobacteria can produce conjugated linoleic acid, which has been associated with health benefits including liver and adipose fatty acid composition (O’Shea et al. 2012). When beneficial microorganisms reach

66

B. Rackerby et al.

the gut, they can also produce bacteriocins which aid in the establishment of producing strains by inhibiting other organisms, such as pathogens (O’Shea et al. 2012). Probiotic supplements can alter the intestinal microbiota by increasing the concentration of whichever organism(s) they contain and selecting against other organisms via competitive exclusion (CE) or bacteriocin production, as well as return the intestinal flora to a preexisting population. Health benefits are strain specific (Quigley 2013; Pandey et al. 2015; O’Shea et al. 2012; Hemarajata and Versalovic 2013; Arora et al. 2013). Since both probiotics and the native gut microbiota consist of living organisms, they are capable of interacting with one another (Arora et al. 2013). Bifidobacterium longum increased the catabolic activity of Bacteroides thetaiotaomicron, while Lactobacillus casei upregulated genes encoding hexosaminidases and arabinosidases. Bifidobacterium animalis induced transcription and replication of B. longum without altering its carbohydrate metabolism (Arora et al. 2013). Probiotics are frequently administered to patients suffering from inflammatory bowel conditions (Quigley 2013; Hemarajata and Versalovic 2013), though their efficacy is not always supported in clinical trials (Quigley 2013). This may be due at least in part to the interactions between living organisms. While many papers described the health benefits of consuming isolated probiotic organisms, much less seems to have been done on how the consumption of fermented foods may modulate the intestinal microbiota. Probiotics can interact with the existing gut microbiome and change its properties and even have the potential to alleviate obesity (Arora et al. 2013). As with obesity, the gut microbiome may also play a role in the onset and progression of type 2 diabetes (Cabello-Olmo et  al. 2019). The gut microbiome can cause obesity and insulin resistance, with mechanisms both independent of and dependent on the gut microbiota playing a role (Saad et  al. 2016). A non-dairy fermented food product was found to induce microbial changes, including an increase in alpha diversity, that appeared to protect against type 2 diabetes and improve glucose metabolism (Cabello-Olmo et  al. 2019). Compared to a non-fermented milk product, a fermented milk product containing dairy starters and B. animalis increased intestinal short-chain fatty acid production and decreased the prevalence of Bilophila wadsworthia in individuals with IBD, which was accompanied by a reduction of symptoms (Veiga et al. 2014). Though consumption of both the fermented and non-fermented milk products modulated gene expression in the endogenous gut microbiome, the fermented milk product had about twice the effect of the non-fermented product (Veiga et al. 2014). Fermented foods can also alter the microbiomes of healthy individuals. For example, kimchi consumption was found to decrease harmful and increase beneficial organisms, though microbial diversity did not differ between low and high amounts of kimchi groups (Jy and Ey 2016). Individuals with a high daily intake of kimchi saw a 50% or greater reduction in 16 bacterial species, including pathogens and organisms belonging to Gammaproteobacteria, while 18 species are used to ferment kimchi, at least doubled. These organisms included B. breve, Lactobacillus acidophilus, L. mindensis, L. reuteri, L. brevis, L. amylolyticus, and Leuconostoc mesenteroides (Jy and Ey 2016). Another study found that Weissella cibaria JW15, a probiotic

Effects of Diet on Human Gut Microbiome and Subsequent Influence on Host…

67

organism isolated from kimchi, had antioxidative and anti-inflammatory properties (Yu et al. 2019). Cheeses and cured meats are commonly produced using commercial starter cultures of L. lactis, Pediococcus acidilactici, and S. thermophilus. Additionally, several species of Staphylococcus are also used in cured meats. In diets where consumption of these foods was increased, the presence of L. lactis, P. acidilactici, and Staphylococcus was more prevalent in fecal samples. Certain fungi can be found in fermented foods, which also remained viable into the gut. This indicates that microorganisms present in fermented foods can survive and even remain metabolically active into the gut (David et al. 2014). There is little evidence on how the consumption of specific fermented foods, or fermented foods in general, impacts the gut microbiota, though a study done on fermented green tea extract found that it can reverse obesity-related changes in gene expression brought about by a high-fat diet. A high-fat diet supplemented with fermented green tea prevented weight gain without a change in food intake. In the gut, it reduced the ratio of Firmicutes-­ Bacteroidetes and reverted the ratio of Bacteroides-Prevotella to a more normal state in high-fat-fed mice (Seo et al. 2018). The general effects of a habitual diet high in fermented foods should be explored and compared to diets supplemented, short and long term, with probiotics.

3  Dairy Foods Milk is a nutrient-rich food source that contains proteins, fats, carbohydrates, vitamins, minerals, and amino acids (Quigley et al. 2013a). Milk can come from many different animals, with cow’s milk being the most widely available in most parts of the world. In a study comparing the effects of human, donkey, and cow milk on the gut microbiome, human and donkey milk were found to increase Bacteroides and Parabacteroides and provide metabolic and immune benefits. Donkey milk also increased levels of Streptococcus, Lactococcus, and Blautia and decreased Akkermansia. Human milk increased Coprobacillus, Parabacteroides, and Syntrophococcus (Trinchese et al. 2015). Yak, camel, and cow milks similarly lowered the proportions of Ruminococcus, Prevotella, and Barnesiella intestinihominis while increasing B. glucerasea, B. dorei, Parabacteroides, and Clostridium saccharogumia after a month of feeding (Wen et al. 2017). A study comparing sheep and cow milk observed that species origin appears to have little impact on the gut microbiota (Rettedal et al. 2019). Between breast, goat, and cow milk, the Lachnospiraceae of breast and goat milk diets was primarily Ruminococcus gnavus, while this family was more diverse with cow milk (Tannock et  al. 2012). Camel milk reduced Romboutsia, Lactobacillus, Turicibacter, and Desulfovibrio and increased Allobaculum, Akkermansia, and Bifidobacterium (Wang et al. 2018a). Within single studies comparing the effects of various milks, the animal source does not appear significant; however, between studies results do not appear consistent.

68

B. Rackerby et al.

There are links between bovine diet, rumen microbiome, and milk microbiome, as well as milk nutrient composition, meaning that the method of cow rearing impacts the milk and changes the nutrients and microbes we consume (Jami et al. 2014; Quigley et al. 2013b). Raw milk contains a wide variety of organisms, from beneficial organisms to spoilage and/or pathogenic microbes. The most prevalent organisms in milk are lactic acid bacteria (LAB), most commonly Lactococcus, Lactobacillus, Leuconostoc, Streptococcus, and Enterococcus. These organisms are responsible for the fermentation of lactose to lactic acid. Propionibacterium is another fermentative organism present in milk (Quigley et al. 2013a). Propionibacteria are grouped by their ability to either metabolize lactose or reduce nitrates and are responsible for the production of organic acids, primarily propionic and acetic acid, and B group vitamins (Quigley et al. 2013a; Piwowarek et al. 2018). They also have impressive lipolytic abilities (Chamba and Irlinger 2004). Bifidobacterium present in milk can confer health benefits as well, along with certain Lactobacillus (Quigley et al. 2013a). Many Lactobacillus spp. found in dairy, including L. paracasei, L. rhamnosus, L. acidophilus, and L. reuteri, are considered probiotic strains and confer certain health benefits when consumed in high enough quantities (Quigley 2013; Arora et al. 2013). Lactobacillus paracasei is able to alter lipid synthesis, nutrient absorption, and intestinal digestion, as well as decrease oxidative stress (Arora et al. 2013). It was shown to restore normal metabolic profiles to postinfectious IBS models, as well as reduce immune activation and gut hypercontractility. Additionally, it was found to reduce antibiotic-induced visceral hypersensitivity (Quigley 2013). When administered with L. rhamnosus, an increase in gluconeogenesis, proteolysis, and branched-chain amino acid catabolism was observed, along with a decrease in the acetate-propionate ratio (Arora et  al. 2013). Lactobacillus rhamnosus PL60 produces conjugated linoleic acid and was found to reduce white adipose tissue and weight gain without changes in food intake (Clarke et al. 2014). Lactobacillus acidophilus and L. reuteri were both found to attenuate visceral pain (Quigley 2013). Even when consumed only at the levels naturally present in dairy products, such as cheese, these organisms demonstrated an increased presence in the gut. Fermented milk containing the probiotic strains B. animalis subsp. lactis, two strains of L. delbrueckii subsp. bulgaricus, L. lactis subsp. cremoris, and S. thermophilus increased only B. animalis when administered to monozygotic twins; however, in gnotobiotic mice whose flora consisted of 15 organisms, the fermented milk resulted in increased expression of genes related to xylooligosaccharide (XOS) catabolism and conversion of carbohydrates into propionate (Arora et  al. 2013). Another fermented milk product of a very similar composition induced production of SCFAs, particularly butyrate, and decreased the abundance of B. wadsworthia, an opportunistic pathogen implicated in IBD, leading to a reduction of symptoms (David et  al. 2014; Veiga et  al. 2014). As previously stated, fermentation status alters the chemical composition of a food in addition to the microbial communities present. These chemical changes can affect the gut microbiome as well. Rats given milk had higher rates of Firmicutes, Lactobacillus, and Collinsella, while rats fed

Effects of Diet on Human Gut Microbiome and Subsequent Influence on Host…

69

yoghurt depleted of starter cultures demonstrated increased Proteobacteria, Bacteroidetes, and Parabacteroides (Rettedal et al. 2019). Lactose is the primary sugar found in milk. An investigation of lactose-free milk and the elderly gut microbiota found that lactose-free milk resulted in higher microbial diversity than regular milk, indicating that lactose-free milk may confer larger health benefits than regular milk (Ntemiri et al. 2019). Despite this, consumption of lactose may present certain health benefits, including aiding in the uptake of divalent cations such as calcium, as well as immune enhancement through synergistic interactions with cathelicidin antimicrobial peptide (Wahlqvist 2015). Though the intestinal microbiota of lactose consumers and nonconsumers does not appear to have been extensively studied, certain changes have been observed. Most notably, lactose consumption significantly increases the presence of bifidobacteria (Wahlqvist 2015; Francavilla et al. 2012). Infants with dairy allergy had low Bifidobacterium and Lactobacillus with high levels of Clostridium, Staphylococcus, and E. coli, and the addition of lactose to the diet increased Bifidobacterium and lactic acid bacteria while lowering Bacteroides and Clostridium to control levels (Francavilla et  al. 2012). In individuals with lactose intolerance, consumption of galactooligosaccharides (GOS) increased levels of Bifidobacterium, Faecalibacterium, and Lactobacillus, while the subsequent reintroduction of lactose increased Roseburia levels. These changes ameliorated lactose intolerance (Azcrate-Peril et al. 2017). It is of interest to lessen the effects of lactose intolerance, as it has been found that lactose may have a positive impact on the gut microbiota (Wahlqvist 2015). As not all individuals who are genetically unable to produce lactase display lactose intolerance symptoms (Wahlqvist 2015), more research on the role of the gut microbiota in lactose intolerance, as well as the effects of lactose on the gut microbiome, should be done. It has been seen that bile acid production and metabolism contributes significantly to host health and is largely influenced by the intestinal microbiota. The gut microbiota which influences bile acids is present and is responsible, to a large degree, for bile acid metabolism (Long et al. 2017). Germ-free mice demonstrated a 300% increase in biliary bile acid absorption, higher cholesterol, and no deconjugation of bile acids in the intestine (Jones et al. 2012a). Due to its interactions with bile acids via bile salt hydrolase activity, L. reuteri 30242 can reduce LDL cholesterol when administered in yoghurt or as a dietary supplement capsule (Jones et al. 2012a b). Intraluminal bile salt deconjugation led to an increased concentration of deconjugated bile salts in the plasma, which correlated with LDL reduction. The level of absorption of both dietary and biliary cholesterol also appeared reduced (Jones et al. 2012a). Lactobacillus plantarum KCTC3928 in mice decreased LDL cholesterol; increased expression of 7α-hydrolase, the enzyme required to break down cholesterol and synthesize bile acid; and increased synthesis and fecal excretion of bile acid (Jones et al. 2012a). This is seen with L. reuteri 30242 as well. The increased excretion of deconjugated bile acids leads to the uptake of serum cholesterol by the liver in order to replace lost bile acids by de novo synthesis, thus reducing serum cholesterol levels (Jones et al. 2012b). Conversely, L. paracasei increased hepatic methylamines and shifted bile acid metabolism to favor the increase of

70

B. Rackerby et al.

enterohepatic recirculation of bile acids (Arora et al. 2013). There also appears to be a factor in milk, fermented or unfermented and including yoghurt, that prevents the synthesis of cholesterol from acetate. Though this factor is present in both types of milk, its levels appear slightly higher in fermented milk (Richardson 1978). In one study, the secretion of bile acid stimulated by the saturated fats contained in milk was found to promote the growth of a Bilophila-containing cluster, which is largely composed of B. wadsworthia (David et al. 2014). Since B. wadsworthia has been implicated in IBD, it seems as though increased non-fermented milk consumption could increase the risk of or aggravate existing IBD through the proliferation of this organism. This organism showed a positive correlation with general saturated fat intake as well (David et al. 2014), indicating that this is not a dairy-specific problem, but a general saturated fat intake problem. When compared to mice fed polyunsaturated fats, mice fed milk fat displayed a shift in bile acid composition, showing increased levels of TCA and an increased abundance of B. wadsworthia (Wahlström et al. 2016).

4  Fresh Produce Fresh produce is a common source of foodborne pathogenic infections, and most of the research surrounding fresh produce has focused on its ability to carry pathogens. There are several ways in which the consumption of fresh produce may influence the human gut microbiota. The first has to do with the microbiome of the produce itself. Despite the fact that most people either rinse or wash their produce prior to consumption, a cursory rinse leaves behind much of the microbiota associated with the produce. The type of produce consumed changes the microbiota a person is exposed to, as different produce harbor different microbial communities. For example, produce grown near the soil surface, such as lettuce, strawberries, tomatoes, and peppers, share a higher relative abundance of Enterobacteriaceae (Berg et al. 2015). Even in bananas, Enterobacteriaceae accounted for 33% of the microbial load and included both pathogenic genera and disease-suppressive organisms, such as Serratia (Berg et al. 2015). Rubus chlorotic mottle virus, a spinach plant pathogen, was detected in the feces of individuals fed a plant-based diet, and RNA transcripts of plant viruses were found in individuals who ate both plant- and animal-based diets, indicating that organisms present on produce do survive the trip along the gastrointestinal tract (David et  al. 2014). Additionally, Bifidobacterium increased after the consumption of red berries (Graf et al. 2015). The second way in which fresh produce can affect the gut microbiome relates to the nutrients contained within the food. Fresh produce primarily contain carbohydrates, specifically fiber and sugars. The Prevotella enterotype is associated with populations which have a high fiber intake (Kashtanova et al. 2016). Bacterial fermentation of carbohydrates results in the formation of SCFAs, which are used in regulatory control of the digestive system and as a major energy source at the cellular level (Clarke et al. 2014). A reduced intake

Effects of Diet on Human Gut Microbiome and Subsequent Influence on Host…

71

of carbohydrates resulted in the reduction of Roseburia and Eubacterium rectale, as well as a decrease of SCFAs present in feces (Kashtanova et al. 2016) Furthermore, certain microbes were shown to be inversely associated with fat intake while being directly correlated with plant-based nutrient consumption (Davenport et al. 2014). Produce also contain cellulose, a substrate for SCFA production whose consumption can increase the levels of beneficial organisms in the gut (Kashtanova et  al. 2016). Fiber intake has been found to be protective against many inflammatory conditions (Shen and Wong 2016), which, given the immunomodulatory properties of the gut microbiome, may be related to a healthier gut microbiota resulting from increased fiber intake. Indeed, the consumption of fruits, vegetables, and other forms of fiber has been associated with higher microbial richness and diversity (Jandhyala et al. 2015). There are several different types of fiber, each of which affects the gut microbiome differently (Yang et al. 2013). The main fibers in fresh produce are pectin and inulin. Pectin leads to significant increases in Bifidobacterium (Yang et al. 2013), and inulin influences hormone production (Clarke et  al. 2014). Consumption of inulin is associated with increases in Bifidobacterium, Lactobacillus, and Enterococcus; however, changes in SCFA concentrations have not been noted (Graf et al. 2015). Inulin was found to lower hepatic triglycerides and hepatic fatty acid uptake, improve insulin sensitivity, and increase mitochondrial capacity, as well as stimulate the growth of B. animalis (Weitkunat et al. 2017). In addition to carbohydrates, fresh produce also contains significant levels of phenolic compounds. Different fruits and vegetables contain different levels of particular polyphenols, and different organisms are responsible for the metabolism of specific compounds. Polyphenols remain inactive unless modified by intestinal microbiota; therefore, the ability for the body to utilize these compounds depends on the presence of particular organisms within the gut (Jandhyala et al. 2015). Once catabolized, these compounds can be absorbed and elicit anti-inflammatory and antioxidant effects (González-Sarrías et al. 2017). Ellagitannins, for example, are of questionable bioavailability until they are metabolized by the intestinal microbiota into urolithins, which are likely responsible for the observed bioactivities (Piwowarski et al. 2015). While urolithins A, B, and C all decrease nitric oxide production and inflammation, urolithin A is the most anti-inflammatory (Piwowarski et al. 2015). Curcumin, found in turmeric, is another polyphenolic compound with multiple bioactivities but poor systemic bioavailability, meaning that even after large oral doses, serum levels were undetectable (Shen et al. 2017). The bioactivity associated with curcumin may be due to modulation of the gut microbiota, as it significantly decreased the abundance of Prevotellaceae and increased Bacteroidaceae and Rikenellaceae. It also decreased microbial richness and diversity. Degradation products and microbial metabolites from curcumin may contribute as well (Shen et al. 2017). Curcumin was also found to alleviate hepatic steatosis, likely through modulation of the gut microbiome (Feng et al. 2017). Dysbiosis is a contributing factor in nonalcoholic fatty liver disease. Curcumin was found to shift the microbiome of high-fat-fed rats to resemble lean rats fed a normal diet and reduced 36/47 OTUs positively correlated with hepatic steatosis, thus alleviating the

72

B. Rackerby et al.

hepatic steatosis (Feng et al. 2017). In vegans, who have increased consumption of polyphenolic compounds due to their plant-based diets, increased metabolism of these compounds was observed (Wu et  al. 2016). Polyphenolic compounds have been found to promote the growth of Akkermansia muciniphila and decrease the ratio of Firmicutes-Bacteroidetes and have the potential to ameliorate the effects of a high-fat diet (Kashtanova et al. 2016; Jin et al. 2017). Akkermansia muciniphila is important for the structural integrity of the gut mucosa (Jin et al. 2017). Examination of seasonal effects on the gut microbiome revealed variations between summer, when a certain population primarily consumed fresh produce, and winter, when the same population consumed produce that had been frozen, canned, or otherwise preserved from the summer months (Davenport et al. 2014). This may be important given that many people consume frozen, canned, or preserved produce year-round out of convenience. Though it is possible that there are differences between fresh and preserved produce, it is more likely that the changes observed had more to do with the overall consumption of produce with the seasons. Bacteroidetes were more prevalent in the summer months, when the general consumption of produce was higher (Davenport et al. 2014). Bacteroidetes are proficient at metabolizing high molecular weight structures and compounds, such as plant cell walls and complex carbohydrates. They also possess many carbohydrate-­ active enzymes (Davenport et al. 2014). Actinobacteria increased with reduced produce consumption in the winter (Davenport et al. 2014). General diversity of the gut microbiome was decreased in the summer when produce consumption was high (Davenport et  al. 2014), which conflicts with other data indicating produce consumption increases diversity (Jandhyala et al. 2015; Wu et al. 2016). While the first study found an increase in the relative abundance of Bacteroidetes, the second found that individuals consuming a diet high in fruits, vegetables, and fiber showed an increase in organisms of the phylum Firmicutes, such as Ruminococcus bromii, Roseburia, and Eubacterium rectale, which are proficient at insoluble carbohydrate metabolism (Jandhyala et al. 2015). Since a diet high in plant-based materials can significantly alter the gut microbiome, it naturally follows that vegans would have a different microbiota than omnivores. Those on a plant-based diet consume higher levels of carbohydrates and lower levels of fat and protein (Wu et al. 2016). There is much conflicting data on the microbiomes of those consuming plant-based diets. While total cell count remains constant between vegans and omnivores, the composition between the two groups was found to be significantly altered in one study, with lower levels of Bacteroides, bifidobacteria, E. coli, and Enterobacteriaceae (Zimmer et al. 2012). Another found higher percentages of Bacteroides, Prevotella, Clostridium clostridioforme, and Faecalibacterium prausnitzii in those consuming vegetarian diets (Graf et  al. 2015). Plant-based diets have been associated with increased diversity, a higher Prevotella-Bacteroides ratio, and increased production of SCFAs, though this study found only modest differences between the gut microbiomes and no change in the prevalence of Prevotella (Wu et al. 2016). The intestinal microbiomes of vegetarians were in between those of vegans and omnivores (Zimmer et al. 2012). Even where only small differences in microbiome were seen, the metabolome of

Effects of Diet on Human Gut Microbiome and Subsequent Influence on Host…

73

vegans and non-vegans was significantly different, likely due to the availability of different nutrients (Wu et al. 2016). When plant- and animal-based diets were compared, the microbiome expressed transcriptional changes in gene expression that were consistent with the gut microbiomes of herbivorous and carnivorous mammals. This includes the preference for amino acid catabolism versus biosynthesis, with catabolism favored in the presence of high protein, and the interconversions of phosphoenolpyruvate and oxaloacetate. This dichotomy is not as dramatic when each diet is compared to a given individual’s baseline (David et al. 2014). Other studies found increased butyrate-producing Clostridium and increased butyrate production, which has been linked to health benefits, in omnivores. The ability of this data to translate to western countries is dubious, as this data was collected from inhabitants of rural southern India, whose omnivorous diets are very different from western omnivorous diets (Graf et al. 2015). Agricultural practices can influence the microbiome of crops, which in turn could potentially lead to changes in the human gut microbiome. Compared to organic crops, conventionally cultivated crops often have reduced microbial diversity (Berg et al. 2015). Additionally, pesticide residues can be found on fruits and vegetables, as well as in honey (Rissato et al. 2007). The potential for commonly used herbicides and pesticides to alter the gut microbiome, either through alteration of the crop microbiome or through direct consumption of residues, should be considered. Glyphosate, the most widely used active ingredient in herbicides, has antimicrobial properties due to its interference with the shikimate pathway and has been found to alter the microbiomes of soil, plants, and animals. Low-dose exposure to both glyphosate and Roundup, administered at the rate considered safe by the U.S. acceptable daily intake, induced significant changes in the gut microbiome during early development (Mao et  al. 2018). This is important, as the early gut microbiome impacts the microbiome later in life (O’Hara and Shanahan 2006; Guarner and Malagelada 2003), and certain diseases have been associated with early-life imbalances in the gut microbiome (Mao et al. 2018). For example, neurological defects in germ-free mice could be corrected only by colonization of neonates (Sommer and Bäckhed 2013). Microbial changes induced by glyphosate and Roundup included increases in Prevotella and Mucispirillum and decreases in Lactobacillus and Aggregatibacter. Changes specific to either glyphosate or Roundup were seen as well (Mao et al. 2018). Pesticide usage, particularly chlorothalonil, has also been shown to affect the intestinal microbiota of honeybees, and pesticide residues have been found in their hives (Kakumanu et al. 2016). Honeybee microbiota commonly consists of Firmicutes, Actinobacteria, and Proteobacteria (Kakumanu et  al. 2016). The infant gut microbiome is primarily composed of Proteobacteria and Actinobacteria, while the adult microbiome is mostly Firmicutes and Bacteroidetes (Quigley 2013). This means that, if it can affect their microbiomes, it can likely affect ours. Many additional studies demonstrate that dysbiosis can be induced by exposure to a wide range of pesticides and fungicides (Jin et al. 2017). In addition to direct interactions between the gut microbiome and pesticides, pesticide usage could reduce plants’ need to produce phytoalexins to defend themselves against infection.

74

B. Rackerby et al.

This could have gastrointestinal repercussions as phytoalexins are micronutrients that promote the gut microbiome (Heiman and Greenway 2016).

5  Western Diet Compared to less developed areas, westernized countries showed a reduction in Prevotella, and the United States had the lowest level of microbial diversity (Graf et al. 2015). Many of the problems associated with the western diet may be related to increased consumption of fats and sugars replacing the consumption of more nutritional foods, causing deficiencies in important dietary components, such as fiber or vitamins. Aside from being a diet high in saturated fats and carbohydrates in the form of processed foods, the western diet delivers, on average, only half of the recommended daily fiber intake (Shen and Wong 2016). Even the US recommended daily intake of fiber is significantly less than the fiber content of traditional diets (Deehan and Walter 2016). Diets low in fiber have been shown to cause a reduced microbial diversity (Deehan and Walter 2016), and decreased microbial diversity has been associated with obesity (Sommer and Bäckhed 2013). Indeed, the high-­ carbohydrate, high-fat western diet has been linked to obesity on many occasions. There does appear to be an important link between obesity and the gut microbiome, as germ-free mice, when fed a high-sugar, high-fat diet, were resistant to obesity (Sommer and Bäckhed 2013). Of course, when fed a normal diet, germ-free mice also required 30% more calories compared to conventional mice in order to maintain body weight (Faderl et al. 2015). This is simply further evidence of the role intestinal microbes play in digestion and nutrient acquisition, though a causal relationship between the gut microbiome and obesity is being developed. Germ-free mice became obese upon transplantation of an obese individual’s microbiota and lost weight upon receiving the microbiota of mice who demonstrated weight loss after gastric bypass surgery (Clarke et al. 2014). The microbiome of obese individuals demonstrates an increase in genes related to carbohydrate metabolism and increased dietary energy extraction (Sommer and Bäckhed 2013). The high-fat, high-sugar western diet has been associated with a drop in Bacteroidetes and a proportional increase in Firmicutes, a compositional change which has been linked with obesity (Clarke et al. 2014; Davenport et al. 2014). The role of increased Firmicutes in obesity may be attributed to their efficiency in nutrient extraction and calorie absorption (Quigley 2013; Clarke et  al. 2014). Other dysbioses that have been associated with obesity are reductions in bifidobacteria with increases in some Firmicutes, such as Staphylococcus, and Proteobacteria, as well as increased Prevotellaceae, which lies within Bacteroidetes. Interestingly, certain members of Bacteroidetes may also prevent obesity (Clarke et al. 2014). A study done in mice found that a high-sugar, high-fat diet in mice resulted in diminished levels of Cyanobacteria and Thaumarchaeota, with significant increases in Firmicutes (Lu et  al. 2017). The Bacteroides enterotype is common among people consuming a western diet (Kashtanova et al. 2016).

Effects of Diet on Human Gut Microbiome and Subsequent Influence on Host…

75

Polysaccharides are often used as food additives for their function as emulsifiers, stabilizers, or bulking agents. The increased consumption of these polysaccharides has been linked to intestinal disorders associated with the gut microbiome (Nickerson and McDonald 2012). Guar gum is a common thickening or stabilizing agent often added to processed foods. A mixture of inulin and partially hydrolyzed guar gum or maltodextrin, also used as a food additive, given to constipated women resulted in a reduction of total Clostridium; however, no other changes in microbiota or SCFA production were noted (Graf et al. 2015). Guar gum supplementation did not reduce body-fat gain or insulin resistance as inulin did; however, it stimulated the growth of B. pseudolongum (Weitkunat et al. 2017), an organism that typically has a low abundance but performs the vital function of resistant starch hydrolysis (Centanni et al. 2018). Similar to inulin, SCFA supplementation offered complete protection against body-fat gain and insulin resistance (Weitkunat et al. 2017). Maltodextrin consumption appears to decrease the populations of lactobacilli and enterococci (Graf et al. 2015) and may also be related to E. coli LF82 adhesion and dysbiosis (Nickerson and McDonald 2012). Resistant maltodextrin, which is different from maltodextrin, may have prebiotic effects. It was found that resistant maltodextrin increased fecal bacterial content and enhanced the growth of Ruminococcus, Eubacterium, Lachnospiraceae, Bacteroides, Holdemania, and Faecalibacterium (Baer et al. 2014). Another study found the effects of resistant maltodextrin on the gut microbiome to be insignificant and inconsistent (Graf et al. 2015). Since there has been increased awareness in the gut microbiome and GI health, prebiotics and probiotics have seen a rise in popularity and are being added to many foods, including granola bars and cookies. Arabinoxylan oligosaccharides fed to obese mice on a western diet promoted the growth of both B. animalis and B. pseudolongum in the cecum and normalized many health conditions associated with the western diet, such as body-fat gain, steatosis, hypercholesterolemia, hyperleptinemia, hyperglycemia, and hyperinsulinemia (Neyrinck et al. 2018). While studies have found that supplementing high-fat diets with certain prebiotics can have beneficial effects (Weitkunat et al. 2017; Neyrinck et al. 2018), it is likely best to eat foods which possess these compounds naturally as they will likely be better sources of other nutrients as well, though there does not appear to be research in this area. The western diet contains a high level of saturated fats, as well as an exceptionally high omega-6-omega-3 fatty acid ratio, as high as 20–30:1, compared to the traditional 1–2:1 (Robertson et al. 2017). This type of high-fat diet may have health implications that reach far beyond obesity. Obesity has been linked to behavioral and anxiety disorders (Sasaki et al. 2014), and links have been found between the gut microbiome and nervous system function (Clarke et al. 2014). SCFAs modulate enteroendocrine secretion of serotonin, and the intestinal microbiota has the capacity to release hundreds of signaling molecules, such as noradrenaline, dopamine, and serotonin, as well as GABA, which is produced by several strains of Lactobacillus (Clarke et al. 2014). A high-fat diet like those found in western countries has been shown to promote anxiety and anhedonic behaviors, as well as interfere with glucose homeostasis, disrupt synaptic plasticity, elevate corticosterone and inflammatory cytokine levels, and activate the innate immune system in as little as 4 months

76

B. Rackerby et al.

(Dutheil et al. 2016). Long-term effects in individuals include impaired homeostasis, diminished hippocampus volume, and impaired cognitive function in areas such as memory, psychomotor function, and attention (Dutheil et al. 2016). Not only are neurological and metabolic functions impaired in those consuming a high-fat diet, but these symptoms also appear in the adult offspring of those consuming a high-fat diet (Sasaki et al. 2014). Excessive consumption of saturated fats during pregnancy led to increased anxiety and inflammation in offspring later in life. Inflammation was linked to alterations in genes related to the glucocorticoid signaling pathway that seemed to be brought about by the perinatal diet. Adolescent offspring in the same situation displayed lower anxiety levels; however, they still had altered expression of genes relating to the glucocorticoid receptor and inflammation in the hippocampus and amygdala. This lack of anxiety may be due to incomplete feedback systems relating to corticosteroid sensitivity in adolescence (Sasaki et al. 2014). It is probable that the altered gut microbiota plays a role in these mechanisms. Stress itself can also influence the microbiome. Stress has been found to decrease microbial diversity and possibly microbial load, in one study reducing the abundance of lesser organisms present in the intestinal community and, in another, causing loss of Verrucomicrobia, a doubling of Clostridium, and the addition of Lactobacillus and Enterococcus in mice (Luna and Foster 2015).

6  Ketogenic Diet The ketogenic diet is high in fat and low in carbohydrates with adequate protein levels (Olson et al. 2018) and is implemented with the goal of switching the body’s metabolism from glucose based to fat based. The general effects of the ketogenic diet on the gut microbiome of subjects with refractory epilepsy were decreased alpha diversity, increased levels of A. muciniphila and Parabacteroides, and decreased gamma-glutamyltranspeptidase activity. Colonization with A. muciniphila and Parabacteroides or transplantation of a ketogenic gut microbiome demonstrates the same anti-seizure activity as the ketogenic diet (Olson et al. 2018). In an autism spectrum disorder (ASD) model, the ketogenic diet decreased total bacterial abundance, reversed the low Firmicutes-Bacteroidetes ratio, and reduced the elevated levels of A. muciniphila present in the BTBRT  +  tf/j mouse model of ASD (Newell et al. 2016). In the first model, the level of A. muciniphila in the control group was very low, which could offer a possible explanation as to why they increased in this study but decreased in the ASD model, where levels were initially elevated. The ketogenic diet primarily affects neural tissue, and interactions between the gut microbiome and neurological function have been discovered (Newell et al. 2016). Many microorganisms produce neurotransmitters, including noradrenaline, dopamine, and serotonin. Several lactobacilli also produce GABA, which is the most important brain inhibitory neurotransmitter (Clarke et al. 2014). In the refractory epilepsy model, the ketogenic diet leads to an increased ratio of GABA to glutamate in the brain, thus reducing seizures (Olson et al. 2018).

Effects of Diet on Human Gut Microbiome and Subsequent Influence on Host…

77

Another study examined the effects of the ketogenic diet on neurovascular integrity in healthy young mice via alterations to the gut microbiome (Ma et al. 2018). Mice on this diet were found to have increased levels of A. muciniphila and Lactobacillus, as well as reductions in their proportions of the inflammatory organisms Desulfovibrio and Turicibacter. After 16 weeks, cerebral blood flow was significantly increased, as was P-glycoprotein transport on the blood-brain barrier. The latter facilitates the removal of amyloid-beta, which is present in Alzheimer’s disease (Ma et al. 2018). It is important to note that this study was done in young mice. Not only the gut microbiome but also the impacts it has on host neurological development appear to be more malleable early in life, and later disease states appear permanent, while interventions later in life have little to no lasting effect (Sommer and Bäckhed 2013; Quigley 2013; Heiman and Greenway 2016; Mao et al. 2018).

7  Coffee, Tea, and Wine Coffee is one of the most consumed beverages in the world, second only to water (Butt and Sultan 2011). Even Britain, a country known for its remarkable tea consumption, drinks around 70 million cups of coffee per day (Van Doorn et al. 2014). Despite this significant and widespread coffee consumption, tea remains one of the world’s most popular beverages as well (Goldbohm et al. 1996). These drinks are significant sources of caffeine and polyphenols (Jandhyala et al. 2015; Kashtanova et al. 2016; Butt and Sultan 2011; Goldbohm et al. 1996). Given the chemical composition of these beverages along with the impressive quantity consumed per individual on a daily basis, these drinks have the capacity to vastly influence the composition of the human gut microbiome (Wang and Ho 2009). While it is known that caffeine has hepatoprotective effects (Nishitsuji et al. 2018) and the gut microbiome has a hand in liver health, no information can be found on what role the gut microbiome may play in the relationship between caffeine metabolism and the liver. Coffee has also been found to reduce liver damage caused by high-fat diets, though the reason for this remains unclear (Vitaglione et al. 2019). Though little could be found on the effects that coffee consumption has on the normal human gut microbiota, several studies have been conducted on the protective role coffee may play on the microbiome in certain disease states. Compared to mice fed only a high-fat diet, mice given a high-fat diet with coffee differed in their levels of Alistipes, Bacteroides, and Odoribacter and had elevated Alcaligenaceae similar to mice fed on whole grain oat flour (Dutheil et al. 2016). Whole grain oat flour and coffee both contain antioxidant dietary fibers as well as polyphenols that interact with the gut microbiota (Vitaglione et  al. 2019; Cowan et  al. 2014). Melanoidins present in coffee behave as dietary fiber and trap polyphenols, carrying them to the colon (Vitaglione et  al. 2019). In a Sprague Dawley rat model fed a normal diet, coffee increased the presence of Clostridium leptum and decreased Bacteroides/Prevotella (Cowan et  al. 2014). The same model fed a high-fat diet demonstrated an improved Firmicutes-Bacteroidetes ratio and reductions in

78

B. Rackerby et al.

Clostridium cluster XI with the addition of coffee to the diet. These rats also saw an increase in both Enterobacteriaceae and Clostridium leptum (Cowan et al. 2014). In a model using TSOD mice, coffee did not improve the characteristic gut dysbiosis, and increased the prevalence of Prevotella (Nishitsuji et al. 2018). The coffee components caffeine and chlorogenic acid did not affect the gut microbiome; however, a slight improvement in the SCFA profile was observed (Nishitsuji et al. 2018). Tea is one of the most commonly consumed beverages in the world. The primary component of tea that has the potential to interact with the intestinal microbiota is polyphenols. Polyphenols comprise over 1/3 of the dry weight of tea (Sun et al. 2018), and most of these are catechins (Gurley et al. 2019). As we saw in our discussion of fresh produce, microbes are required for the processing of phenolic compounds before they can be used by the body. Here, we see that high polyphenol levels can cause changes in the gut microbiome as well. Almost all of the polyphenols contained in tea pass through the digestive system and are able to interact with microbes in the colon, rather than being absorbed by the body at an earlier time (Sun et al. 2018; Kemperman et al. 2013). Different teas have different polyphenol compositions and therefore may have different interactions with the gut microbiome. For example, Ningbo oolong tea was found to contain high levels of epigallocatechin-3-O-(3″-O-methyl)-gallate, a compound with known health benefits, while black and green tea did not (Sun et al. 2018). Since green tea is the second most popular drink in the world and is thought to have antiobesity effects, most studies focus on green tea (Gurley et al. 2019; Janssens et al. 2016). One study found that green tea consumption did not elicit changes in the gut microbiome; however, this study had a small sample size and did not appear to control for variations in diet (Janssens et al. 2016). In general, tea consumption lowered the ratio of Firmicutes-Bacteroidetes (Sun et al. 2018; Gurley et al. 2019; Kemperman et  al. 2013; Zhang et  al. 2018). This reduced ratio was achieved either through an increase in Bacteroidetes and a decrease in Firmicutes (Wang et al. 2018b) or a decrease in Firmicutes with unaffected levels of Bacteroidetes (Kemperman et  al. 2013). Long-­term consumption of green tea polyphenols increased Bacteroidetes and Oscillospira, which have been associated with a lean phenotype, and reduced Peptostreptococcaceae, which has been linked with colorectal cancer (Wang et  al. 2018b). Decaffeinated green tea promoted the growth of Akkermansia (Gurley et al. 2019). A study on black tea found increases in Klebsiella, Enterococcus, and Akkermansia with decreases in bifidobacteria, B. coccoides, Anaeroglobus, and Victivallis, as well as an overall reduction in Actinobacteria, while an in vitro study looking only at catechin found increases in B. coccoides, Eubacterium rectale, Bifidobacterium, and Escherichia coli, with a decrease in Clostridium histolyticum (Janssens et  al. 2016). Similarly, Clostridium histolyticum was found to decrease with the administration of black, green, and oolong tea, as did Bacteroides-Prevotella (Sun et al. 2018). All three teas increased the prevalence of Bifidobacterium, with the impact of oolong the most profound, followed by black and finally green. Proliferation of the Lactobacillus/Enterococcus group was stimulated as well (Sun et al. 2018). In a diet-induced obesity model, green tea polyphenols had a prebiotic-like activity similar to fructo-oligosaccharides and were able to reverse obesity-induced

Effects of Diet on Human Gut Microbiome and Subsequent Influence on Host…

79

dysbiosis. The phylum-level decrease in the Firmicutes-Bacteroidetes ratio resulted from family-­level changes that consisted of increases in Prevotellaceae and Bacteroidaceae, with decreases in Eubacteriaceae, Lachnospiraceae, Ruminococcaceae, and Clostridiaceae. At the genus level, this looked like increases in Prevotella, Bacteroides, Megamonas, and Sutterella, with decreases in Eubacterium, Clostridium, Roseburia, Faecalibacterium, Coprococcus, Ruminococcus, and Phascolarctobacterium (Zhang et  al. 2018). With these changes in microbial community structure, one study found an increase in SCFA production (Sun et  al. 2018), while another discovered that polyphenols may inhibit butyrate-­producing bacteria, as a reversible decrease in SCFA production was observed, along with an apparent decrease in microbial metabolism (Kemperman et  al. 2013). Tea also caused a reduction in genes related to Salmonella infection, as well as bacterial chemotaxis and mobility (Gurley et al. 2019). In many parts of the world, it is common to add milk to tea and coffee. Milk has the potential to decrease the bioavailability of phenolic compounds through chemical interactions between milk components, such as fat and casein, and polyphenolic compounds. Tea increased plasma catechin levels whether it contained milk or not, though the increase was more pronounced with plain black tea (Vijayakuma et al. 2005). The effects of milk on tea are linked to, though not solely caused by, the fat content of the milk. The antioxidant ability was reduced the most when skim milk was added, and whole milk reduced it the least (Ryan and Petit 2010). This study found a 2–15% reduction compared to tea with cold water added and a 7–25% reduction compared to the standard; however, another study did not find significant reductions (Ryan and Petit 2010). Two other studies found that the addition of milk to tea did not affect the plasma levels of flavanols or catechin (Hollman et al. 2001; van het Hof et al. 1998); however, most of the polyphenols survive into the colon for processing by microbes rather than being absorbed by the body. Neither of these studies investigated the effects of tea with milk on the gut microbiome. Wine is an important part of culture along the Mediterranean and is therefore an integral part of the diet. Consumption of red wine and dealcoholized red wine correlated with increases in Bifidobacterium, Enterococcus, Eggerthella lenta, and members of the phylum Fusobacteria (Graf et al. 2015). Red wine is also thought to increase the prevalence of Prevotella, Bacteroides, and Bifidobacterium (Kashtanova et al. 2016). Red wine had more profound effects on the gut microbiome than dealcoholized red wine, indicating that alcohol may interact synergistically with other wine constituents. Alcohol alone did not cause deviations from baseline values (Graf et al. 2015).

8  Conclusion Perhaps the most significant trend we have seen throughout this chapter is that the early-life diet seems to have a larger impact on the gut microbiome than diet later in life and that the effects of this diet and microbiome on development and function are

80

B. Rackerby et al.

lifelong. Furthermore, the effects can persist across generations, with maternal diet during pregnancy impacting the development, especially neurological development, of the offspring later in life. As it turns out, we can alter 30–40% of our adult gastrointestinal microbiome, while the other 60–70% is controlled by factors such as genetics, epigenetics, and maternal factors such as maternal health, diet, and breastfeeding (Kashtanova et al. 2016). It has been noted that a more diverse diet leads to a more diverse intestinal microbiome; however, this is becoming increasingly difficult to achieve, as 75% of the world’s food consists of a measly 12 plants and 5 animal species (Heiman and Greenway 2016). People today often search for a certain “miracle food” to provide optimal health; however, the chemical and microbial interactions in food, in the gut, and in the body as a whole are far too complex for such a simple solution. Indeed, it has been assessed that the benefits of certain diets are due to the interactions between nutrients present in the diet and that the effects of any one nutrient are too small to be measured, thus requiring an analysis of the diet as a whole (Del Chierico et al. 2014). As our understanding of the various factors involved in human health evolves, even accepted knowledge may need to be reevaluated. Acknowledgments  This book chapter was partially supported by the Korean-American Scientists and Engineers Association (KSEA) Young Investigator Grant (YIG) awarded to Si Hong Park. The Building University-Industry linkages through Learning and Discovery (BUILD) supported to authors Bryna Rackerby, Daria Van De Grift, and Si Hong Park.

References Arora, T., Singh, S., & Sharma, R. (2013). Probiotics: Interaction with gut microbiome and antiobesity potential. Nutrition, 29(4), 591–596. Azcrate-Peril, M., Ritter, A., & Savaiano, D. (2017). Impact of short-chain galactooligosaccharides on the gut microbiome of lactose-intolerant individuals. Proc Natl Acad Sci U S A, 114(3), E367–E375. Baer, D., Stote, K. S., Henderson, T., et al. (2014). The metabolizable energy of dietary resistant maltodextrin is variable and alters fecal microbiota composition in adult men. The Journal of Nutrition, 144(7), 1023–1029. Berg, G., Erlacher, A., & Grube, M. (2015). The Edible plant microbiome: importance and health issues. In B. Lugtenberg (Ed.), Principles of plant-microbe interactions (pp. 419–426). Switzerland: Springer. Butt, M., & Sultan, T. (2011). Coffee and its consumption: Benefits and risks. Critical Reviews in Food Science and Nutrition, 51(4), 363–373. Cabello-Olmo, M., Oneca, M., Torre, P., Sainz, N., et al. (2019). A fermented food product containing lactic acid bacteria protects ZDF rats from the development of Type 2 diabetes. Nutrients, 11(10), 2530. Centanni, M., Lawley, B., Butts, C., et al. (2018). Bifidobacterium pseudolongum in the ceca of rats fed hi-maize starch has characteristics of a keystone species in Bifidobacterial blooms. Applied and Environmental Microbiology, 84(15), 1–13. Chamba, J. F., & Irlinger, F. (2004). Secondary and adjunct cultures. In P. Fox, P. McSweeney, T. Cogan, & T. Guinee (Eds.), Cheese: Chemistry, physics and microbiology (pp. 191–206). Amsterdam: Academic Press.

Effects of Diet on Human Gut Microbiome and Subsequent Influence on Host…

81

Clarke, G., Stilling, R. M., & Kennedy, P. J. (2014). Minireview: gut microbiota: the neglected endocrine organ. Journal of Molecular Endocrinology, 28(8), 1221–1238. Cowan, T., Palmnäs, M., Yang, J., et al. (2014). Chronic coffee consumption in the diet-induced obese rat: Impact on gut microbiota and serum metabolomics. The Journal of Nutritional Biochemistry, 25(4), 489–495. Davenport, R., Mizrahi-Man, O., Michelini, K., et  al. (2014). Seasonal variation in human gut microbiome composition. PLoS One, 9(3), e90731. David, L., Maurice, C., Carmody, R., et al. (2014). Diet rapidly and reproducibly alters the human gut microbiome. Nature, 505(7484), 559–563. De Filippis, F., Pellegrini, N., Vannini, L., et al. (2016). High-level adherence to a Mediterranean diet beneficially impacts the gut microbiota and associated metabolome. Gut, 65, 1–10. Deehan, E., & Walter, J. (2016). The fiber gap and the disappearing gut microbiome: Implications for human nutrition. Trends in Endocrinology and Metabolism, 27(5), 239–242. Del Chierico, F., Vernocchi, P., Dallapiccola, B., et al. (2014). Mediterranean diet and health: Food effects on gut microbiota and disease control. International Journal of Molecular Sciences, 5(7), 11678–11699. Dutheil, S., Ota, K., Wohleb, E., et al. (2016). High-fat diet induced anxiety and anhedonia: Impact on brain homeostasis and inflammation. Neuropsychopharmacology, 41(7), 1874–1887. Faderl, M., Noti, M., Corazza, N., et al. (2015). Keeping bugs in check: The mucus layer as a critical component in maintaining intestinal homeostasis. IUBMB Life, 67, 275–285. Feng, W., Wang, H., Zhang, P., et al. (2017). Modulation of gut microbiota contributes to curcumin-­ mediated attenuation of hepatic steatosis in rats. Biochimica et Biophysica Acta, 1861(7), 1801–1812. Francavilla, R., Calasso, M., & Calace, L. (2012). Effect of lactose on gut microbiota and metabolome of infants with cow’s milk allergy. Pediatric Allergy and Immunology, 23(5), 420–427. Goldbohm, R. A., Hertog, M., Brants, H., et al. (1996). Consumption of black tea and cancer risk: A prospective cohort study. Journal of the National Cancer Institute, 88(2), 93–100. González-Sarrías, A., Espín, J., & Tomás-Barberán, F. (2017). Non-extractable polyphenols produce gut microbiota metabolites that persist in circulation and show anti-inflammatory and free radical-scavenging effects. Trends in Food Science and Technology, 69, 281–288. Graf, D., Di Cagno, R., Fåk, F., et al. (2015). Contribution of diet to the composition of the human gut microbiota. Microbial Ecology in Health and Disease, 26(26164), 1–11. Guarner, F., & Malagelada, J. R. (2003). Gut flora in health and disease. The Lancet, 361, 512–519. Gurley, B., Miousse, I., Nookaew, I., et  al. (2019). Decaffeinated green tea extract does not elicit hepatoxic effects and modulates the gut microbiome in lean B6C3F1 mice. Nutrients, 11(776), 1–14. Heiman, M., & Greenway, F. (2016). A healthy gastrointestinal microbiome is dependent on dietary diversity. Molecular Metabolism, 5(5), 317–320. Hemarajata, P., & Versalovic, J. (2013). Effects of probiotics on gut microbiota: Mechanisms of intestinal immunomodulation and neuromodulation. Therapeutic Advances in Gastroenterology, 6(1), 39–51. Hollman, P., Van Het Hof, K., Tijburg, L., et al. (2001). Addition of milk does not affect the absorption of flavonols from tea in man. Free Radical Research, 34, 293–300. ISAPP. (2016). ISAPP videos. https://isappscience.org/resources/isapp-videos/. Accessed 7 Jul 2019. Jami, E., White, B., & Mizrahi, I. (2014). Potential role of the Bovine Rumen microbiome in modulating milk composition and feed efficiency. PLoS One, 9(1), e85423. Jandhyala, S., Talukdar, R., Subramanyam, C., et al. (2015). Role of the normal gut microbiota. World Journal of Gastroenterology, 21(29), 8787–8803. Janssens, P. L. H. R., Penders, J., Hursel, R., Budding, A. E., Savelkoul, P. H. M., & Westerterp-­ Plantenga, M. S. (2016). Long-term green tea supplementation does not change the human gut microbiota. PLoS One, 11(4), e0153134.

82

B. Rackerby et al.

Jin, Y., Wu, S., Zeng, Z., et  al. (2017). Effects of environmental pollutants on gut microbiota. Environmental Pollution, 222, 1–9. Jones, M., Martoni, C. J., & Prakash, S. (2012a). Cholesterol lowering inhibition of sterol absorption by Lactobacillus reuteri NCIMB 30242 a randomized controlled trial. European Journal of Clinical Nutrition, 66, 1234–1241. Jones, M., Martoni, J., Parent, M., et al. (2012b). Cholesterol-lowering efficacy of a microencapsulated bile salt hydrolase-active Lactobacillus reuteri NCIMB 30242 yoghurt formulation in hypercholesterolaemic adults. The British Journal of Nutrition, 107, 1505–1513. Jy, K., & Ey, C. (2016). Changes in Korean adult females’ intestinal microbiota resulting from Kimchi Intake. Journal of Nutrition & Food Sciences, 06(02), 1–9. Kakumanu, M., Reeves, A., Anderson, D., et al. (2016). Honey bee gut microbiome is altered by in-hive pesticide exposures. Frontiers in Microbiology, 7, 1–11. Kashtanova, D., Popenko, A., Tkacheva, O., et al. (2016). Association between the gut microbiota and diet: Fetal life, early childhood, and further life. Nutrition, 32(6), 620–627. Kemperman, R., Gross, G., Mondot, S., et  al. (2013). Impact of polyphenols from black tea and red wine grape juice on a gut model microbiome. Food Research International, 53(2), 659–669. join. Long, S., Gahan, G., & Joyce, S. (2017). Interactions between gut bacteria and bile in health and disease. Molecular Aspects of Medicine, 56, 54–65. Lu, C., Sun, T., Li, Y., et al. (2017). Modulation of the gut microbiota by krill oil in mice fed a high-sugar high-fat diet. Frontiers in Microbiology, 8(905), 1–11. Luna, R. A., & Foster, J. A. (2015). Gut brain axis: Diet microbiota interactions and implications for modulation of anxiety and depression. Current Opinion in Biotechnology, 32, 35–41. Ma, D., Wang, A. C., Parikh, I., et al. (2018). Ketogenic diet enhances neurovascular function with altered gut microbiome in young healthy mice. Scientific Reports, 8(6670), 1–10. Mao, Q., Manservisi, F., Panzacchi, S., et al. (2018). The Ramazzini Institute 13-week pilot study on glyphosate and Roundup administered at human-equivalent dose to Sprague Dawley rats: effects on the microbiome. Environmental Health, 17(1), 50. Newell, C., Bomhof, M., Reimer, R., et al. (2016). Ketogenic diet modifies the gut microbiota in a murine model of autism spectrum disorder. Molecular Autism, 7(37), 2–6. Neyrinck, A., Hiel, S., Bouzin, C., et  al. (2018). Wheat-derived arabinoxylan oligosaccharides with bifidogenic properties abolishes metabolic disorders induced by western diet in mice. The Journal of Nutrition, 144(7), 1023–1029. Nickerson, K., & McDonald, C. (2012). Crohn’s disease-associated adherent-invasive Escherichia coli adhesion is enhanced by exposure to the ubiquitous dietary polysaccharide maltodextrin. PLoS One, 7(12), e52132. Nishitsuji, K., Watanabe, S., Xiao, J., et al. (2018). Effect of coffee or coffee components on gut microbiome and short-chain fatty acids in a mouse model of metabolic syndrome. Scientific Reports, 8(16173), 1–10. Ntemiri, A., Ribière, C., Stanton, C., et al. (2019). Retention of microbiota diversity by lactose-free milk in a mouse model of elderly gut microbiota. Journal of Agricultural and Food Chemistry, 67(7), 2098–2112. O’Hara, A. M., & Shanahan, F. (2006). The gut flora as a forgotten organ. EMBO Reports, 7(7), 688–693. O’Shea, E., Cotter, P., Stanton, C., et al. (2012). Production of bioactive substances by intestinal bacteria as a basis for explaining probiotic mechanisms: Bacteriocins and conjugated linoleic acid. International Journal of Food Microbiology, 152(3), 189–205. Olson, C., Vuong, H., Yano, J., et al. (2018). The gut microbiota mediates the anti-seizure effects of the ketogenic diet. Cell, 173(7), 1728–1741.e1–e6. Pandey, K., Naik, S., & Vakil, B. (2015). Probiotics, prebiotics and synbiotics – A review. Journal of Food Science and Technology, 52(12), 7577–7587. Paul Ross, R., Morgan, S., & Hill, C. (2002). Preservation and fermentation: Past, present and future. International Journal of Food Microbiology, 79(1), 3–16.

Effects of Diet on Human Gut Microbiome and Subsequent Influence on Host…

83

Piwowarek, K., Lipińska, E., Hać-Szymańczuk, E., et al. (2018). Propionibacterium spp.-source of propionic acid, vitamin B12, and other metabolites important for the industry. Applied Microbiology and Biotechnology, 102(2), 515–538. Piwowarski, J. P., Kiss, A. K., Granica, S., et al. (2015). Urolithins, gut microbiota-derived metabolites of ellagitannins, inhibit LPS-induced inflammation in RAW 264.7 murine macrophages. Molecular Nutrition & Food Research, 59(11), 2168–2177. Quigley, E. (2013). Gut bacteria in health and disease. Gastroenterología y Hepatología, 9(9), 560–569. Quigley, L., O’Sullivan, O., Stanton, C., et  al. (2013a). The complex microbiota of raw milk. FEMS Microbiology Reviews, 37(5), 664–698. Quigley, L., McCarthy, R., O’Sullivan, O., et al. (2013b). The microbial content of raw and pasteurized cow milk as determined by molecular approaches. Journal of Dairy Science, 96(8), 4928–4937. Rettedal, A., Altermann, E., Roy, N., et al. (2019). The effects of unfermented and fermented cow and sheep milk on the gut microbiota. Frontiers in Microbiology, 10(458), 1–12. Richardson, T. (1978). The hypocholesteremic effect of milk  – A review. Journal of Food Protection, 41(3), 226–235. Rissato, S., Galhiane, M., de Almeida, M., et al. (2007). Multiresidue determination of pesticides in honey samples by gas chromatography–mass spectrometry and application in environmental contamination. Food Chemistry, 101(4), 1719–1726. Robertson, R., Seira Oriach, C., Murphy, K., et al. (2017). Omega-3 polyunsaturated fatty acids critically regulate behaviour and gut microbiota development in adolescence and adulthood. Brain, Behavior, and Immunity, 59, 21–37. Ryan, L., & Petit, S. (2010). Addition of whole, semiskimmed, and skimmed bovine milk reduces the total antioxidant capacity of black tea. Nutrition Research, 40(1), 14–20. Saad, M. J. A., Santos, A., & Prada, P. O. (2016). Linking gut microbiota and inflammation to obesity and insulin resistance. Physiology, 31(4), 283–293. Sandoval, D., & Seeley, R. (2010). The microbes made me eat it. Science, 328(5975), 179–180. Sasaki, A., de Vega, W., Sivanathan, S., et al. (2014). Maternal high-fat diet alters anxiety behavior and glucocorticoid signaling in adolescent offspring. The Journal of Neuroscience, 272, 92–101. Saxe, L. (2019). Fermented Foods are up to 149%: As long as they’re unfamiliar. Forbes. Available via https://www.forbes.com/sites/lizzysaxe/2019/02/06/fermented-foods-are-up-149-percentas-long-as-theyre-unfamiliar/#59cac643673f. Accessed 7 Jul 2019. Seo, D.-B., Jeong, H., Cho, D., et al. (2018). Fermented green tea extract alleviates obesity and related complications and alters gut microbiota composition in diet-induced obese mice. Journal of Medicinal Food, 18(5), 1–8. Shen, S., & Wong, C. (2016). Bugging inflammation: role of the gut microbiota. Clinical and Translational Immunology, 5, e72. Shen, L., Liu, L., & Ji, H.-F. (2017). Regulative effects of curcumin spice administration on gut microbiota and its pharmacological implications. Food & Nutrition Research, 61(1), 1361780. Sommer, F., & Bäckhed, F. (2013). The gut microbiota — masters of host development and physiology. Nature Reviews Microbiology, 11, 227–238. Sun, H., Chen, Y., Cheng, M., et al. (2018). The Modulatory effect of polyphenols from green tea, oolong tea, and black tea on human intestinal microbiota in vitro. Journal of Food Science and Technology, 55(1), 399–407. Tannock, G., Lawley, B., Munro, K., et al. (2012). Comparison of the compositions of the stool microbiotas of infants fed goat milk formula, cow milk-based formula, or breast milk. Applied and Environmental Microbiology, 79(9), 3040–3048. Trinchese, G., Cavaliere, G., Canani, R. B., et al. (2015). Human, donkey and cow milk differently affects energy efficiency and inflammatory state by modulating mitochondrial function and gut microbiota. The Journal of Nutritional Biochemistry, 26(11), 1136–1146. van het Hof, K., Kivits, G., Tijburg, W., et al. (1998). Bioavailability of catechins from tea the effect of milk. European Journal of Clinical Nutrition, 52, 356–359.

84

B. Rackerby et al.

Van Doorn, G., Wuillemin, D., & Spence, C. (2014). Does the colour of the mug influence the taste of the coffee? Flavour, 3(10), 1–7. Veiga, P., Pons, N., Agrawal, A., et al. (2014). Changes of the human gut microbiome induced by a fermented milk product. Scientific Reports, 4(1), 6328. Vijayakuma, R., Sagar, G. V., Sreeramulu, D., et al. (2005). Addition of milk does not alter the antioxidant activity of black tea. Annals of Nutrition & Metabolism, 49(3), 189–195. Vitaglione, P., Mazzone, G., Lembo, V., et al. (2019). Coffee prevents fatty liver disease induced by a high-fat diet by modulating pathways of the gut-liver axis. Journal of Nutritional Science, 8(e15), 1–11. Wahlqvist, M. (2015). Lactose nutrition in lactase nonpersisters. Asia Pacific Journal of Clinical Nutrition, 24(1), S21–S25. Wahlström, A., Sayin, S., Marschall, H.-U., et al. (2016). Intestinal crosstalk between bile acids and microbiota and its impact on host metabolism. Cell Metabolism, 24(1), 41–50. Wang, Y., & Ho, C.-T. (2009). Polyphenolic chemistry of tea and coffee: A century of progress. Journal of Agricultural and Food Chemistry, 57(18), 8109–8114. Wang, Z., Zhang, W., Wang, B., et al. (2018a). Influence of Bactrian camel milk on the gut microbiota. Journal of Dairy Science, 101(7), 5758–5769. Wang, J., Tang, L., Hongyuan, Z., et al. (2018b). Long term treatment with green tea polyphenols modifies the gut microbiome of female sprague dawley rats. The Journal of Nutritional Biochemistry, 56, 55–64. Weitkunat, K., Stuhlmann, C., Postel, A., et al. (2017). Short-chain fatty acids and inulin, but not guar gum, prevent diet-induced obesity and insulin resistance through differential mechanisms in mice. Scientific Reports, 7(6109), 1–13. Wen, Y., He, Q., Ding, J., et al. (2017). Cow, yak, and camel milk diets differentially modulated the systemic immunity and fecal microbiota of rats. Science Bulletin, 62(6), 405–414. Wu, G., Compher, C., Chen, E., et al. (2016). Comparative metabolomics in vegans and omnivores reveal constraints on diet-dependent gut microbiota metabolite production. Gut, 65(1), 63–72. Yang, J., Martínez, I., Walter, J., et al. (2013). In vitro characterization of the impact of selected dietary fibers on fecal microbiota composition and short chain fatty acid production. Anaerobe, 23, 74–81. Yu, H.-S., Lee, N.-K., Choi, A.-J., et al. (2019). Anti-inflammatory potential of probiotic strain Weissella cibaria JW15 isolated from Kimchi through regulation of NF-kB and MAPKs pathways in LPS-Induced RAW 264.7 cells. Journal of Microbiology and Biotechnology, 29(7), 1022–1032. Zhang, X., Zhang, M., Ho, C.-T., et al. (2018). Metagenomics analysis of gut microbiota modulatory effect of green tea polyphenols by high fat diet-induced obesity mice model. Journal of Functional Foods, 46, 268–277. Zimmer, J., Lange, B., Frick, J.-S., et al. (2012). A vegan or vegetarian diet substantially alters the human colonic faecal microbiota. European Journal of Clinical Nutrition, 66(1), 53–60. Zoetendal, E., Akkermans, A., Akkermans-van Vliet, W., et al. (2001). The host genotype affects the bacterial community in the human gastrointestinal tract. Microbial Ecology in Health and Disease, 13(3), 129–134.

Probiotics and Prebiotics on Intestinal Flora and Gut Health Mengfei Peng, Nana Frekua Kennedy, Andy Truong, Blair Arriola, and Ahlam Akmel

1  Introduction All bacterial species in the gut intestine live in symbiosis and share mutualistic relationships with other gut microbes and their host. One of the largest influencers of gut microflora symbiosis is diet. A healthy gastrointestinal microbiome is dependent on dietary diversity. The gut is filled with energy, either undigested or digested, that can be transformed in different ways by each of the millions of microbiotic species that exist in the gut. Human beings started to develop their initial gut intestinal microflora when consuming their mother’s breast milk, during which the diversity in the gut microorganism especially commensal bacteria start to build up a balanced gut microbiome. As solid food is introduced, more exotic bacteria get introduced and throw off the established environment of the gut. Young children transitioning from a liquid diet to a solid adult diet can potentially have a more diverse gut microbiome than their own parents because of the testing of new food along the way. While from the parent’s side, the habitual diets as a result of their lifestyle could also contribute to creating their children’s personalized microbiome. Studies have shown that many dietary factors, such as fiber and polyphenols, can modify the balance of gut bacteria. For example, one study performed on subjects with a fiber-blend formula expressed fewer negative symptoms of bowel urgencies, specifically with a smaller decrease in the amount of bacteria loss in the gut intestine compared to the control with a fiber-free diet. (Koecher et al. 2015). In a separate study, dietary polyphenols could affect the gut bacterial balance indirectly through their transformation products compared to original plant products, which leads to increased proliferation of bacteria in the gut compared to the controls

M. Peng (*) · N. F. Kennedy · A. Truong · B. Arriola · A. Akmel Department of Animal and Avian Sciences, University of Maryland, College Park, MD, USA e-mail: [email protected] © Springer Nature Switzerland AG 2020 D. Biswas, S.O. Rahaman (eds.), Gut Microbiome and Its Impact on Health and Diseases, https://doi.org/10.1007/978-3-030-47384-6_4

85

86

M. Peng et al.

(Zhang et al. 2015). Carbohydrates, proteins, and fats are the major components that are incorporated in most diets. The amount and type of fat, protein, and ­carbohydrate is known to play a large role in the composition of gut microbiota. Butyrate and acetate are known to be bioactive metabolites of microbial degradation of proteins, fats, and carbohydrates, which also have positive influences on gut health in the host (Riaz Rajoka et al. 2017). Different therapeutic strategies exist in order to modify and contribute to gut health. Some of these major factors include the usage of fecal matter transplants, or addition of prebiotics/probiotics to one’s diet. The practice of fecal transplants is to transfer the stool of a healthy donor into the gastrointestinal tract of a recipient in order to replenish bacterial balance. One study covered the effects of inducing alcoholic liver disease into mice and combating it with two different methods. One involved fecal transplants using fecal matter from alcohol-resistant donor mice. The other method had to deal with using a prebiotic, pectin, to reduce the effects of liver inflammation. The study found that both methods lead to prevention of steatosis, liver inflammation, and restored gut homeostasis (Ferrere et al. 2017).

2  Gastrointestinal Microbial Ecosystem and Its Impact The gut microbiota consists of different microorganisms such as bacteria and fungi that have a commensal relationship with the human gut. Commensal bacteria comprise around 1000 different species, and in total, there are over 100 trillion microorganisms in the human gastrointestinal tract. These organisms can be affected by many factors including things like prebiotics, probiotics, synbiotics, diet, environment, pH value, intestinal motility, and host secretions. Studies conducted on the gut microbiota in twins have shown that apart from the heritable factor involved in the gut, a large proponent of our gut’s condition is determined by environmental factors (Goodrich et al. 2014). The gut microbiota as an entire system can provide direct effects on our immune, metabolic, and neurobehavioral traits. The role of the gut microbiota varies greatly from being able to contribute directly to host nutrient metabolism, drug metabolism, structural integrity, protection against pathogens, and providing capacities for fermentation of nondigestible substrates. This complicated system starts to develop into its adult stage at an early age. Even though an infant’s gut microbiota may be seen as underdeveloped, their gut typically resembles the adult flora by the age of 3 (Jandhyala et al. 2015). Moreover, one can see that typically, people with bowel disease, obesity, type 1 and 2 diabetes, and other related diseases have a lower bacterial diversity compared to healthy controls. On the other hand, diversity is usually an indicator of a healthy gut. (Valdes et al. 2018).

Probiotics and Prebiotics on Intestinal Flora and Gut Health

87

2.1  G  ut Microbial Homeostasis and Commensal Bacteria on Gut Immunity Development of the gut microbial system starts before birth and is a long and complex process. A human’s large intestine contains the greatest number of microbes in the body that maintain large networks of relationships in its ecosystem to develop the health of the individual. Many studies have shown that creation of the gut is idiosyncratic with large variations between infants (Chong et al. 2018). Therefore, there are a lot of gaps in our knowledge of the specifics that lead to control of the emerging gut microbiota developed by infants. For example, it was once thought that the gut was sterile before birth, but more recent studies have identified bacteria and bacterial products in the placenta. The utilization of high-throughput sequencing and molecular phylogenetic recently has created a detailed outline of the normal human gut microbiota, and studies have revealed the highly specific relationships between microbial species and certain microenvironments in the human gut. There have been several studies performed to compare gene expression profiles of the epithelial layer between germ-free and control animals that show direct responses to bacteria at a molecular level (Samuel et al. 2008). Other studies have looked at using only a single microbe in otherwise germ-free animals to determine which microbes are the ones contributing to the specific relationships (Lee et  al. 2013). These molecular mutualisms were proved as beneficial to the growth of the gut microbiota and its impact on health. Following this, at maturity, the gut intestine can resist pathogenic bacteria with two different barriers, a mechanical barrier and an immune barrier. A mechanical barrier contains intestinal epithelial cells, enterocytes, and mucus, while the immune barrier has a larger variety of defenses, consisting of things like intraepithelial lymphocytes, natural killer cells, Peyer’s plaques, and secreted immunoglobulin A. All of these variables can be affected by commensal bacteria, and its ability to contribute to resistance of colonization of pathogenic bacteria through competition for nutrients is called colonization resistance. Another way that commensal bacteria contribute to gut immunity is through the production of short-chain fatty acids (SCFAs), which lower the pH of the gut environment. These commensal bacteria are required for proper gut function, and studies have shown that animals bred under germ-free conditions developed many morphological, structural, and functional abnormalities (Zhang et al. 2015).

2.2  G  ut Microbial Dysbiosis Causing Acute and Chronic Health Issues Numerous commensal bacteria in our gut persist throughout our entire lifetime, while some are just considered transient and only pass through our system. The reach of influence that the gut has on its host is immense, with even more ­complexities

88

M. Peng et al.

that contribute to its creation. Alongside direct influence on the defense system of the gut, commensal bacteria contribute to the gut ecosystem in many ways. For instance, commensal bacteria can regulate gut motility, make vitamins, transform bile acid and steroids, absorb minerals, destroy toxins, etc. (Zhang et  al. 2015). However, showing all of the benefits that a balanced gut microbiome can provide to a host also reveals that a disrupted gut microbial ecosystem can lead to health issues for its host. Other than the correlation between gut microbiome and prevalence of diseases, there are direct factors that a dysbiotic gut contributes to compromised health. For example, development of gut dysbiosis can induce the initiation of activating host immune and inflammation responses that cause metabolic abnormalities, which further cause and sustain disease states in a host (Peng et al. 2018). A large number of microbes are influenced by an inflammatory milieu because they can survive hostile inflammatory milieu where other commensal bacteria cannot survive in the same environment. Therefore, it is to the bacteria’s benefit to maintain an inflammatory state in order to prevent competition by other microorganisms, which can further spiral downward into a vicious cycle that can lead to chronic diseases (Lee et al. 2003). Another example was shown in a study of germ-­ free mice where the positive relationship between producers of lipopolysaccharide endotoxin and increased obesity/insulin resistance was suggested through the track of changes in the gut permeability and inflammatory biomarkers (Fei and Zhao 2013). Furthermore, one important and expanding field is the gut-brain axis which allows communication between our central nervous system and the enteric nervous system. The gut microbiota was found to be sensitive to stress and stress mediators like catecholamine, and studies have established the association between dysbiosis of the gut, stress, and depressive order (Lee et al. 2003). In addition, studies have also been performed on germ-free mice expressing anxiety-like behavior which was associated with alterations in hormones and their gene expressions, and it was found that intestinal microbiota can influence human cognitive function by affecting the hypothalamus-pituitary-adrenal axis (Carding et al. 2015).

3  Probiotics and Their Advantages on Gut Health Benefits Probiotics benefit gut health by stimulating the metabolic activity and growth of commensal gut microbes which are essential for human beings efficiently perform their regulatory intestinal functions. These commensal or beneficial bacteria located in the gut intestine are responsible for supplying essential nutrients, synthesizing vitamin K, aiding in the digestion of cellulose, and promoting angiogenesis and enteric nerve function (Zhang et  al. 2015). Without the presence of these crucial microbes, a strong increase in the risk of gut health complications including bowel disorders and gut inflammations will be associated. Through systematic selection, various strains of probiotics providing health benefits in terms of reducing the risk of related diseases used in the food industry and for therapeutics.

Probiotics and Prebiotics on Intestinal Flora and Gut Health

89

3.1  Probiotic Selection and Common Strains The scientific definition of probiotics is a live microbial food supplement that beneficially affects the host by improving the intestinal microbial balance. The objectives of probiotic use include preventing the proliferation of pathogens in the gut, improving host’s gut digestion, delivering improved nutrition to hosts, enhancing host immune responses to disease, and improving gut environmental quality. In the case of probiotic foods, the health effect is usually based on the alteration of the gastrointestinal microflora and targeting the gut microbes located in the intestinal tract where most digestion and absorption are taking place. However, the application of probiotics is normally independent of the site of action, such as the oral cavity, the intestine, the vagina, and the skin, and the route of administration. The most common probiotics that are in use are various strains of lactic acid bacteria (LAB) including Lactobacillus, Lactococcus, and Bifidobacterium. LAB are Gram-positive, catalase-negative bacteria that produce lactic acid as a result of carbohydrate fermentation (Kechagia et al. 2013). It is also important to note that Streptococcus thermophilus and Lactococcus lactis are the top two lactic acid commercial probiotics used with dairy products. In common cases, phenotypic tests followed by genetic tests are performed in order to identify and select the probiotic strains. The characteristics of acid/bile tolerance, adhesion to mucosal and epithelial surfaces, antimicrobial activity against pathogenic bacteria, and bile salt hydrolase activity from strains are generally performed to determine the functionality of the probiotic. However, there are discrepancies of whether or not these tests can be reliable due to the lack of standardization. Therefore, there are no specific qualifications for probiotics, and it is beneficial to factor in the target location and targeted physiological function (Kechagia et al. 2013). The probiotic chosen must follow certain standards; for example, probiotics must be nonpathogenic, nontoxic, and nonallergenic; must be from human origin; must be genetically stable and capable of remaining viable for long periods in field condition; must be capable of surviving and metabolizing in the gastrointestinal tract (e.g., resistant to low pH, organic acids, bile juice, saliva and gastric acid) and secreting byproducts in the gut environment; must be able to modulate immune response and provide resistance to disease through improved immunity or by the production of antimicrobial substance in the guts; must possess good adhesion/colonization ability to human intestinal tract and influence on gut mucosal permeability; must be antagonistic against carcinogenic/pathogenic organism; and must possess clinically proven health benefit, e.g., preventing/alleviating gastrointestinal disorders, persistent diarrhea, Clostridium difficle-induced colitis or other antibiotics associated diarrhea, acute infantile gastroenteritis, etc. (Kechagia et al. 2013; Peng and Biswas 2017).

90

M. Peng et al.

3.2  P  robiotics Combating Enteric Bacterial Pathogens and Preventing Diseases Probiotics possess several advantages in providing health benefits on their host. For example, they produce lactic acids and lower the pH of intestines, therefore inhibiting bacterial villains such as Clostridium, Salmonella, Shigella, and pathogenic E. coli. Probiotics also decrease the production of a variety of toxic or carcinogenic metabolites by bacterial pathogens, and they secret a wide range of antimicrobial substances like acidophilin and bacteriocin to control pathogenic bacteria. Furthermore, probiotics aid in the absorption of minerals, especially calcium, due to increased intestinal acidity, produce β-D-galactosidase that break down lactose, produce vitamins (vitamin B and vitamin K), and also act as barriers to prevent harmful bacteria from colonizing the gut intestine (Kechagia et al. 2013; Peng and Biswas 2017). The effectiveness of probiotics on out-competing/combating pathogenic bacteria is well known from different mechanisms. For instance, probiotic strains are able to reduce plasma levels of bacterial endotoxin concentrations by inhibiting bacterial translocation across gastrointestinal lumen into the bloodstream; they adhere and colonize the gut mucosa to tighten the gut mucosal barriers and therefore decrease the translocation of bacterial pathogens and further infections, which may occur as a result of the ability of probiotics to tighten the mucosal barrier; probiotics disallow the colonization by disease-provoking bacteria through competition for nutrients, immune system upregulation, production of antitoxins, and upregulation of intestinal mucin genes; probiotics produce hydrogen peroxide and benzoic acids as well to inhibit pathogenic and acid-sensitive bacteria. Moreover, probiotics in producing and secreting bioactive metabolites also indirectly protect the host’s gut from pathogenic infections. One of the functional metabolites from probiotics is SCFA. They assist in lowering colon luminal pH and foster the growth of nonpathogenic commensal bacteria by SCFA production, one type of which, acetic acid, has antimicrobial activity against molds, yeasts, and pathogenic bacteria. SCFAs facilitate the absorption of water and electrolytes that in turn helps minimize the risk of diarrhea as well as its volume. Acetate, as one example, stimulates contractions of the ileum, shortens ileal emptying, increases colonic blood flow, and enhances ileal motility, whereas butyrate is the preferred energy substrate for the colonocyte, and it provides extra nutrition for ileal and colonic epithelial cells, which assists in maintenance of the integrity of colon. Probiotics can impact the immune system and therefore help prevent several diseases including foodborne illness, irritable bowel syndrome, chronic gut inflammation, constipation, food allergies, and various cancers (Riaz Rajoka et al. 2017). Although it is still under further research, several studies have shown that incorporating probiotics early on life the children are less likely to develop allergies. Additionally, it is found that using probiotics in infants is a safe alternative in helping the child develop a stronger immune system (Kechagia et al. 2013).

Probiotics and Prebiotics on Intestinal Flora and Gut Health

91

Certain probiotics that contribute to reducing carcinogenesis through several proposed mechanisms such as direct cholesterol assimilation, cholesterol absorption, and fermented byproduct production (Kechagia et  al. 2013). Though more work is still essential for understanding the specific effectiveness and mechanisms of selected probiotic strains, it is believed that members of the Lactobacillus (specifically L. acidophilus and L. casei), Lactococcus, and Bifidobacterium are the strains that have been found to decrease the levels of carcinogenic enzymes, for example, glycosidase, β-glucuronidase, and nitroreductase, which are being produced by intestinal flora located in the colon through converting pre-carcinogens into carcinogens. Moreover, probiotics also assist in reducing fecal concentrations of these carcinogenic enzymes, secondary bile salts, and absorption of mutagens that may contribute to colon carcinogenesis. Besides, several other mechanisms in inhibiting colon cancer have been proposed which include enhancing the host’s immune responses, altering the metabolic activity of the intestinal microflora, binding and degrading carcinogens, producing anti-mutagenic compounds, and altering the physiochemical conditions in the colon (Peng et al. 2018). Probiotics can help prevent irritable bowel syndrome by creating a better balance of the microbes in the gut (Peng et al. 2018). The cause of irritable bowel syndrome (IBS) is not known, but there are several ideas as to what causes it. Some believe it is caused by a disruption between the connection of the gut and the brain. By incorporating the right probiotic and strain, you can help rebuild the connection between the gut and the brain by improving the functioning of other mechanisms (Kennedy et al. 2014). It is also believed that IBS could also be caused by a weak immune system, which leads to the irregular movement of the large intestine (Barbara et al. 2011). The probiotics can help strengthen the immune system because they improve interactions with lymphoid tissues; the epithelium induces phagocytosis and IgA secretion, modifies T-cell responses, and enhances Th1 and alters Th2 responses (Markowiak and Ślizewska 2017). All of these will improve the host’s immune system and response time to infections. Gut bacteria are essential when it comes to breaking down and processing natural compounds that our intestinal tract wouldn’t be able to do on its own. For example, bacteria in our gut help transform lignans into a form we are able to digest and utilize to improve the immune system. Lignans help with preventing several different types of cancer and cardiovascular diseases (Zhang et al. 2015). Probiotics are also active in the improvement of lactose intolerance which is a genetically determined beta-galactosidase deficiency resulting in the inability to hydrolyze lactose into monosaccharides glucose and galactose (Kechagia et  al. 2013). When probiotics are supplemented into the diet of individuals with lactose intolerant, it helps to block the production of gut intestinal bacterial enzymes which degrade host-undigested lactose reaching the large intestine and cause diarrhea and decreases the risk of unnecessary reactions to lactose-containing dairy products (Kechagia et al. 2013). Furthermore, probiotics also have the potential in allergy relief through modifying the structure of antigens as well as reducing the immunogenicity, intestinal permeability of allergen, and pro-inflammatory cytokines that are elevated in patients with a variety of allergic disorders. Additionally, studies

92

M. Peng et al.

using L. rhamnosus GG and B. lactis BB12 have shown that atopic dermatitis, a condition that causes severe skin rashes in up to 15% of babies, can be prevented in 50% of cases if mothers ingest probiotics during pregnancy and newborns ingest them during the first 6 months of life (Meneghin et al. 2012).

4  P  rebiotics and Functional Foods in Shaping Gut Microbiota Prebiotics are short-chain carbohydrates that are not digestible by enzymes but promote the growth of probiotics which benefit the health of the host (Al-Sheraji et al. 2013). Prebiotics can be consumed naturally through functional foods and or synthetically as dietary pills or supplemented foods (Florowska et al. 2016). Through promoting probiotics, the fermentation creates an environment that favors the beneficial bacteria more than the pathogenic bacteria, and this further benefits the host by increasing the absorbance of minerals and generating SCFAs that provide an energy source to the surrounding tissues (Topping and Clifton 2001). Different diets can affect the macrobiotic environment of an individual; for example, both omnivorous versus vegan diets and gluten-free versus fiber-rich diets contribute to shaping the diverse gastrointestinal system microbiome of the people throughout the world.

4.1  P  rebiotic Characterization, Functions, and Prebiotic-­Based Commercial Functional Foods Gut health is an important factor in maintaining a human’s health condition. To promote the growth of probiotics and create an unfavorable environment for pathogens, prebiotics have been found and developed. Prebiotics are short-chain carbohydrates that are not digestible by enzymes and are known to enhance growth of probiotics to improve the health of the gut in humans (Al-Sheraji et  al. 2013). Prebiotics are defined according to the following: be able to reach the colon undigested, not be absorbed by the gastrointestinal system, and promote the growth of only probiotics. Generally, prebiotics are found naturally contained in fruits, vegetables, and whole grains, such as garlic, onions, bananas, and wheat bran and flour (Florowska et al. 2016). However, synthetic methods to obtain prebiotics are also developed and utilized to provide a better source by supplementing other foods, which may allow individuals with a specific food allergy or in dietary lifestyle choices to consuming prebiotics. Prebiotics can be isolated through several methods. They are produced by microbes, isolated from plants, or though enzymes either by synthesizing them or degrading polysaccharides (Al-Sheraji et al. 2013). There are many prebiotics being researched, but only a few have been approved and are currently being added as a

Probiotics and Prebiotics on Intestinal Flora and Gut Health

93

supplement to foods (Slavin 2013). Fructooligosaccharides (FOS) and galactooligosaccharides (GOS) are two carbohydrates confirmed to be prebiotics (Florowska et al. 2016). GOS are a derivative of lactose found in milk from mammals, and FOS can be produced from sucrose enzymatically or by hydrolyzing inulin, both of which can be derived through plants (Crout and Vic 1998). Through these methods, prebiotics can be mass produced and supplemented in foods, giving individuals with dietary restrictions another option that will not negatively impact their health. As carbohydrates, prebiotics are fermented by the probiotics, favoring the commensal or beneficial gut microbes over the pathogenic bacteria (Cummings et al. 2001). The colon is a great place for bacteria to thrive, where it is a controlled stable environment with constant temperature and nutrient flow. Prebiotics provide probiotics the competitive edge by being carbohydrates that they can properly ferment and metabolize. Limited space pushes out other bacteria and provides difficulty for them to survive, and the growth promotion of the probiotics also reduces the pH condition in the gut environment (Florowska et al. 2016). In addition, the stimulated fermentation process in probiotics increases the concentration of SCFAs which is an energy source for the tissues in the colon and bacteria (Topping and Clifton 2001). Prebiotic intake has been associated with better absorption of minerals, calcium and magnesium (Carabin and Gary Flamm 1999). Calcium is important for the gastrointestinal system specifically because calcium ions contribute in passive diffusion for the surrounding epithelial cells and it is also needed for proper function in other parts of the body and tissues (Bandyopadhyay and Mandal 2014). Calcium is essential for basic bodily functions, blood clotting, and muscle contractions, and it is lost through shed skin, nails, and hair (Beto 2015). Magnesium is a necessary cofactor for enzymes that require adenosine triphosphate (ATP). ATP is the cell’s way to transport energy to maintain proper function. Processes like DNA replication and RNA synthesis both require ATP which in turn needs magnesium (Sidnell 2008). A study on adolescents showed that there was an increase in calcium absorption when consuming 8 g of inulin a day which leads to a higher mineral density in bones (Slavin 2013). In mice, both magnesium absorption and calcium absorption were increased after GOS had been provided to their diet; however, the specific mechanisms under it have not been determined yet (Martin et al. 2010). Functional foods are food products that have been proven to be beneficial physiologically. Different from medications, through simply boosting the health of the consumer via their diet, prebiotics, probiotics, and antioxidants are all considered functional foods (Al-Sheraji et al. 2013). Specifically, prebiotics also have unique properties that allow them to enhance the texture of the foods added to and prolong the shelf life of food products without having a negative effect on their tastes (Bosscher 2009). Dairy products like yogurt and cheese are often probiotic-­ containing foods and in some cases combined with the addition of prebiotics/ prebiotic-­like components, which establishes a system of symbiotic (Collins and Gibson 1999). Symbiotic systems can provide the probiotic strains an advantage through promoting their growth and postbiotic production most likely due to prior contact before ingestion (Conlon and Bird 2015).

94

M. Peng et al.

4.2  D  iet-Dependent Blueprint in Modulating Intestinal Microbiota Different diets can either have significant or negligible effect on the intestinal microbiota, whereas, regardless of prebiotic effects on promoting growth and metabolism of probiotics, medication can also have a prominent effect upon probiotics in the gut intestine (Reijnders et  al. 2016). A study on a large population showed that certain drugs, progesterone and osmotic laxatives to name a few, had a very large effect on the microbiota (Falony et al. 2016). This effect caused higher gastrointestinal infection in individuals (Jackson et al. 2016). Antibiotics also have an overall effect on the bacteria in the gut as their purpose is to inhibit the growth of bacteria. They can be specific but can still affect the beneficial bacteria in the gut (Hayes and Vargas 2016). More studies are needed in order to determine how exactly antibiotics affect humans. Humans have varied responses to antibiotics; previous attempted studies are unable to collect proper data and be consistent enough with the results (Valdes et al. 2018). Various diets with functional foods containing probiotics and prebiotics can modulate unhealthy gastrointestinal which provide the host with a better gut immune system as well (Kelly et al. 2007). Infants gain most of the important nutrients from their mother during breastfeeding, during which time of period their immune system and gastrointestinal system are also built up (Harmsen et al. 2000). It was found that no probiotics were detected in the newborn stools but their population was gradually increased once the infants got older and solid foods were introduced to them (Harmsen et al. 2000). Additionally, the diversity of the microbiota increasing in complexity with age as various foods become introduced to the system, whereas it varies drastically based on geographic location, diet, and personal lifestyle (Nicholson et al. 2012). Restrictions on diet range from personal preference to physical difficulties like allergies. There is little research on comparisons of a vegan diet to an omnivore diet, but one study looked at the serum metabolites of both groups and detected a significant difference between groups. When looking at the fecal bacterial populations, there was only a slight difference found between vegan-diet and omnivorediet individuals (Sridharan et al. 2014). Another study focused on omnivore-fed individuals with either a high-fiber but low-fat diet or a high-fat but low-fiber diet, and it was found that the distinct diet resulted in little alterations of the fecal microbial population (Sridharan et  al. 2014). Although both studies were performed on small groups (between 10 and 20 individuals) and performed over a short period of time, they suggested that a vegan diet does not differ much from an omnivorous diet in terms of fecal microbial population but might be an effective factor on influencing the metabolism of the gut intestinal microbes themselves (Valdes et al. 2018). It was also found that maintaining a gluten-free diet, which has become a popular choice to lose weight, has been shown to drastically alter the microbial environment of the gastrointestinal system by raising the fecal levels of Akkermansia species (Marietta et  al. 2013). Furthermore, fermentable oligosaccharide, disaccharide, ­monosaccharide, and polyol (Magge and Lembo 2012) diets

Probiotics and Prebiotics on Intestinal Flora and Gut Health

95

rich in various categories of sugar/carbohydrates (Magge and Lembo 2012) have been associated with individuals suffering from bowel disorders and related gastrointestinal issues, for example, irritable bowel syndrome. Several food ingredients from FODMAP diets include fructose, lactose, sorbitol, and xylitol (Magge and Lembo 2012). As a matter of fact, slowly excluding FODMAP-related food consumption is one of the methods and goals in reducing the symptom or risk of intestinal discomfort and therefore eventually leads to a better overall healthier gut intestinal microbiota (Magge and Lembo 2012; Valdes et al. 2018). Health issues like cardiovascular diseases and obesity are found more prevalent in western society, and they often rest on the overconsumption of food products high in sodium and sugar (Turnbaugh et  al. 2008). Artificial sweeteners such as sucralose, aspartame, and saccharin, approved to be safe for consumption, are used for adding sweetness with fewer calories (Nettleton et al. 2016). However, tests on mice being given sucralose for 6 weeks resulted in the enrichment of bacterial pro-­ inflammatory genes in the murine gut intestine as well as disruption in their fecal metabolites, showing the negative influence of sucralose-containing diet on gastrointestinal microbiota (Bian et al. 2017). Emulsifiers, naturally found in animal products like egg yolks, are typically proteins and phospholipids which also attribute to unhealthy microbiota alterations (Hasenhuettl and Hartel 2008). An experiment on mice was conducted on evaluating the effectiveness of low-concentration emulsifiers carboxymethylcellulose and polysorbate 80, and the researchers observed that the mice provided with these two emulsifiers were associated with microbiota encroachment and altered species composition when compared to the control mice, and they further induced low-grade gut intestinal inflammation and promoted metabolic syndrome/adiposity (Chassaing et al. 2015). On the other hand, the diet that consists of a higher amount of animal proteins with saturated fats and simple sugars is not recommended compared to fruits and vegetables which contain functional ingredients beneficial to human health especially prebiotics (Bandyopadhyay and Mandal 2014). According to previously performed studies, beneficial microbes including Lactobacillus and Bifidobacterium in the gastrointestinal system were found to be significantly less in terms of both species diversity and total quantity in the children from North America and urban Italy who commonly have diets consisted more of animal proteins and saturated fats than children in rural Africa and South America whose diets were enriched by plants containing more fiber (Conlon and Bird 2015).

5  T  herapeutic Strategies Aiming at Restoring Balance of Gut Microbial Ecosystem The gut microbial ecosystem is composed of numerous types of microbiota that reside in the host digestive tract (Haller 2018). Some of the roles of the microbiota include supporting immune function, nutrient metabolism, and maintaining the overall health of the gut mucosal barrier (Jandhyala et al. 2015). Imbalance in the

96

M. Peng et al.

gut microbial ecosystem increases the inhabitance of harmful pathogens, which can then negatively impact the health of the host. When the gut ecosystem is imbalanced, it increases the chance of the host organism developing diseases such as inflammatory bowel disease, irritable bowel syndrome, cardiovascular disease, and obesity (Flint et al. 2012). The detailed role of the gut microbial and the impact of an imbalanced gut microbial ecosystem is still under study and not fully understood (Valdes et al. 2018); however, understanding the negative effects of a disrupted environment has increased the level of research on possible ways to restore the gut microbiota ecosystem. Some of the given methods to improve the balance of the gut microbiota are by probiotic, prebiotic, synbiotic, and transplant of bacteria and fecal microbiota.

5.1  Probiotics, Prebiotics, and Synbiotics Formulation Probiotics have many essential features that provide beneficial properties to the host digestive system. Among the various features, the ability to inhibit harmful pathogens while improving the health of the digestive tract is a feature that makes probiotics a strategic method in many therapeutic approaches (Sreeja and Prajapati 2013). The balance of gut microbiota is influenced by various factors such as changes in diet and the use of antibiotic drugs. These factors can lead to an imbalance in the gut ecosystem and decrease the presence of useful functional bacteria (Govender et al. 2014). To help combat this problem, probiotics can colonize and replenish the gut microbial system (Govender et  al. 2014). The common types of bacteria used as probiotics are the Bifidobacterium and Lactobacillus strains. These strains are typically used because of their tolerance to gastric acid and their capability to adhere to the mucosal surface (Fioramonti et al. 2003). A comprehensive list of various probiotics for their practices in the restoration of the balance of the gut microbial ecosystem is summarized in Table 1. Given the beneficial properties of probiotics, taking probiotic supplements can advance the gut microbiota system. The supplements are mainly formulated with mixtures of probiotics that consists of Lactobacillus acidophilus, Bifidobacterium Table 1  Analysis of probiotic bacteria and the beneficial properties Common probiotics Bifidobacterium (B. breve and B. longum)

Enterococcus (E. faecium) Escherichia (E. coli Nissle) Lactobacillus (L. acidophilus, L. casei, L. paracasei, L. plantarum, L. rhamnosus, and L. salivarius)

Benefits Inhibits irritable bowel disease, provides immune support, and protects against agents causing diarrhea Treats inflammation of the gastrointestinal tracts and infection caused by Salmonella Prevents tumor and cancerous activities Balances intestinal ecosystem, enhances immune response, protects against diarrhea, and promotes vitamin intake

Probiotics and Prebiotics on Intestinal Flora and Gut Health

97

bifidum, Lactobacillus Salivarius, B. infantis, and B. longum (Peng et  al. 2018). These mixtures are then administered in two major forms: conventional pharmaceutical products and nonconventional commercial foods (Govender et  al. 2014). In conventional pharmaceutical products, probiotics are delivered in a capsule or a tablet form (Govender et al. 2014). These forms of delivery are found to be effective since the coating of the capsules and tablets ensure the supplements extend to the digestive tract without severe impact (Govender et  al. 2014). In nonconventional commercial foods, probiotics are formulating by adding different strains of probiotics into manufactured foods that are fermented (Saxelin 2008). A mistaken notion about fermented foods is the idea that all fermented foods contain live bacteria, whereas most fermented foods are thermally purified after production, which eliminates the functional bacteria (Rezac et al. 2018). The only products that contain live probiotics are products that have a label indicating the presence of active microbes (Rezac et al. 2018). Probiotics are normally formulated into fermented foods such as dairy products which allows a prolonged lifespan for probiotics (Rezac et  al. 2018). These forms of delivery are found to be effective, but the formulation process can still influence the amount of probiotic delivered (Govender et al. 2014). The use of prebiotics to help balance the gut microbiota is another therapeutic strategy of focus. Major types of foods that are used in therapeutic approaches are foods that contain “fructooligosaccharides (FOS), inulin, and galactooligosaccharides (GOS)” (Gibson 1999). Fermentable foods that are naturally found in foods and considered to be prebiotic include starch-rich whole grains, flaxseed gum, and fenugreek gum (Patel and Goyal 2012). Prebiotics are also extracted and used as food additives to increase fermentation (Patel and Goyal 2012). The prebiotics are formulated by extracting the prebiotics from plant sources and then adding the extracts into other diets (Patel and Goyal 2012). For example, the polysaccharide levan can be extracted from Zymomonas mobilis and hydrolyzed to obtain oligofructans which beneficially affect the host by selective stimulation of probiotic bacteria in the digestive system (Patel and Goyal 2012). Additional methods of prebiotic production include immobilization of galactosidase, osmotic dehydration, separation by ion exchange chromatography, and hydrothermal degradation. (Patel and Goyal 2012). After extraction of the prebiotics, the content can be inserted into other foods to help provide the necessary diet needed to help improve the gut flora. In milk production, the extraction and production of inulin prebiotics can be used to improve the fermentation process in milk products (Patel and Goyal 2012). Overall, prebiotics are naturally found in certain foods, but they can also function as additives into other diets through extraction. The use of prebiotic is a safe application since it contains no microorganisms; instead, it selectively works to help improve the growth of useful microbes found in the gut flora (Markowiak and Ślizewska 2017). Synbiotics are products that contain both prebiotic and probiotic properties as additive supplements to help balance the gut microbiota (Markowiak and Ślizewska 2017). In the Journal of Leukocyte Biology publication, Su et al. studied the survival of probiotic strains in fecal samples after administering a combination of prebiotic and probiotic supplements to mice models (Su et al. 2007). The result showed that FOS and inulin prebiotics helped stimulate growth of B. lactis probiotic strain

98

M. Peng et al.

and helped in the lifespan of the Lactobacillus casei probiotic strain (Su et al. 2007). A naturally occurring synbiotic process is the consumption of breast milk. The human breast milk contains oligosaccharides and lactic acid bacteria which are considered a symbiotic food (Su et al. 2007). As infants breastfeed, they ingest synbiotic supplements that will help influence the formation of the gut colony and form balance of microbes. Synbiotics provide a viable environment for probiotics and help improve the health of the host digestive system (Markowiak and Ślizewska 2017). Synbiotics are important therapeutically applications because they have properties such as antibacterial, anticancerogenic, and anti-allergic effects (Markowiak and Ślizewska 2017). The application of prebiotics and probiotics as supplement can help provide beneficial properties but requires further research to understand the implications (Markowiak and Ślizewska 2017).

5.2  F  ecal Microbiota Transplantation and Bacterial Consortium Transplantation Fecal microbiota transplantation is the procedure of transferring stool sample from one host to another host (Li et al. 2015). The microbial habitation in the digestive system requires a balance to help the host have a healthy digestive system. A disruption of the intestinal microbiota may result in dysfunction of the mucosal barrier and lead to intestinal sensory and motor changes (Li et al. 2015). When the imbalance requires significant restoration, one efficient technique that is used at restoring the balance is the use of fecal microbiota transplantation. The method of restoration can be through enema administration, nasogastric tube, and colonoscopy (Aroniadis 2013). For a transplant to be performed, the ideal donor should have not taken antibiotics for the preceding 3 months and should not have diseases such as HIV, hepatitis B or C, and a current communicable disease (Aroniadis 2013). Once an ideal donor is identified, a stool sample is obtained and diluted so the content can channel through a syringe (Aroniadis 2013). The use of fecal microbiota transplantation provides an assuring therapeutic improvement in the digestive system and can be a strategy used for patient requiring a fecal microbiota reestablishment (Li et al. 2015). Dysbiotic gut microbiota can cause the dysfunction of the mucosal barrier (Li et al. 2015). An imbalance can cause infections and other diseases in the digestive system. To reestablish the ecosystem of the digestive system, a bacterial consortium transplantation has shown a promising result considering that it provides better control and stability (Li et  al. 2015). Method of balance includes selectively combining different gut bacteria from a donor’s digestive tract (Gagliardi et  al. 2018). The types of gut bacteria combined in a bacterial consortia transplantation include Acidaminococcus intestinalis, Bacteroides ovatus, B. adolescentis, B. longum, Blautia producta, Clostridium cocleatum, Collinsella aerofaciens, Dorea longicatena, Escherichia coli, Eubacterium desmolans, E. eligens, E. limosum, E. rectale, E. ventriosum, Faecalibacterium prausnitzii, Lachnospira pectinoschiza, Lactobacillus casei, L.paracasei, Parabacteroides distasonis, Raoultella sp.,

Probiotics and Prebiotics on Intestinal Flora and Gut Health

99

Roseburia faecalis, R. intestinalis, Ruminococcus torques, R. obeum, and Streptococcus mitis (Gagliardi et  al. 2018). The transplant has shown a prompt reestablishment in the digestive system microbiota and helped contribute in an anti-­inflammatory activity in patients with inflammatory bowel disease (Li et al. 2016). The use of bacterial consortium transplantation as a therapeutically approach can help provide a rapid improvement to the digestive system ecosystem.

5.3  L  imitations and Future Investigation on Advanced Approach The application of probiotic, prebiotic, and synbiotic and transplant of the fecal microbial and bacterial consortium are important therapeutic strategies that have positive effects to help balance the digestive system ecosystem. These methods are useful but can have limitations because of the method of delivery or the lack of further studies. In the case of probiotics, most consumed in commercial foods lack the properties needed to survive once inside the digestive system (Rezac et al. 2018). When probiotics are exposed to bacteriophages or antibiotics, their functionalities are limited because of their lack of resistance (Govender et al. 2014). It might be fundamental to have further research to creating resistant genes that can be potentially passed on to beneficial microbial. The use of prebiotics for therapeutic method is effective to provide a long-term stable supplement (Markowiak and Ślizewska 2017) with properties that promote the cultivation of beneficial microbes in the digestive system (Patel and Goyal 2012). Further investigation on the influence of both prebiotics and probiotics is still yet to be confirmed, but various studies have shown positive enhanced effects when prebiotics and probiotics are administered together (Markowiak and Ślizewska 2017). Since there are limited studies on the effects of synbiotics, there needs to be further studies to understand the implications of combining prebiotics and probiotics (Markowiak and Ślizewska 2017). When it comes to fecal microbiota and bacterial consortium transplants, there have been studies that have shown successful regulation of the gut flora, but future studies are still required to understand how the immune response influences the procedure and improved delivery/administration methods of transplantation are also necessary for future treatment of enteric infections and chronic bowel inflammations (Li et  al. 2015, 2016).

6  Conclusion When looking at the gut microbiota, many factors can be analyzed that vary from the gut’s ability for homeostasis and the gut’s overall immunity, the wide arrangements lead to gut microflora symbiosis, and the effects of gut microbial dysbiosis on acute and chronic health issues in humans. The ability to modify and regulate our

100

M. Peng et al.

gut microbiota to be used for disease therapy and intervention strategies is immensely powerful and constantly rising. Several benefits observed from the utilization of probiotic strains and prebiotic-like food ingredients include improvement of intestinal health, enhancement of immune response, reduction of serum cholesterol, and aids in preventing cancer. Mechanisms the beneficial microbes targeting can be through producing bioactive metabolites like SCFAs and vitamin K.  They also improve the immune system through the interactions with lymphoid tissues; the epithelium induces phagocytosis and IgA secretion, modifies T-cell responses, and enhances Th1 and alters Th2 responses. Furthermore, newly established fecal microbiota transplantation and bacterial consortium transplantation which are currently under developing and improving are also promising therapeutic strategies in restoring gut microbiota from dysbiosis.

References Al-Sheraji, S. H., Ismail, A., Manap, M. Y., Mustafa, S., Yusof, R. M., Hassan, F. A. (2013). Prebiotics as functional foods: A review, Journal of Functional Foods, 5(4), 1542–1553, ISSN 1756-4646, https://doi.org/10.1016/j.jff.2013.08.009. Aroniadis, O.  C. (2013). Fecal microbiota transplantation: Past, present and future. Current Opinion in Gastroenterology, 29(1), 79–84. Bandyopadhyay, B., & Mandal, N.  C. (2014). Probiotics, prebiotics and synbiotics  – In health improvement by modulating gut microbiota: The concept revisited. International Journal of Current Microbiology and Applied Sciences, 3, 410–420. Barbara, G., Cremon, C., Carini, G., Bellacosa, L., Zecchi, L., De Giorgio, R., Corinaldesi, R., & Stanghellini, V. (2011). The immune system in irritable bowel syndrome. Journal of Neurogastroenterology and Motility, 17(4), 349–359. Beto, J. A. (2015). The role of calcium in human aging. Clinical Nutrition Research. https://doi. org/10.7762/cnr.2015.4.1.1. Bian, X., Chi, L., Gao, B., Tu, P., Ru, H., & Lu, K. (2017). Gut microbiome response to sucralose and its potential role in inducing liver inflammation in mice. Frontiers in Physiology. https:// doi.org/10.3389/fphys.2017.00487. Bosscher, D. (2009). Fructan prebiotics derived from inulin. In: Prebiotics and probiotics science and technology. Springer, New York, NY. https://doi.org/10.1007/978-0-387-79058-9_6. Carabin, I.  G., & Gary Flamm, W. (1999). Evaluation of safety of inulin and oligofructose as dietary fiber. Regulatory Toxicology and Pharmacology. https://doi.org/10.1006/ rtph.1999.1349. Carding, S., Verbeke, K., Vipond, D. T., Corfe, B. M., & Owen, L. J. (2015). Dysbiosis of the gut microbiota in disease. Microbial Ecology in Health and Disease. https://doi.org/10.3402/mehd. v26.26191. Chassaing, B., Koren, O., Goodrich, J. K., Poole, A. C., Srinivasan, S., Ley, R. E., & Gewirtz, A. T. (2015). Dietary emulsifiers impact the mouse gut microbiota promoting colitis and metabolic syndrome. Nature. https://doi.org/10.1038/nature14232. Chong, C. Y. L., Bloomfield, F. H., & O’Sullivan, J. M. (2018). Factors affecting gastrointestinal microbiome development in neonates. Nutrients, 10(3), 274. Collins, M.  D., & Gibson, G.  R. (1999). Probiotics, prebiotics, and synbiotics: Approaches for modulating the microbial ecology of the gut. American Journal of Clinical Nutrition, 69(5), 1052S–1057S.

Probiotics and Prebiotics on Intestinal Flora and Gut Health

101

Conlon, M. A., & Bird, A. R. (2015). The impact of diet and lifestyle on gut microbiota and human health. Nutrients, 7(1), 17–44. Crout, D. H. G., & Vic, G. (1998). Glycosidases and glycosyl transferases in glycoside and oligosaccharide synthesis. Current Opinion in Chemical Biology. https://doi.org/10.1016/ S1367-5931(98)80041-0. Cummings, J. H., Macfarlane, G. T., & Englyst, H. N. (2001). Prebiotic digestion and fermentation. American Journal of Clinical Nutrition, 73(2 Suppl), 415S–420S. Falony, G., Joossens, M., Vieira-Silva, S., Wang, J., Darzi, Y., Faust, K., Kurilshikov, A., Bonder, M. J., Valles-Colomer, M., Vandeputte, D., Tito, R. Y., Chaffron, S., Rymenans, L., Verspecht, C., De Sutter, L., Lima-Mendez, G., D’hoe, K., Jonckheere, K., Homola, D., Garcia, R., Tigchelaar, E.  F., Eeckhaudt, L., Fu, J., Henckaerts, L., Zhernakova, A., Wijmenga, C., & Raes, J. (2016). Population-level analysis of gut microbiome variation. Science. https://doi. org/10.1126/science.aad3503. Fei, N., & Zhao, L. (2013). An opportunistic pathogen isolated from the gut of an obese human causes obesity in germfree mice. The ISME Journal. https://doi.org/10.1038/ismej.2012.153. Ferrere, G., Wrzosek, L., Cailleux, F., Turpin, W., Puchois, V., Spatz, M., Ciocan, D., Rainteau, D., Humbert, L., Hugot, C., Gaudin, F., Noordine, M.  L., Robert, V., Berrebi, D., Thomas, M., Naveau, S., Perlemuter, G., & Cassard, A. M. (2017). Fecal microbiota manipulation prevents dysbiosis and alcohol-induced liver injury in mice. Journal of Hepatology. https://doi. org/10.1016/j.jhep.2016.11.008. Fioramonti, J., Theodorou, V., & Bueno, L. (2003). Probiotics: What are they? What are their effects on gut physiology? Best Practice and Research Clinical Gastroenterology, 17(5), 711–724. Flint, H.  J., Scott, K.  P., Louis, P., & Duncan, S.  H. (2012). The role of the gut microbiota in nutrition and health. Nature Reviews. Gastroenterology & Hepatology, 9, 577–589. https://doi. org/10.1038/nrgastro.2012.156. Florowska, A., Krygier, K., Florowski, T., & Dłuzewska, E. (2016). Prebiotics as functional food ingredients preventing diet-related diseases. Food & Function, 7(5), 2147–2155. Gagliardi, A., Totino, V., Cacciotti, F., Iebba, V., Neroni, B., Bonfiglio, G., Trancassini, M., Passariello, C., Pantanella, F., & Schippa, S. (2018). Rebuilding the gut microbiota ecosystem. International Journal of Environmental Research and Public Health, 15(8), 1679. Gibson, G.  R. (1999). Dietary modulation of the human gut microflora using the prebiotics Oligofructose and inulin. The Journal of Nutrition. https://doi.org/10.1093/jn/129.7.1438s. Goodrich, J.  K., Waters, J.  L., Poole, A.  C., Sutter, J.  L., Koren, O., Blekhman, R., Beaumont, M., Van Treuren, W., Knight, R., Bell, J. T., Spector, T. D., Clark, A. G., & Ley, R. E. (2014). Human genetics shape the gut microbiome. Cell. https://doi.org/10.1016/j.cell.2014.09.053. Govender, M., Choonara, Y. E., Kumar, P., Du Toit, L. C., Van Vuuren, S., & Pillay, V. (2014). A review of the advancements in probiotic delivery: Conventional vs. Non-conventional formulations for intestinal flora supplementation. AAPS PharmSciTech, 15(1), 29–43. Haller D. (eds) The Gut Microbiome in Health and Disease. Springer, Cham. https://doi. org/10.1007/978-3-319-90545-7. Harmsen, H. J. M., Wildeboer-Veloo, A. C. M., Raangs, G. C., Wagendorp, A. A., Klijn, N., Bindels, J.  G., & Welling, G.  W. (2000). Analysis of intestinal flora development in breast-fed and formula-­fed infants by using molecular identification and detection methods. Journal of Pediatric Gastroenterology and Nutrition. https://doi.org/10.1097/00005176-200001000-00019. Hasenhuettl G., Hartel R. (eds) Food Emulsifiers and Their Applications. Springer, Cham. https:// doi.org/10.1007/978-3-030-29187-7. Hayes, S.  R., & Vargas, A.  J. (2016). Probiotics for the prevention of pediatric antibiotic-­ associated diarrhea. Explore: The Journal of Science & Healing. https://doi.org/10.1016/j. explore.2016.08.015. Jackson, M. A., Goodrich, J. K., Maxan, M. E., Freedberg, D. E., Abrams, J. A., Poole, A. C., Sutter, J. L., Welter, D., Ley, R. E., Bell, J. T., Spector, T. D., & Steves, C. J. (2016). Proton

102

M. Peng et al.

pump inhibitors alter the composition of the gut microbiota. Gut. https://doi.org/10.1136/ gutjnl-2015-310861. Jandhyala, S.  M., Talukdar, R., Subramanyam, C., Vuyyuru, H., Sasikala, M., & Reddy, D.  N. (2015). Role of the normal gut microbiota. World Journal of Gastroenterology. https://doi. org/10.3748/wjg.v21.i29.8787. Kechagia, M., Basoulis, D., Konstantopoulou, S., Dimitriadi, D., Gyftopoulou, K., Skarmoutsou, N., & Fakiri, E. M. (2013). Health benefits of probiotics: A review. ISRN Nutrition. https://doi. org/10.5402/2013/481651. Kelly, D., King, T., & Aminov, R. (2007). Importance of microbial colonization of the gut in early life to the development of immunity. Mutation Research. https://doi.org/10.1016/j. mrfmmm.2007.03.011. Kennedy, P.  J., Cryan, J.  F., Dinan, T.  G., & Clarke, G. (2014). Irritable bowel syndrome: A microbiome-­ gut-brain axis disorder? World Journal of Gastroenterology, 20(39), 14105–14125. Koecher, K.  J., Thomas, W., & Slavin, J.  L. (2015). Healthy subjects experience bowel changes on enteral diets: Addition of a fiber blend attenuates stool weight and gut bacteria decreases without changes in gas. Journal of Parenteral and Enteral Nutrition. https://doi. org/10.1177/0148607113510523. Lee, S. O., Kim, C. S., Cho, S. K., Choi, H. J., Ji, G. E., & Oh, D. K. (2003). Bioconversion of linoleic acid into conjugated linoleic acid during fermentation and by washed cells of Lactobacillus reuteri. Biotechnology Letters, 25, 935–938. https://doi.org/10.1023/A:1024084203052. Lee, S. M., Donaldson, G. P., Mikulski, Z., Boyajian, S., Ley, K., & Mazmanian, S. K. (2013). Bacterial colonization factors control specificity and stability of the gut microbiota. Nature, 501, 426–429. https://doi.org/10.1038/nature12447. Li, M., Liang, P., Li, Z., Wang, Y., Zhang, G., Gao, H., Wen, S., & Tang, L. (2015). Fecal microbiota transplantation and bacterial consortium transplantation have comparable effects on the re-establishment of mucosal barrier function in mice with intestinal dysbiosis. Frontiers in Microbiology. https://doi.org/10.3389/fmicb.2015.00692. Li, M., Li, Z., Wen, S., Liu, Y., Wang, Y., & Tang, L. (2016). Transplantation of a bacterial consortium ameliorates trinitrobenzenesulfonic acid-induced colitis and intestinal dysbiosis in rats. Future Microbiology. https://doi.org/10.2217/fmb-2015-0002. Magge, S., & Lembo, A. (2012). Low-FODMAP diet for treatment of irritable bowel syndrome. Gastroenterología y Hepatología, 8(11), 739–745. Marietta, E. V., Gomez, A. M., Yeoman, C., Tilahun, A. Y., Clark, C. R., Luckey, D. H., Murray, J. A., White, B. A., Kudva, Y. C., & Rajagopalan, G. (2013). Low incidence of spontaneous type 1 diabetes in non-obese diabetic mice raised on gluten-free diets is associated with changes in the intestinal microbiome. PLoS One. https://doi.org/10.1371/journal.pone.0078687. Markowiak, P., & Ślizewska, K. (2017). Effects of probiotics, prebiotics, and synbiotics on human health. Nutrients, 9(9), 1021. Martin, B. R., Braun, M. M., Wigertz, K., Bryant, R., Zhao, Y., Lee, W. H., Kempa-Steczko, A., & Weaver, C. M. (2010). Fructo-oligosaccharides and calcium absorption and retention in adolescent girls. Journal of the American College of Nutrition. https://doi.org/10.1080/07315724 .2010.10719855. Meneghin, F., Fabiano, V., Mameli, C., & Zuccotti, G. V. (2012). Probiotics and atopic dermatitis in children. Pharmaceuticals (Basel), 5(7), 727–744. Nettleton, J.  E., Reimer, R.  A., & Shearer, J. (2016). Reshaping the gut microbiota: Impact of low calorie sweeteners and the link to insulin resistance? Physiology & Behavior, 164(Pt B), 488–493. Nicholson, J. K., Holmes, E., Kinross, J., Burcelin, R., Gibson, G., Jia, W., & Pettersson, S. (2012). Host-gut microbiota metabolic interactions. Science, 336(6086), 1262–1267. Patel, S., & Goyal, A. (2012). The current trends and future perspectives of prebiotics research: A review. 3 Biotech. https://doi.org/10.1007/s13205-012-0044-x.

Probiotics and Prebiotics on Intestinal Flora and Gut Health

103

Peng, M., & Biswas, D. (2017). Short chain and polyunsaturated fatty acids in host gut health and foodborne bacterial pathogen inhibition. Critical Reviews in Food Science and Nutrition. https://doi.org/10.1080/10408398.2016.1203286. Peng, M., Patel, P., Vinod, N., Cassandra, B., Michael, C., & Debabrata, B. (2018). Feasible options to control colonization of enteric pathogens with designed synbiotics. In R. R. Watson & V. R. Preedy (Eds.), Dietary interventions in gastrointestinal diseases. Elsevier Academic Press, 135–149, ISBN 9780128144688, https://doi.org/10.1016/B978-0-12-814468-8.00011-9. Reijnders, D., Goossens, G. H., Hermes, G. D. A., Neis, E. P. J. G., van der Beek, C. M., Most, J., Holst, J. J., Lenaerts, K., Kootte, R. S., Nieuwdorp, M., Groen, A. K., Olde Damink, S. W. M., Boekschoten, M. V., Smidt, H., Zoetendal, E. G., Dejong, C. H. C., & Blaak, E. E. (2016). Effects of gut microbiota manipulation by antibiotics on host metabolism in obese humans: A randomized double-blind placebo-controlled trial. Cell Metabolism. https://doi.org/10.1016/j. cmet.2016.06.016. Rezac, S., Kok, C. R., Heermann, M., & Hutkins, R. (2018). Fermented foods as a dietary source of live organisms. Frontiers in Microbiology, 9, 1785. Riaz Rajoka, M. S., Shi, J., Mehwish, H. M., Zhu, J., Li, Q., Shao, D., Huang, Q., & Yang, H. (2017). Interaction between diet composition and gut microbiota and its impact on gastrointestinal tract health. Food Science and Human Wellness. https://doi.org/10.1016/j.fshw.2017.07.003. Samuel, B. S., Shaito, A., Motoike, T., Rey, F. E., Backhed, F., Manchester, J. K., Hammer, R. E., Williams, S. C., Crowley, J., Yanagisawa, M., & Gordon, J. I. (2008). Effects of the gut microbiota on host adiposity are modulated by the short-chain fatty-acid binding G protein-coupled receptor, Gpr41. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/ pnas.0808567105. Saxelin, M. (2008). Probiotic formulations and applications, the current probiotics market, and changes in the marketplace: A European perspective. Clinical Infectious Diseases. https://doi. org/10.1086/523337. Sidnell, A. (2008). Essentials of human nutrition. Nutrition Bulletin. https://doi. org/10.1111/j.1467-3010.2008.00698.x. Slavin, J. (2013). Fiber and prebiotics: Mechanisms and health benefits. Nutrients, 5(4), 1417–1435. Sreeja, V., & Prajapati, J.  B. (2013). Probiotic formulations: Application and status as pharmaceuticals-­a review. Probiotics and Antimicrobial Proteins. https://doi.org/10.1007/ s12602-013-9126-2. Sridharan, G. V., Choi, K., Klemashevich, C., Wu, C., Prabakaran, D., Pan, L. B., Steinmeyer, S., Mueller, C., Yousofshahi, M., Alaniz, R. C., Lee, K., & Jayaraman, A. (2014). Prediction and quantification of bioactive microbiota metabolites in the mouse gut. Nature Communications. https://doi.org/10.1038/ncomms6492. Su, P., Henriksson, A., & Mitchell, H. (2007). Prebiotics enhance survival and prolong the retention period of specific probiotic inocula in an in  vivo murine model. Journal of Applied Microbiology. https://doi.org/10.1111/j.1365-2672.2007.03469.x. Topping, D. L., & Clifton, P. M. (2001). Short-chain fatty acids and human colonic function: Roles of resistant starch and nonstarch polysaccharides. Physiological Reviews, 81, 1031–1064. https://doi.org/10.1152/physrev.2001.81.3.1031. Turnbaugh, P. J., Bäckhed, F., Fulton, L., & Gordon, J. I. (2008). Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome. Cell Host & Microbe. https://doi.org/10.1016/j.chom.2008.02.015. Valdes, A. M., Walter, J., Segal, E., & Spector, T. D. (2018). Role of the gut microbiota in nutrition and health. BMJ. https://doi.org/10.1136/bmj.k2179. Zhang, Y. J., Li, S., Gan, R. Y., Zhou, T., Xu, D. P., & Li, H. B. (2015). Impacts of gut bacteria on human health and diseases. International Journal of Molecular Sciences, 16(4), 7493–7519.

Role of the Gut Flora in Human Nutrition and Gut Health Zabdiel Alvarado-Martinez, Stephanie Filho, Megan Mihalik, Rachel Rha, and Michelle Snyder

1  Introduction With the increase in studies revolving around the gut microbiome, more data has emerged establishing the gut microbiome as one of the most important factors for maintaining animal and human health. The roles of the gut microbiome are immensely diverse, but much attention has been placed on how it is involved in the process of digestion and it contributes to host nutrition (Laparra and Sanz 2010). Much research is still being performed in order to understand the exact dynamics that take place between the host and its microbiome, and what the specific outcome of this interaction will be (Hillman et al. 2017). The gut microbiome is composed of a very diverse ecosystem of microbes inhabiting specific regions within the gastrointestinal tract, but it can be greatly influenced by external factors, making the gut microbiome very fluid and diverse. Environmental factors, such as climate, exposure to chemicals, minerals, and pollution, are important to consider, but the food that the host consumes will come into direct contact with the microbes in the gastrointestinal tract, potentially influencing their metabolism and growth. For similar reasons, the microbiome might differ from individual to individual, in terms of the groups of microbes that will be found in specific areas and what their numbers might be. In addition to this, factors intrinsic to the host, such as genetics and

Zabdiel Alvarado-Martinez, Stephanie Filho, Megan Mihalik, Rachel Rha, and Michelle Snyder have contributed equally with all other contributors. Z. Alvarado-Martinez (*) Department of Biology-Molecular and Cellular Biology, University of Maryland, College Park, MD, USA e-mail: [email protected] S. Filho · M. Mihalik · R. Rha · M. Snyder Department of Animal and Avian Sciences, University of Maryland, College Park, MD, USA © Springer Nature Switzerland AG 2020 D. Biswas, S.O. Rahaman (eds.), Gut Microbiome and Its Impact on Health and Diseases, https://doi.org/10.1007/978-3-030-47384-6_5

105

106

Z. Alvarado-Martinez et al.

metabolism, will also have an effect on these microbial populations, how they interact with the host cells, and what effect they will bring about. It is important to mention that when taking into consideration the many variables that will influence the host and its microbiome, finding a universal standard for the optimal ratios of microorganisms that should be in the gut microbiota is very difficult and must take into account many of the external and intrinsic factors that are constantly at play in these systems. However, with the collective knowledge that has been amassed so far, certain parameters have been identified that can be used as general guidelines for promoting a healthy gut microbiome. With these guidelines in mind, certain measures can be put into action by specific individuals in order to bring about the benefits of a balanced gut microbiome (Hemarajata and Versalovic 2013). Also, understanding the different roles that specific groups of microbes have within their community gives important insight into their potential as benefiters to the host and how they reduce the influence of those microbes that might be detrimental to health.

2  M  icrobial Distribution in Gut Health and Nutrient Absorption The process of colonization by the microbes that make up the host’s normal flora commences as early as parturition, when the infant’s body is seeded with microbes from the mother’s flora and from the environment (Milani et al. 2017). This microbial flora will consist of bacteria, fungi, archaea, and viruses, some of which will become indigenous to the host, but may experience changes throughout their lifetime. A great number of the microbial population is found residing in the gastrointestinal tract. Bacteria are the predominant microbe in the GI tract, comprising 1011 microorganisms per gram of wet weight (Wexler 2007). Bacteria make up about 99% of the total microbes, while fungi, archaea, and viruses make up 4000 square feet of surface area. Proteins found on epithelial cells of the adjoining cells of the tract form tight junctions between the cells. This makes a semipermeable barrier that helps the intestinal wall to regulate the transfer of water and solutes to the bloodstream while preventing the entry of unwanted substances inside the cell (Arrieta et al. 2006; Cheadle et al. 2013; Miyoshi and Takai 2005). The term leaky gut is often used to describe the increased permeability of the intestine. When the tight junctions between the intestinal cells begin to break down, pathogens and foreign antigens such as undigested food and microbes “leak” through the wall of the gut (Boyle and Finlay 2005). Pro-inflammatory cytokines TNF-α and interferon-gamma found to be responsible for initiating tight junction disruption which results in compromisation of intestinal barrier function (Bruewer et  al. 2003; Sugi et  al. 2001). Although the “leaky gut” hypothesis is not firmly accepted throughout the medical community as a diagnosis but an increase in the amount of research into the condition has shown a correlation between increased inflammation and increased intestinal permeability. Bloating, food sensitivities, maldigestion, allergies, fatigue, gas, cramping, etc. are some of the acute varying symptoms of leaky gut syndrome (Arrieta et al. 2006). These may only occur after the consumption of certain types of food or when the body is under duress. Leaky gut is hard to diagnosis because the symptoms could be associated with other digestive conditions. The causative agent of intestinal inflammation can vary between individuals but some common sources are diet, alcohol, autoimmune disorders, pathogens and even the genetics of an individual can be a contributing factor (Mu et al. 2017). Any kind of intestinal imbalance can be primarily related to poor or imbalanced diet. Researchers have also agreed that leaky gut has become more prevalent in the United States due to high-fat and low-fiber “western diet” (Campos 2017). Dietary fiber is an important food source for many gut floras. Intake of less fiber affects the diversity and abundance of gut flora leaving the intestinal cell layer more exposed (Zou et al. 2018). Habitual consumption of a large volume of alcohol could disrupt the intestinal tight junction. In the gut, alcohol is metabolized into acetaldehyde by various gram-negative bacteria, as well as by the epithelial cells. A high level of acetaldehyde in the gut has been associated with increased permeability of the gut to endotoxin (lipopolysaccharide) (Ferrier et  al. 2006). A significant presence of endotoxin in the bloodstream causes septic shock. Leaky gut or inflammation of the gut has been related to many chronic enteric disorders, but it is not clearly understood if it is the initial cause of the disease or an unfortunate side effect. Researchers are starting to look at the gut microbiome as a potential contributing factor to chronic metabolic diseases.

138

A. Aditya et al.

2.3.1  Celiac Disease Celiac disease (CD), aka celiac sprue, gluten-sensitive enteropathy, is an autoimmune inflammatory disorder of the digestive tract usually triggered by dietary prolamins in genetically susceptible individuals (HLA-DQ2 and HLA-DQ8 haplotypes). Prolamins are a group of protein consists of gluten, gliadin, secalin, and hordein present in grains like wheat, rye, barley, and oat. Being rich in proline and glutamine residues, gluten activates both innate and adaptive immunity which start the cascade of events that leads to celiac disease (Balakireva and Zamyatnin 2016; Harris et al. 2012; Sanz et al. 2011). In intestinal lamina propria, prolamin peptide is deaminated by tissue transglutaminase (tTG) which is recognized by HLA class II (e.g., HLA DQ2 and HLA DQ8) of antigen-presenting cell (APC). The deaminated peptide is then presented to T cells. The activated T cells release cytokines (e.g., IFN-γ) which further activates macrophages, dendritic cells, and activated macrophage-derived matrix metalloproteinases (MMP). This activation results in the release of inflammatory cytokines, e.g., IL-1β, IL-8, TNF-α, and MCP-1, which can cause atrophy of the villus and increased intestinal permeability (Marasco et  al. 2016; Marsh 1997). The intestinal surface has multiple types of toll-like receptors (TLRs) that can recognize a variety of bacterial products based on pathogen-associated molecular pattern (PAMP) or even specific constituents of grains and exert immunomodulatory effects (Round and Mazmanian 2009). An overexpression of mucosal TLR4 and TLR2 is observed in CD patients which is relatable to dysbiosis and alteration of intestinal barrier function (Szebeni et al. 2007). The gut microbiota contributes to the formation of the vascular structure of villi by increasing epithelial cell proliferation and ensuring its integrity (Ashida et al. 2012; Stappenbeck et al. 2002). A comparative study of the fecal samples of CD patients and the age-matched control group documented a high proportion of Bacteroides, Prevotella, C. histolitycum, C. coccoides, Eubacterium rectal, Atopobium, and sulfate-reducing bacterial groups in CD (Collado et al. 2007). Another group reported the characteristic presence of Lactobacillus curvatus, Leuconostoc mesenteroides, and L. carnosum and a reduction in Bifidobacterium population diversity in CD patients (Marasco et  al. 2016; Sanz et al. 2007). CD patients on a gluten-containing diet showed a higher number of E. coli and Staphylococcus; the number came down to a normal level when those patients were on gluten-free diet (Collado et al. 2009). 2.3.2  Irritable Bowel Syndrome (IBS) Irritable bowel syndrome (IBS) is perceived as a chronic functional disorder resulting in muscular contraction of the colon and associated with a wide range of symptoms mainly periodic abdominal cramp, altered bowel habits, gas, bloating, diarrhea, and constipation (Bertram et al. 2001; Pimentel et al. 2000). About 11% of people around the globe are suffering from IBS with a higher susceptibility in females and younger adults (Lovell and Ford 2012). Certain types of IBS have been reported with constipation-predominant IBS (IBS-C), diarrhea-predominant IBS (IBS-D),

Gut Microbiome in Inflammation and Chronic Enteric Infections

139

mixed IBS, and unclassified IBS (Lacy et  al. 2016). Multiple factors have been reported to be associated with the development of IBS that makes it very difficult to come up with a clear mechanistic pathway. Previous history of enteric infection, immunomodulation, alterations in brain-gut connection, changes in visceral sensation and motility, colonic distension, and most importantly alteration in the gut microflora are thought to be the leading cause of the IBS (Chey et al. 2015; Ghoshal et al. 2012; Parkes et al. 2012; Saulnier et al. 2011). Altered gut flora can trigger changes in gut permeability, motility, visceral perception, and food processing, ultimately resulting in IBS symptoms. A lower prevalence of Bifidobacterium catenulatum in the brushings of duodenal mucosa (Kerckhoffs et al. 2009) and a reduced colonization pattern of Lactobacillus, Bifidobacterium, and Faecalibacterium prausnitzii (Liu et  al. 2017) have been reported in IBS patients as compared to the healthy group. An overexpression of TLRs is observed in IBS patients that may be responsible for an immune response to enteric pathogens. Generally, TLR-4 recognizes LPS of gram-negative bacterium’s outer membrane and signals the secretion of pro-inflammatory cytokines resulting in fever, inflammation, tissue damage, shock, and even death (Jeffery et al. 2012; Shendure and Ji 2008). 2.3.3  Inflammatory Bowel Disease (IBD) Inflammatory bowel disease (IBD) is significantly different from IBS despite several similarities making each uniquely difficult to treat. IBD is a chronic condition resulting in inflammation of the gut. Some common manifestation associated with IBD includes weight loss, bloody diarrhea, and abdominal pain. It can even put the patients at risk of developing colon cancer (Zimmerman 2003). The two types of IBD are ulcerative colitis (UC) and Crohn’s disease (CD). Ulcerative Colitis (UC) Ulcerative colitis (UC) is a chronic inflammatory disorder of the large intestine or colon. The inflammation of the colonic mucus lining results in the formation of tiny open sores or ulcers, which ends in producing pus and mucus. The entire colon or a part of it (descending colon, sigmoid colon, rectum, etc.) can be infected (Cohen et al. 2000). Bloody diarrhea and abdominal pain are most commonly associated with UC (Timmer et al. 2007). UC has a higher annual prevalence rate in Caucasians followed by North Americans than the rest of the world (Logan and Bowlus 2010). This might indicate the association of lifestyle and other environmental factors to the occurrence of UC (Conrad et al. 2014). Although the complete pathogenesis of UC is yet to be elucidated, it can be mediated by genetic susceptibility, dysbiosis, and epigenetic factors (Shen et  al. 2018). The microbial connection to the pathogenesis of UC is a widely debated topic because of the variegated outcomes form the studies that have been conducted.

140

A. Aditya et al.

So far, there is no definitive evidence of any microbial species being the driving force behind the disease (Alipour et al. 2016). However, research has shown that the biodiversity of the gut microbiome is compromised by 25% in UC patients compared with healthy controls (Michail et al. 2012; Shen et al. 2018). The shift between the dominant normal flora and pathogenic microbes remodels their role in host immunity and production of helpful metabolites. Roseburia hominis and F. prausnitzii, two Firmicutes that produce butyrate, a short-chain fatty acid (SCFA), were significantly reduced in UC patients (Machiels et al. 2014). Besides, studies of fecal and tissue microbiome of UC patients demonstrated a significant decline in A. muciniphila, Ruminococcus gnavus, and Butyricicoccus pullicaecorum (Bajer et al. 2017; Duboc et al. 2013; Shang et al. 2017). In addition to the decrease in certain microbes, relocation of normal microbiota from their usual niche, e.g., B. fragilis, to bloodstream and abundance of certain pathogens such as Mycobacterium avium subspecies paratuberculosis, adherent-invasive E. coli (AIEC), C. difficile, Helicobacter spp., Salmonella spp., Yersinia spp., Fusobacterium varium, norovirus, and Listeria spp. have been documented (Ohkusa et al. 2003; Scaldaferri et al. 2013; Shen et al. 2018). This prevalence and paucity of different gut bacterial species lead to different effects on host T-cell differentiation which paves the way to inflammation and ultimately UC. Hence, many researchers reported UC to be caused by the abnormal immune response by the host immune system to the gut microbiota by producing cytokine and inflammatory mediators (Head and Jurenka 2003). LPS-A of some gram-negative bacteria (e.g., B. fragilis) affects the Th1/Th2 ratio that has an effect on the secretion of TNF-α and IL-12 via stimulating NF-κB and TLR2 (Wang et al. 2006). The segmented filamentous bacteria (SFB) help to proliferate regulatory T cells (Treg) and promote IL-22 secretion (Gaboriau-­ Routhiau et al. 2009). SCFA secreted by Clostridium spp. stimulate intestinal epithelial cells to produce TGF-β which confer mucosal immune tolerance (Atarashi et al. 2013). These scenarios in combination with other epigenetic factors may lead to the development of UC. Crohn’s Disease (CD) Crohn’s disease (CD) is the second type of IBD that can be equally debilitating when compared to UC. The inflammation seen in CD patients is spread throughout all layers of the bowel. Depending on the affected area, CD can be divided into several subcategories, namely, ileocolitis (commonly affecting the ileum and colon), ileitis (affecting only the ilium), gastroduodenal Crohn’s disease (affecting the stomach and duodenum), jejunoileitis (patchy areas of inflammation in the jejunum), and Crohn’s (granulomatous) colitis (affecting the colon and anus). Several risk factors have been attributed to CD like smoking, left-handedness, and adult appendectomy. Regular use of oral contraceptive, nonsteroidal anti-inflammatory drugs, and antibiotics also contributes to the development of CD by causing inflammation of the bowl (Head and Jurenka 2004).

Gut Microbiome in Inflammation and Chronic Enteric Infections

141

Several mechanisms of microbial association to CD have been thought for a long time, but a specific responsible agent has never been proved. The mechanisms include alteration of the gut microbiota composition (Darfeuille-Michaud et  al. 1998), intestinal infection resulting from the immune response to a specific pathogen (Balfour Sartor 1997), and a faulty mucosal barrier which is frequently exposed to gut microbiota and their antigens and toxins (Hollander 1986; Ibbotson et  al. 1992). One study suggests that in CD patients, there is a decrease in Faecalibacterium, Christensenellaceae, Methanobrevibacter, and Oscillospira bacteria. It is thought to be responsible for interaction with the immune system in the gut to maintain homeostasis (Pascal et  al. 2017). With the loss of the aforementioned beneficial bacteria, it is thought that Fusobacterium, E. coli, L. monocytogenes, Y. enterocolitica, M. avium subspecies paratuberculosis, measles virus, and other potentially pathogenic microbes could take advantage toward CD (Martin et al. 2004). Like UC, there is no known cure, but therapies can aid in the reduced severity of symptoms and even induce remission. Both forms of IBD discussed are relatively prevalent and common today. Research as to how they develop and why they develop is still ongoing, and specifically, the question of how the gut microbiota is involved is of extreme interest. As more research is done and published, it is only a matter of time before the pathogenesis behind both UC and CD will be deciphered and fully understood.

3  Biotherapeutics for Gut Eubiosis A healthy human gut microbiota contributes to nurturing a synergistic relation among the host, host immune system, and host-microbial community which consists of bacteria, archaea, fungi, protozoa, virus, etc. (Lazar et al. 2018). However, the healthy composition of gut microbiota is continuously influenced by factors like age, antibiotic therapy, altered peristalsis, geographic location, intrinsic host components, irradiation, lifestyle, stress, and most importantly diet (Hawrelak 2004; Shin et al. 2016). There are multiple strategies aimed at restoring/maintaining eubiosis. These strategies include promoting in situ microbial growth through probiotics, prebiotics, and synbiotics; bacteriophage therapy; fecal microbiota transplantation; and bacterial consortium transplantation (Gagliardi et al. 2018). Fecal microbiota transplant (FMT) is quite an old concept. During the fourth century in China, fecal suspensions were used to cure food poisoning. It is being applied sporadically for about 50 years to treat diseases like bacterial dysentery and pseudomembranous colitis (Borody and Khoruts 2012; Lewin 2001). At present, FMT is a promising strategy to treat recurrent C. difficile diarrhea (CDI) that is incurable by standard therapeutic antibiotics (Cammarota et al. 2014; Schwan et al. 1983). In FMT, fresh feces are collected from a healthy donor and blended with saline followed by sieving. The filtrate is inserted into the small intestine of the patient via a tube from either the mouth, nose, or colon (Borody et al. 2013). The idea behind this therapy is that the healthy balanced gut microbiome of the donor

142

A. Aditya et al.

will help to reintroduce some beneficial microbes back to the gut of the recipient. To reduce any associated risk, the donor’s stool is screened carefully for the absence of harmful microbes like Listeria, Vibrio, C. difficile, H. pylori and Giardia antigen, cryptosporidium, isospora, norovirus, hepatitis B and C, Epstein-Barr virus, Campylobacter jejuni, and Blastocystis, HIV 1, 2 (de Vrieze 2013). However, the possibility of transmitting noninfectious diseases, e.g., diabetes, autism, atherosclerosis, and colorectal cancer, is a big concern of FMT (Hota et al. 2019). Besides, infection from the transferred microorganisms in immunocompromised people and possible hypersensitivity reactions in the recipient need to be explored (Gagliardi et al. 2018; Liu et al. 2017; de Vrieze 2013). Due to the undiscovered long-term consequences of FMT, it is yet to be approved by the U.S.  Food and Drug Administration (FDA). Another strategy similar to FMT is known as bacterial consortium transplantation (BCT) which can ameliorate gut dysbiosis in a more controlled and relatively stable way (Li et al. 2015). An artificial combination of 33 precisely characterized bacteria purified from feces was successful to cure recurrent CDI in two patients. They were infected with hypervirulent C. difficile strain (ribotype 078) and failed three vancomycin or metronidazole courses (Petrof et al. 2013). Since the bacteria are accurately characterized, this strategy can be personalized to treat different kinds/levels of dysbiosis with advanced potentiality (Gagliardi et al. 2018; Petrof et al. 2013). Rebuilding the gut ecosystem by the application of probiotics, prebiotics, prebiotic-­like/functional foods, and their combination (aka synbiotics) is being extensively studied. The most common probiotics include multiple species of Lactobacillus (Moal and Servin 2014), Bifidobacterium, Streptococcus, and Lactococcus. Other than these, Saccharomyces boulardii, Bacillus spp., and E. coli strain Nissle 1917 have specific applications to help in curing diarrhea, UC, uncomplicated diverticular disease, etc. (Gagliardi et al. 2018; Gareau et al. 2010). Only a few are autochthonous gut flora, while the majority of these probiotics are acquired from fermented foods (Berg 1996; Gareau et al. 2010; Walter 2008). Probiotics are capable of metabolizing many indigestible dietary components like non-starch polysaccharides and oligosaccharides, collectively known as prebiotics (Macfarlane et al. 2008; Roberfroid 2007). Human diet also contains many prebiotic-like components to promote probiotics and commensal flora growth while suppressing pathogenic proliferation. Multiple studies have reported that phenolic compounds extracted from berry fruits can eliminate the growth of some most common foodborne pathogens (E. coli O157:H7, S. typhimurium, and Campylobacter jejuni) while exerting growth-promoting effect on probiotics and commensal flora in a dose-dependent manner (Aditya et al. 2019; Salaheen et al. 2016; Tabashsum et al. 2018). Another relatively new concept is postbiotics which refers to bioactive metabolites and/or structural components of probiotics which provides beneficial effects to human (Aguilar-Toalá et al. 2018). This idea has the potential in developing personalized probiotics aimed to exert specific functions in the host. According to Peng et  al. (2018), genetically modified strain of linoleic acid overproducing L. casei can inhibit pathogenic E. coli, S. typhimurium, and stimulated

Gut Microbiome in Inflammation and Chronic Enteric Infections

143

anti-inflammatory response in vitro (Peng et al. 2018). Isomers of linoleic acid, i.e., conjugated linoleic acids, also have anticarcinogenic properties (O’Shea et al. 2012). Bacterial viruses or bacteriophages or phages are viruses that infect specific bacteria and utilize their resources and finally lyse that bacteria to proliferate (Lin et al. 2017; White and Orlova 2019). Prior to the era of large-scale antibiotic production, phages showed the enormous potential to treat bacterial infections, centered mostly in the then Soviet Union (d’Herelle 1931). A cocktail of phage containing SP15, SP21, and SP22 reduced E. coli O157:H7 in both in vitro and in vivo models (Tanji et al. 2005). Phage SS is found to be effective in controlling Klebsiella pneumoniae-­ mediated lobar pneumonia in mice (Chhibber et al. 2008). Phages have a vast potential to control foodborne pathogens. Application of phages in the preservation of fermented foods (cheese, yogurt, etc.), meat, fruits, and vegetables is well documented in literature (Leverentz et  al. 2001; Rios et  al. 2016; Viazis et  al. 2011). Phages can reduce the pathogenic microbial load and horizontal bacterial transmissions, such as E. coli, Salmonella spp., P. aeruginosa, C. difficile, and Campylobacter spp. coming from food-producing animals and birds (Andreatti Filho et al. 2007; Carrillo et al. 2005; Huff et al. 2002; McVay et al. 2007; Ramesh et al. 1999; Wills et al. 2005). Although phages were proved to be very promising in some clinical applications, they are not free of risks. Since phages replicate in the host and are released into the gut, they are potentially able to enter the host bloodstream which may elicit an adverse immune response. A very narrow host range of the phages is also a concern (Loc-Carrillo and Abedon 2011). These potential therapies can rebuild an ideal ecosystem that will benefit the host in several ways. It helps to stimulate immune cells such as macrophages, B cells, and T cells to optimize the release of antibodies, cytokines, and other immune mediators. Other benefits involve aid in the digestion process, competition with pathogens for nourishment and receptor proteins, production of bacteriocins, pH change, etc. (Daliri and Lee 2015; Gagliardi et al. 2018). However, any potential risks associated with these strategies are not fully documented yet.

4  Direction for Future Research on the Gut Microbiome Scientists and researchers have started to conclude that the gut microbiome plays a much larger role in the overall function of the body. The interrelationship of the gut microbiome has far-reaching effects on the understanding of why and how dysbiosis occurs and can impact many diseases and disorders throughout the body. With the advancement of molecular and genomic tools in the last 20 years, there is a significant growth in the number of gut microbiome-focused studies. The National Institutes of Health (NIH) Human Microbiome Project (HMP) characterized the microbiota of 300 healthy people to obtain a broad picture of the variations and similarities of the human microflora (NIH Human Microbiome Project 2018). By the year 2024, the human microbiome market will be valued at around $3.2 billion

144

A. Aditya et al.

(Transparency Market Research 2019). Already, there are 796 trials focusing on the microbiome analysis in Pubmed data (NIH Human Microbiome Project 2018). The ongoing study of the gut microbiome could have effects on how researchers and doctors approach various chronic illnesses and autoimmune disorders. Emerging evidences continue to point to the gut microbiome as a source of food allergies and sensitivities. Understanding how the intestinal barrier works and how it can become damaged may explain how allergies arise. This could also lead to a better understanding of autoimmune diseases such as rheumatoid arthritis and lupus (Mudd and Brenchley 2016). This shows the hope to discover cures to today’s untreatable disease in the future.

5  Conclusion As a significant component of the human body, the role of gut microorganisms is becoming more evident in health and diseases. It is already established that they are a convenient source of bioactive metabolites and pharmabiotic molecules. However, it should be noted that because of the lack of human model, the knowledge we have gained so far is primarily based on in  vitro and in  vivo animal model studies. A human body shows diverse response to any perturbation to the gut microbial composition that may be related to variation in the immune system, genetic background, environment, age, intestinal structure, and most importantly the indigenous gut microbial composition (Rolhion and Chassaing 2016) which can lead to many complications ranging from chronic metabolic diseases to neuronal disorders. It is hypothesized that a complete understanding of the history of microbial colonization in humans will help to design effective strategies to maintain eubiosis and prevent many unwanted diseases.

References Aditya, A., Alvarado-Martinez, Z., Nagarajan, V., Peng, M., & Biswas, D. (2019). Antagonistic effects of phenolic extracts of Chokeberry pomace on E. coli O157: H7 but not on probiotic and normal bacterial flora. Journal of Berry Research, 9, 459–472. Aguilar-Toalá, J.  E., Garcia-Varela, R., Garcia, H.  S., Mata-Haro, V., González-Córdova, A.  F., Vallejo-Cordoba, B., & Hernández-Mendoza, A. (2018). Postbiotics: An evolving term within the functional foods field. Trends in Food Science and Technology, 75, 105–114. Akil, L., & Ahmad, H. A. (2011). Relationships between obesity and cardiovascular diseases in four southern states and Colorado. Journal of Health Care for the Poor and Underserved, 22, 61–72. Alipour, M., Zaidi, D., Valcheva, R., Jovel, J., Martínez, I., Sergi, C., Walter, J., Mason, A.  L., Wong, G. K.-S., Dieleman, L. A., et al. (2016). Mucosal barrier depletion and loss of bacterial diversity are primary abnormalities in paediatric ulcerative colitis. Journal of Crohn’s and Colitis, 10, 462–471.

Gut Microbiome in Inflammation and Chronic Enteric Infections

145

Andreatti Filho, R.  L., Higgins, J.  P., Higgins, S.  E., Gaona, G., Wolfenden, A.  D., Tellez, G., & Hargis, B. M. (2007). Ability of bacteriophages isolated from different sources to reduce Salmonella enterica Serovar Enteritidis in vitro and in vivo. Poultry Science, 86, 1904–1909. Arrieta, M. C., Bistritz, L., & Meddings, J. B. (2006). Alterations in intestinal permeability. Gut, 55, 1512–1520. Ashida, H., Ogawa, M., Kim, M., Mimuro, H., & Sasakawa, C. (2012). Bacteria and host interactions in the gut epithelial barrier. Nature Chemical Biology, 8, 36–45. Association, A.D. (2004). Gestational diabetes mellitus. Diabetes Care Alex, 27, S88–S90. Atarashi, K., Tanoue, T., Oshima, K., Suda, W., Nagano, Y., Nishikawa, H., Fukuda, S., Saito, T., Narushima, S., Hase, K., et al. (2013). Treg induction by a rationally selected mixture of Clostridia strains from the human microbiota. Nature, 500, 232–236. Bäckhed, F., Ding, H., Wang, T., Hooper, L.  V., Koh, G.  Y., Nagy, A., Semenkovich, C.  F., & Gordon, J.  I. (2004). The gut microbiota as an environmental factor that regulates fat storage. Proceedings of the National Academy of Sciences of the United States of America, 101, 15718–15723. Bajer, L., Kverka, M., Kostovcik, M., Macinga, P., Dvorak, J., Stehlikova, Z., Brezina, J., Wohl, P., Spicak, J., & Drastich, P. (2017). Distinct gut microbiota profiles in patients with primary sclerosing cholangitis and ulcerative colitis. World Journal of Gastroenterology, 23, 4548–4558. Balakireva, A. V., & Zamyatnin, A. A. (2016). Properties of gluten intolerance: Gluten structure, evolution, pathogenicity and detoxification capabilities. Nutrients, 8, 644. Balfour Sartor, R. (1997). Enteric microflora in IBD: Pathogens or commensals? Inflammatory Bowel Diseases, 3, 230–235. Berg, R. D. (1996). The indigenous gastrointestinal microflora. Trends in Microbiology, 4, 430–435. Bertin, Y., Girardeau, J.  P., Chaucheyras-Durand, F., Lyan, B., Pujos-Guillot, E., Harel, J., & Martin, C. (2011). Enterohaemorrhagic Escherichia coli gains a competitive advantage by using ethanolamine as a nitrogen source in the bovine intestinal content. Environmental Microbiology, 13, 365–377. Bertram, S., Kurland, M., Lydick, E., Locke, G. R. I., & Yawn, B. P. (2001). The Patient’s perspective of irritable bowel syndrome. The Journal of Family Practice, 50, 521. Bornstein, J., & Lawrence, R. D. (1951). Two types of diabetes mellitus, with and without available plasma insulin. British Medical Journal, 1, 732. Borody, T. J., & Khoruts, A. (2012). Fecal microbiota transplantation and emerging applications. Nature Reviews. Gastroenterology & Hepatology, 9, 88–96. Borody, T. J., Paramsothy, S., & Agrawal, G. (2013). Fecal microbiota transplantation: Indications, methods, evidence, and future directions. Current Gastroenterology Reports, 15, 337. Boyle, E.  C., & Finlay, B.  B. (2005). Leaky guts and lipid rafts. Trends in Microbiology, 13, 560–563. Bruewer, M., Luegering, A., Kucharzik, T., Parkos, C.  A., Madara, J.  L., Hopkins, A.  M., & Nusrat, A. (2003). Proinflammatory cytokines disrupt epithelial barrier function by apoptosis-­ independent mechanisms. Journal of Immunology, 171, 6164–6172. Cammarota, G., Ianiro, G., Bibbò, S., & Gasbarrini, A. (2014). Fecal microbiota transplantation: A new old kid on the block for the management of gut microbiota-related disease. Journal of Clinical Gastroenterology, 48, S80–S84. Marcelo Campos (2017). Leaky gut: What is it, and what does it mean for you? Cani, P. D., Amar, J., Iglesias, M. A., Poggi, M., Knauf, C., Bastelica, D., Neyrinck, A. M., Fava, F., Tuohy, K. M., Chabo, C., et al. (2007). Metabolic endotoxemia initiates obesity and insulin resistance. Diabetes, 56, 1761–1772. Cani, P.  D., Delzenne, N.  M., Amar, J., & Burcelin, R. (2008). Role of gut microflora in the development of obesity and insulin resistance following high-fat diet feeding. Pathologie et Biologie, 56, 305–309. Carrillo, C. L., Atterbury, R. J., El-Shibiny, A., Connerton, P. L., Dillon, E., Scott, A., & Connerton, I.  F. (2005). Bacteriophage therapy to reduce campylobacter jejuni colonization of broiler chickens. Applied and Environmental Microbiology, 71, 6554–6563.

146

A. Aditya et al.

Chakraborti, C.  K. (2015). New-found link between microbiota and obesity. World Journal of Gastrointestinal Pathophysiology, 6, 110–119. Chassaing, B., Koren, O., Carvalho, F. A., Ley, R. E., & Gewirtz, A. T. (2014). AIEC pathobiont instigates chronic colitis in susceptible hosts by altering microbiota composition. Gut, 63, 1069–1080. Cheadle, G. A., Costantini, T. W., Lopez, N., Bansal, V., Eliceiri, B. P., & Coimbra, R. (2013). Enteric glia cells attenuate cytomix-induced intestinal epithelial barrier breakdown. PLoS One, 8, e69042. Chey, W. D., Kurlander, J., & Eswaran, S. (2015). Irritable bowel syndrome: A clinical review. JAMA, 313, 949–958. Chhibber, S., Kaur, S., & Kumari, S. (2008). Therapeutic potential of bacteriophage in treating Klebsiella pneumoniae B5055-mediated lobar pneumonia in mice. Journal of Medical Microbiology, 57, 1508–1513. Cohen, R. D., Woseth, D. M., Thisted, R. A., & Hanauer, S. B. (2000). A meta-analysis and overview of the literature on treatment options for left-sided ulcerative colitis and ulcerative proctitis. The American Journal of Gastroenterology, 95, 1263–1276. Collado, M.  C., Calabuig, M., & Sanz, Y. (2007). Differences between the fecal microbiota of coeliac infants and healthy controls. Current Issues in Intestinal Microbiology, 8, 9–14. Collado, M. C., Donat, E., Ribes-Koninckx, C., Calabuig, M., & Sanz, Y. (2009). Specific duodenal and faecal bacterial groups associated with paediatric coeliac disease. Journal of Clinical Pathology, 62, 264–269. Conrad, K., Roggenbuck, D., & Laass, M. W. (2014). Diagnosis and classification of ulcerative colitis. Autoimmunity Reviews, 13, 463–466. d’Herelle, F. (1931). Bacteriophage as a treatment in acute medical and surgical infections. Bulletin of the New York Academy of Medicine, 7, 329–348. Daliri, E. B.-M., & Lee, B. H. (2015). New perspectives on probiotics in health and disease. Food Science and Human Wellness, 4, 56–65. Darfeuille-Michaud, A., Neut, C., Barnich, N., Lederman, E., Di Martino, P., Desreumaux, P., Gambiez, L., Joly, B., Cortot, A., & Colombel, J.-F. (1998). Presence of adherent Escherichia coli strains in ileal mucosa of patients with Crohn’s disease. Gastroenterology, 115, 1405–1413. de Vrieze, J. (2013). The promise of poop. Science, 341, 954–957. Duboc, H., Rajca, S., Rainteau, D., Benarous, D., Maubert, M.-A., Quervain, E., Thomas, G., Barbu, V., Humbert, L., Despras, G., et al. (2013). Connecting dysbiosis, bile-acid dysmetabolism and gut inflammation in inflammatory bowel diseases. Gut, 62, 531–539. Eckburg, P. B., Bik, E. M., Bernstein, C. N., Purdom, E., Dethlefsen, L., Sargent, M., Gill, S. R., Nelson, K.  E., & Relman, D.  A. (2005). Diversity of the human intestinal microbial flora. Science, 308, 1635–1638. Ellekilde, M., Selfjord, E., Larsen, C. S., Jakesevic, M., Rune, I., Tranberg, B., Vogensen, F. K., Nielsen, D. S., Bahl, M. I., Licht, T. R., et al. (2014). Transfer of gut microbiota from lean and obese mice to antibiotic-treated mice. Scientific Reports, 4, 5922. Ferreyra, J.  A., Wu, K.  J., Hryckowian, A.  J., Bouley, D.  M., Weimer, B.  C., & Sonnenburg, J. L. (2014). Gut microbiota-produced succinate Promotes C. difficile infection after antibiotic treatment or motility disturbance. Cell Host & Microbe, 16, 770–777. Ferrier, L., Bérard, F., Debrauwer, L., Chabo, C., Langella, P., Buéno, L., & Fioramonti, J. (2006). Impairment of the intestinal barrier by ethanol involves enteric microflora and mast cell activation in rodents. The American Journal of Pathology, 168, 1148–1154. Gaboriau-Routhiau, V., Rakotobe, S., Lécuyer, E., Mulder, I., Lan, A., Bridonneau, C., Rochet, V., Pisi, A., De Paepe, M., Brandi, G., et al. (2009). The key role of segmented filamentous bacteria in the coordinated maturation of gut helper T cell responses. Immunity, 31, 677–689. Gagliardi, A., Totino, V., Cacciotti, F., Iebba, V., Neroni, B., Bonfiglio, G., Trancassini, M., Passariello, C., Pantanella, F., & Schippa, S. (2018). Rebuilding the gut microbiota ecosystem. International Journal of Environmental Research and Public Health, 15, 1679.

Gut Microbiome in Inflammation and Chronic Enteric Infections

147

Gareau, M.  G., Sherman, P.  M., & Walker, W.  A. (2010). Probiotics and the gut microbiota in intestinal health and disease. Nature Reviews. Gastroenterology & Hepatology, 7, 503–514. Ghoshal, U. C., Shukla, R., Ghoshal, U., Gwee, K.-A., Ng, S. C., & Quigley, E. M. M. (2012). The gut microbiota and irritable bowel syndrome: Friend or foe? International Journal of Inflammation, 2012, 151085. Giel, J. L., Sorg, J. A., Sonenshein, A. L., & Zhu, J. (2010). Metabolism of bile salts in mice influences spore germination in Clostridium difficile. PLoS One, 5, e8740. Hallen-Adams, H.  E., & Suhr, M.  J. (2016). Fungi in the healthy human gastrointestinal tract. Virulence, 8, 352–358. Han, J.-L., and Lin, H.-L. (2014). Intestinal microbiota and type 2 diabetes: from mechanism insights to therapeutic perspective. World J Gastroenterol, 20, 17737–17745. Harris, L. A., Park, J. Y., Voltaggio, L., & Lam-Himlin, D. (2012). Celiac disease: Clinical, endoscopic, and histopathologic review. Gastrointestinal Endoscopy, 76, 625–640. Hawrelak, J.  A. (2004). The causes of intestinal dysbiosis: A review. Alternative Medicine Review, 9, 18. Head, K. A., & Jurenka, J. S. (2003). Inflammatory bowel disease Part 1: Ulcerative colitis–pathophysiology and conventional and alternative treatment options. Alternative Medicine Review – A Journal of Clinical Therapeutics, 8, 247–283. Head, K., & Jurenka, J. S. (2004). Inflammatory bowel disease. Part II: Crohn’s disease–pathophysiology and conventional and alternative treatment options. Alternative Medicine Review – A Journal of Clinical Therapeutics, 9, 360–401. Hollander, D. (1986). Increased intestinal permeability in patients with Crohn’s disease and their relatives: A possible etiologic factor. Annals of Internal Medicine, 105, 883. Hota, S. S., McNamara, I., Jin, R., Kissoon, M., Singh, S., & Poutanen, S. M. (2019). Challenges establishing a multi-purpose fecal microbiota transplantation stool donor program in Toronto, Canada. The Official Journal of the Association of Medical Microbiology and Infectious Disease Canada, 4, 1–9. Hotamisligil, G. S., Shargill, N. S., & Spiegelman, B. M. (1993). Adipose expression of tumor necrosis factor-alpha: Direct role in obesity-linked insulin resistance. Science, 259, 87–91. Huff, W. E., Huff, G. R., Rath, N. C., Balog, J. M., & Donoghue, A. M. (2002). Prevention of Escherichia coli infection in broiler chickens with a bacteriophage aerosol spray. Poultry Science, 81, 1486–1491. Ibbotson, J. P., Lowes, J. R., Chahal, H., Gaston, J. S. H., Life, P., Kumararatne, D. S., Sharif, H., Alexander-Williams, J., & Allan, R. N. (1992). Mucosal cell-mediated immunity to mycobacterial, enterobacterial and other microbial antigens in inflammatory bowel disease. Clinical and Experimental Immunology, 87, 224–230. Jeffery, I. B., O’Toole, P. W., Öhman, L., Claesson, M. J., Deane, J., Quigley, E. M. M., & Simrén, M. (2012). An irritable bowel syndrome subtype defined by species-specific alterations in faecal microbiota. Gut, 61, 997–1006. Joseph, B., Przybilla, K., Stühler, C., Schauer, K., Slaghuis, J., Fuchs, T. M., & Goebel, W. (2006). Identification of Listeria monocytogenes genes contributing to intracellular replication by expression profiling and mutant screening. Journal of Bacteriology, 188, 556–568. Kamdar, K., Khakpour, S., Chen, J., Leone, V., Brulc, J., Mangatu, T., Antonopoulos, D. A., Chang, E. B., Kahn, S. A., Kirschner, B. S., et al. (2016). Genetic and metabolic signals during acute enteric bacterial infection alter the microbiota and drive progression to chronic inflammatory disease. Cell Host & Microbe, 19, 21–31. Kerckhoffs, A.  P., Samsom, M., van der Rest, M.  E., de Vogel, J., Knol, J., Ben-Amor, K., & Akkermans, L. M. (2009). Lower Bifidobacteria counts in both duodenal mucosa-associated and fecal microbiota in irritable bowel syndrome patients. World Journal of Gastroenterology, 15, 2887–2892. Khosravi, Y., Seow, S.  W., Amoyo, A.  A., Chiow, K.  H., Tan, T.  L., Wong, W.  Y., Poh, Q.  H., Sentosa, I. M. D., Bunte, R. M., Pettersson, S., et al. (2015). Helicobacter pylori infection can

148

A. Aditya et al.

affect energy modulating hormones and body weight in germ free mice. Scientific Reports, 5, 8731. Lacy, B. E., Mearin, F., Chang, L., Chey, W. D., Lembo, A. J., Simren, M., & Spiller, R. (2016). Bowel disorders. Gastroenterology, 150, 1393–1407.e5. Lane, J.  A., Murray, L.  J., Harvey, I.  M., Donovan, J.  L., Nair, P., & Harvey, R.  F. (2011). Randomised clinical trial: Helicobacter pylori eradication is associated with a significantly increased body mass index in a placebo-controlled study. Alimentary Pharmacology & Therapeutics, 33, 922–929. Larsen, N., Vogensen, F. K., van den Berg, F. W. J., Nielsen, D. S., Andreasen, A. S., Pedersen, B. K., Al-Soud, W. A., Sørensen, S. J., Hansen, L. H., & Jakobsen, M. (2010). Gut microbiota in human adults with type 2 diabetes differs from non-diabetic adults. PLoS One, 5, e9085. Lazar, V., Ditu, L.-M., Pircalabioru, G.  G., Gheorghe, I., Curutiu, C., Holban, A.  M., Picu, A., Petcu, L., & Chifiriuc, M. C. (2018). Aspects of gut microbiota and immune system interactions in infectious diseases, immunopathology, and cancer. Frontiers in Immunology, 9, 1830. Lender, N., Talley, N. J., Enck, P., Haag, S., Zipfel, S., Morrison, M., & Holtmann, G. J. (2014). Review article: Associations between helicobacter pylori and obesity–An ecological study. Alimentary Pharmacology & Therapeutics, 40, 24–31. Leverentz, B., Conway, W. S., Alavidze, Z., Janisiewicz, W. J., Fuchs, Y., Camp, M. J., Chighladze, E., & Sulakvelidze, A. (2001). Examination of bacteriophage as a biocontrol method for Salmonella on fresh-cut fruit: A model study. Journal of Food Protection, 64, 1116–1121. Lewin, R. A. (2001). More on merde. Perspectives in Biology and Medicine, 44, 594–607. Ley, R.  E., Turnbaugh, P.  J., Klein, S., & Gordon, J.  I. (2006). Microbial ecology: Human gut microbes associated with obesity. Nature, 444, 1022–1023. Li, M., Liang, P., Li, Z., Wang, Y., Zhang, G., Gao, H., Wen, S., & Tang, L. (2015). Fecal microbiota transplantation and bacterial consortium transplantation have comparable effects on the re-establishment of mucosal barrier function in mice with intestinal dysbiosis. Frontiers in Microbiology, 6, 692. Lin, D. M., Koskella, B., & Lin, H. C. (2017). Phage therapy: An alternative to antibiotics in the age of multi-drug resistance. World Journal of Gastrointestinal Pharmacology and Therapeutics, 8, 162–173. Liu, H.-N., Wu, H., Chen, Y.-Z., Chen, Y.-J., Shen, X.-Z., & Liu, T.-T. (2017). Altered molecular signature of intestinal microbiota in irritable bowel syndrome patients compared with healthy controls: A systematic review and meta-analysis. Digestive and Liver Disease, 49, 331–337. Loc-Carrillo, C., & Abedon, S.  T. (2011). Pros and cons of phage therapy. Bacteriophage, 1, 111–114. Logan, I., & Bowlus, C.  L. (2010). The geoepidemiology of autoimmune intestinal diseases. Autoimmunity Reviews, 9, A372–A378. Lovell, R. M., & Ford, A. C. (2012). Global prevalence of and risk factors for irritable bowel syndrome: A meta-analysis. Clinical Gastroenterology and Hepatology, 10, 712–721.e4. Macfarlane, G. T., Steed, H., & Macfarlane, S. (2008). Bacterial metabolism and health-related effects of galacto-oligosaccharides and other prebiotics. Journal of Applied Microbiology, 104, 305–344. Machiels, K., Joossens, M., Sabino, J., De Preter, V., Arijs, I., Eeckhaut, V., Ballet, V., Claes, K., Van Immerseel, F., Verbeke, K., et  al. (2014). A decrease of the butyrate-producing species Roseburia hominis and Faecalibacterium prausnitzii defines dysbiosis in patients with ulcerative colitis. Gut, 63, 1275–1283. Maier, L., Barthel, M., Stecher, B., Maier, R. J., Gunn, J. S., & Hardt, W.-D. (2014). Salmonella typhimurium strain ATCC14028 requires H2-hydrogenases for growth in the gut, but not at systemic sites. PLoS One, 9, e110187. Marasco, G., Di Biase, A. R., Schiumerini, R., Eusebi, L. H., Iughetti, L., Ravaioli, F., Scaioli, E., Colecchia, A., & Festi, D. (2016). Gut microbiota and celiac disease. Digestive Diseases and Sciences, 61, 1461–1472. Marchesi, J. R. (2014). The human microbiota and microbiome. Wallingford: CABI.

Gut Microbiome in Inflammation and Chronic Enteric Infections

149

Marsh, M.  N. (1997). Transglutaminase, gluten and celiac disease: Food for thought. Nature Medicine, 3, 725–726. Martin, H.  M., Campbell, B.  J., Hart, C.  A., Mpofu, C., Nayar, M., Singh, R., Englyst, H., Williams, H. F., & Rhodes, J. M. (2004). Enhanced Escherichia coli adherence and invasion in Crohn’s disease and colon cancer 11The authors thank Professor T. K. Korhonen (Division of General Microbiology, University of Helsinki, Finland), who kindly donated Escherichia coli IH11165; Professor J.-F. Colombel (Laboratoire de Recherche sur les Maladies Inflammatoire de l’Intestine, Centre Hospitalier Universitaire, Lille, France) and Professor A.  Darfeuille-­ Michaud (Faculte de Pharmacie, Clermont-Ferrand, France), who kindly donated the Crohn’s disease ileal isolates LF10 and LF82; and Dr. Keith Leiper (Gastroenterology Unit, Royal Liverpool & Broadgreen University Hospitals Trust, Liverpool, UK) for his cooperation in obtaining colorectal tissue specimens. As a consequence of the work described herein, a patent application has been filed by the University of Liverpool regarding the use of soluble plantain fiber in Crohn’s disease. Gastroenterology, 127, 80–93. McKenney, P. T., & Pamer, E. G. (2015). From hype to hope: The gut microbiota in enteric infectious disease. Cell, 163, 1326–1332. McVay, C.  S., Velásquez, M., & Fralick, J.  A. (2007). Phage therapy of Pseudomonas aeruginosa infection in a mouse burn wound model. Antimicrobial Agents and Chemotherapy, 51, 1934–1938. Michail, S., Durbin, M., Turner, D., Griffiths, A. M., Mack, D. R., Hyams, J., Leleiko, N., Kenche, H., Stolfi, A., & Wine, E. (2012). Alterations in the gut microbiome of children with severe ulcerative colitis. Inflammatory Bowel Diseases, 18, 1799–1808. Mitchell, N. S., Catenacci, V. A., Wyatt, H. R., & Hill, J. O. (2011). Obesity: Overview of an epidemic. The Psychiatric Clinics of North America, 34, 717–732. Miyoshi, J., & Takai, Y. (2005). Molecular perspective on tight-junction assembly and epithelial polarity. Advanced Drug Delivery Reviews, 57, 815–855. Moal, V.  L.-L., & Servin, A.  L. (2014). Anti-infective activities of Lactobacillus strains in the human intestinal microbiota: From probiotics to gastrointestinal anti-infectious biotherapeutic agents. Clinical Microbiology Reviews, 27, 167–199. Mu, Q., Kirby, J., Reilly, C. M., & Luo, X. M. (2017). Leaky gut as a danger signal for autoimmune diseases. Frontiers in Immunology, 8, 598. Mudd, J. C., & Brenchley, J. M. (2016). Gut mucosal barrier dysfunction, microbial dysbiosis, and their role in HIV-1 disease progression. The Journal of Infectious Diseases, 214, S58–S66. Musso, G., Gambino, R., & Cassader, M. (2011). Interactions between gut microbiota and host metabolism predisposing to obesity and diabetes. Annual Review of Medicine, 62, 361–380. Ng, K. M., Ferreyra, J. A., Higginbottom, S. K., Lynch, J. B., Kashyap, P. C., Gopinath, S., Naidu, N., Choudhury, B., Weimer, B.  C., Monack, D.  M., et  al. (2013). Microbiota-liberated host sugars facilitate post-antibiotic expansion of enteric pathogens. Nature, 502, 96–99. NIH Human Microbiome Project (2018). Institute for Genome Sciences, University of Maryland School of Medicine, https://www.hmpdacc.org/overview/ O’Shea, E. F., Cotter, P. D., Stanton, C., Ross, R. P., & Hill, C. (2012). Production of bioactive substances by intestinal bacteria as a basis for explaining probiotic mechanisms: Bacteriocins and conjugated linoleic acid. International Journal of Food Microbiology, 152, 189–205. Ohkusa, T., Okayasu, I., Ogihara, T., Morita, K., Ogawa, M., & Sato, N. (2003). Induction of experimental ulcerative colitis by Fusobacterium varium isolated from colonic mucosa of patients with ulcerative colitis. Gut, 52, 79–83. Parkes, G. C., Rayment, N. B., Hudspith, B. N., Petrovska, L., Lomer, M. C., Brostoff, J., Whelan, K., & Sanderson, J. D. (2012). Distinct microbial populations exist in the mucosa-associated microbiota of sub-groups of irritable bowel syndrome. Neurogastroenterology and Motility, 24, 31–39. Pascal, V., Pozuelo, M., Borruel, N., Casellas, F., Campos, D., Santiago, A., Martinez, X., Varela, E., Sarrabayrouse, G., Machiels, K., et al. (2017). A microbial signature for Crohn’s disease. Gut, 66, 813–822.

150

A. Aditya et al.

Peng, M., Tabashsum, Z., Patel, P., Bernhardt, C., & Biswas, D. (2018). Linoleic acids overproducing Lactobacillus casei limits growth, survival, and virulence of Salmonella typhimurium and Enterohaemorrhagic Escherichia coli. Frontiers in Microbiology, 9, 2663. Petriz, B. A., Castro, A. P., Almeida, J. A., Gomes, C. P., Fernandes, G. R., Kruger, R. H., Pereira, R. W., & Franco, O. L. (2014). Exercise induction of gut microbiota modifications in obese, non-obese and hypertensive rats. BMC Genomics, 15, 511. Petrof, E. O., Gloor, G. B., Vanner, S. J., Weese, S. J., Carter, D., Daigneault, M. C., Brown, E. M., Schroeter, K., & Allen-Vercoe, E. (2013). Stool substitute transplant therapy for the eradication of Clostridium difficile infection: ‘RePOOPulating’ the gut. Microbiome, 1, 3. Pimentel, M., Chow, E. J., & Lin, H. C. (2000). Eradication of small intestinal bacterial overgrowth reduces symptoms of irritable bowel syndrome. The American Journal of Gastroenterology, 95, 3503–3506. Qin, J., Li, Y., Cai, Z., Li, S., Zhu, J., Zhang, F., Liang, S., Zhang, W., Guan, Y., Shen, D., et al. (2012). A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature, 490, 55–60. Ramesh, V., Fralick, J.  A., & Rolfe, R.  D. (1999). Prevention of Clostridium difficile -induced ileocecitis with bacteriophage. Anaerobe, 5, 69–78. Rastelli, M., Knauf, C., & Cani, P. D. (2018). Gut microbes and health: A focus on the mechanisms linking microbes, obesity, and related disorders. Obesity, 26, 792–800. Rios, A. C., Moutinho, C. G., Pinto, F. C., Del Fiol, F. S., Jozala, A., Chaud, M. V., Vila, M. M. D. C., Teixeira, J. A., & Balcão, V. M. (2016). Alternatives to overcoming bacterial resistances: State-­ of-­the-art. Microbiological Research, 191, 51–80. Roberfroid, M. (2007). Prebiotics: The concept revisited. The Journal of Nutrition, 137, 830S–837S. Rolhion, N., & Chassaing, B. (2016). When pathogenic bacteria meet the intestinal microbiota. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 371, 20150504. Round, J. L., & Mazmanian, S. K. (2009). The gut microbiota shapes intestinal immune responses during health and disease. Nature Reviews. Immunology, 9, 313–323. Salaheen, S., Jaiswal, E., Joo, J., Peng, M., Ho, R., OConnor, D., Adlerz, K., Aranda-Espinoza, J. H., & Biswas, D. (2016). Bioactive extracts from berry byproducts on the pathogenicity of Salmonella typhimurium. International Journal of Food Microbiology, 237, 128–135. Santacruz, A., Collado, M. C., García-Valdés, L., Segura, M. T., Martín-Lagos, J. A., Anjos, T., Martí-Romero, M., Lopez, R. M., Florido, J., Campoy, C., et al. (2010). Gut microbiota composition is associated with body weight, weight gain and biochemical parameters in pregnant women. The British Journal of Nutrition, 104, 83–92. Sanz, Y., Sánchez, E., Marzotto, M., Calabuig, M., Torriani, S., & Dellaglio, F. (2007). Differences in faecal bacterial communities in coeliac and healthy children as detected by PCR and denaturing gradient gel electrophoresis. FEMS Immunology and Medical Microbiology, 51, 562–568. Sanz, Y., Palma, G. D., & Laparra, M. (2011). Unraveling the ties between celiac disease and intestinal microbiota. International Reviews of Immunology, 30, 207–218. Sato, J., Kanazawa, A., Ikeda, F., Yoshihara, T., Goto, H., Abe, H., Komiya, K., Kawaguchi, M., Shimizu, T., Ogihara, T., et al. (2014). Gut dysbiosis and detection of “live gut bacteria” in blood of Japanese patients with type 2 diabetes. Diabetes Care, 37(8), 2343–2350. Saulnier, D. M., Riehle, K., Mistretta, T., Diaz, M., Mandal, D., Raza, S., Weidler, E. M., Qin, X., Coarfa, C., Milosavljevic, A., et al. (2011). Gastrointestinal microbiome signatures of pediatric patients with irritable bowel syndrome. Gastroenterology, 141, 1782–1791. Savage, D.  C. (1977). Microbial ecology of the gastrointestinal tract. Annual Review of Microbiology, 31, 107–133. Scaldaferri, F., Gerardi, V., Lopetuso, L. R., Del Zompo, F., Mangiola, F., Boškoski, I., Bruno, G., Petito, V., Laterza, L., Cammarota, G., et al. (2013). Gut microbial flora, prebiotics, and probiotics in IBD: Their current usage and utility. BioMed Research International, 2013, 435268. Schwan, A., Sjolin, S., Trottestam, U., & Aronsson, B. (1983). Relapsing clostridium difficile enterocolitis cured by rectal infusion of homologous faeces. The Lancet, 322, 845.

Gut Microbiome in Inflammation and Chronic Enteric Infections

151

Sekirov, I., & Finlay, B. B. (2009). The role of the intestinal microbiota in enteric infection. The Journal of Physiology, 587, 4159–4167. Shang, Q., Sun, W., Shan, X., Jiang, H., Cai, C., Hao, J., Li, G., & Yu, G. (2017). Carrageenan-­ induced colitis is associated with decreased population of anti-inflammatory bacterium, Akkermansia muciniphila, in the gut microbiota of C57BL/6J mice. Toxicology Letters, 279, 87–95. Shen, Z.-H., Zhu, C.-X., Quan, Y.-S., Yang, Z.-Y., Wu, S., Luo, W.-W., Tan, B., & Wang, X.-Y. (2018). Relationship between intestinal microbiota and ulcerative colitis: Mechanisms and clinical application of probiotics and fecal microbiota transplantation. World Journal of Gastroenterology, 24, 5–14. Shendure, J., & Ji, H. (2008). Next-generation DNA sequencing. Nature Biotechnology, 26, 1135–1145. Shin, J.-H., Sim, M., Lee, J.-Y., & Shin, D.-M. (2016). Lifestyle and geographic insights into the distinct gut microbiota in elderly women from two different geographic locations. Journal of Physiological Anthropology, 35, 31. Stappenbeck, T. S., Hooper, L. V., & Gordon, J. I. (2002). Developmental regulation of intestinal angiogenesis by indigenous microbes via Paneth cells. Proceedings of the National Academy of Sciences of the United States of America, 99, 15451–15455. Sugi, K., Musch, M. W., Chang, E. B., & Field, M. (2001). Inhibition of Na+,K+-ATPase by interferon γ down-regulates intestinal epithelial transport and barrier function. Gastroenterology, 120, 1393–1403. Szebeni, B., Veres, G., Dezsofi, A., Rusai, K., Vannay, A., Bokodi, G., Vásárhelyi, B., Korponay-­ Szabó, I. R., Tulassay, T., & Arató, A. (2007). Increased mucosal expression of Toll-like receptor (TLR)2 and TLR4 in coeliac disease. Journal of Pediatric Gastroenterology and Nutrition, 45, 187–193. Tabashsum, Z., Peng, M., Salaheen, S., Comis, C., & Biswas, D. (2018). Competitive elimination and virulence property alteration of Campylobacter jejuni by genetically engineered Lactobacillus casei. Food Control, 85, 283–291. Tanji, Y., Shimada, T., Fukudomi, H., Miyanaga, K., Nakai, Y., & Unno, H. (2005). Therapeutic use of phage cocktail for controlling Escherichia coli O157:H7 in gastrointestinal tract of mice. Journal of Bioscience and Bioengineering, 100, 280–287. Thiennimitr, P., Winter, S.  E., Winter, M.  G., Xavier, M.  N., Tolstikov, V., Huseby, D.  L., Sterzenbach, T., Tsolis, R. M., Roth, J. R., & Bäumler, A. J. (2011). Intestinal inflammation allows Salmonella to use ethanolamine to compete with the microbiota. Proceedings of the National Academy of Sciences, 108, 17480–17485. Timmer, A., McDonald, J. W., & MacDonald, J. K. (2007). Azathioprine and 6-mercaptopurine for maintenance of remission in ulcerative colitis. Cochrane Database of Systematic Reviews. https://doi.org/10.1002/14651858.CD000478.pub2. Transparency Market Research (TMR) (2019). Published on Apr 8, 2019, ­https://www.transparencymarketresearch.com/pressrelease/human-microbiome-market.htm Viazis, S., Akhtar, M., Feirtag, J., & Diez-Gonzalez, F. (2011). Reduction of Escherichia coli O157:H7 viability on leafy green vegetables by treatment with a bacteriophage mixture and trans-cinnamaldehyde. Food Microbiology, 28, 149–157. Walter, J. (2008). Ecological role of lactobacilli in the gastrointestinal tract: Implications for fundamental and biomedical research. Applied and Environmental Microbiology, 74, 4985–4996. Wang, Q., McLoughlin, R. M., Cobb, B. A., Charrel-Dennis, M., Zaleski, K. J., Golenbock, D., Tzianabos, A. O., & Kasper, D. L. (2006). A bacterial carbohydrate links innate and adaptive responses through Toll-like receptor 2. The Journal of Experimental Medicine, 203, 2853–2863. Weisberg, S. P., McCann, D., Desai, M., Rosenbaum, M., Leibel, R. L., & Ferrante, A. W. (2003). Obesity is associated with macrophage accumulation in adipose tissue. The Journal of Clinical Investigation, 112, 1796–1808. Wellen, K. E., & Hotamisligil, G. S. (2005). Inflammation, stress, and diabetes. The Journal of Clinical Investigation, 115, 1111–1119.

152

A. Aditya et al.

White, H. E., & Orlova, E. V. (2019). Bacteriophages: Their structural organisation and function. In R. Savva (Ed.), Bacteriophages: Perspect and future. London: IntechOpen. Wills, Q. F., Kerrigan, C., & Soothill, J. S. (2005). Experimental bacteriophage protection against Staphylococcus aureus abscesses in a rabbit model. Antimicrobial Agents and Chemotherapy, 49, 1220–1221. Yoo, S.-R., Kim, Y.-J., Park, D.-Y., Jung, U.-J., Jeon, S.-M., Ahn, Y.-T., Huh, C.-S., McGregor, R., & Choi, M. S. (2013). Probiotics L. plantarum and L. curvatus in combination alter hepatic lipid metabolism and suppress diet-induced obesity. Obesity (Silver Spring Md), 21, 2571–2578. Zhang, X., Shen, D., Fang, Z., Jie, Z., Qiu, X., Zhang, C., Chen, Y., & Ji, L. (2013). Human gut microbiota changes reveal the progression of glucose intolerance. PLoS One, 8, e71108. Zimmerman, J. (2003). Extraintestinal symptoms in irritable bowel syndrome and inflammatory bowel diseases: Nature, severity, and relationship to gastrointestinal symptoms. Digestive Diseases and Sciences, 48, 743–749. Zou, J., Chassaing, B., Singh, V., Pellizzon, M., Ricci, M., Fythe, M. D., Kumar, M. V., & Gewirtz, A. T. (2018). Fiber-mediated nourishment of gut microbiota protects against diet-induced obesity by restoring IL-22-mediated colonic health. Cell Host & Microbe, 23, 41–53.e4.

Role of Gut Microbiome in Colorectal Cancer Xiaolun Sun

1  Epidemiology of CRC Although the large intestine only makes up about 20% of the length of the digestive tract and 6% of its mucosal surface area (Helander and Fandriks 2014), colorectal cancer (CRC) is the number one cancer diagnosed in gastrointestinal (GI) tract and accounts for more than 44% of new cases of GI cancers in the United States (USA) (Siegel et  al. 2019). Fortunately, with widespread colonoscopy screening and advancement of research, age-adjusted rate of new CRC cases had consistently declined from 56 per 100,000 population in 1999 to 38 per 100,000 population in 2015 (CDC 2019), although total case counts were mildly reduced from 150,014 in 1999 to 140,788 in 2015 (Fig. 1a). Consistently, age-adjusted rate of CRC death had consistently dropped from 21 per 100,000 population in 1999 to 14 per 100,000 population in 2015, although total case counts were mildly reduced from 57,222 in 1999 to 52,396 in 2015 (Fig. 1b). As a result, colorectal cancer is the third-most common cause of all cancers in both men and women and is the second leading cause of cancer-related deaths in the USA (Siegel et al. 2019). Hence, there remains a long way to go to dramatically reduce CRC new cases and death rates, and it is a matter of urgency to investigate the underlying mechanism of CRC and to discover new therapeutic approaches.

X. Sun (*) Center of Excellence for Poultry Science, University of Arkansas, Fayetteville, AR, USA e-mail: [email protected] © Springer Nature Switzerland AG 2020 D. Biswas, S.O. Rahaman (eds.), Gut Microbiome and Its Impact on Health and Diseases, https://doi.org/10.1007/978-3-030-47384-6_7

153

154

X. Sun

Fig. 1  Age-adjusted CRC new cases and deaths during 1999–2015. (a) Rates of the new cases of and deaths from CRC in the United States. (b) Total counts of new cases of and deaths from CRC

Fig. 2  Sequential molecular and cellular events in CRC. Mutations and dysregulation of the genes and molecular signaling pathways lead to cellular transformation and translocation and CRC initiation and progression

2  Etiopathogenetic Factors of CRC The progress of CRC follows sequential genetic mutations acquired over the course of many years, a process known as the adenoma–carcinoma sequence. This process leads to a defined progression of histological, genetic, and epigenetic alterations, resulting in changes of the morphology and function of the epithelial and the surrounding stroma tissues (Fig. 2). Adenomas often begin mutations in the intestinal epithelial stem cells of Wnt signaling pathway molecules, such as adenomatous polyposis coli (APC) or catenin beta 1 (CTNNB1), leading to hyperactivation of Wnt signaling in early adenomas (Jones et al. 2008). Deregulation of Wnt signaling is often followed with mutations in MAPK signaling of Kirsten rat sarcoma viral oncogene homolog or proto-oncogene and GTPase (KRAS), B-Raf proto-oncogene, serine/threonine kinase (BRAF), neuroblastoma RAS viral oncogene homolog (NRAS), Erb-B2 receptor tyrosine kinase 3 (ERBB3), and ERBB2 (Colussi et  al. 2013). Additional mutations of mothers against decapentaplegic homolog family member 4 (SMAD4) are followed with the activation of the phosphatidylinositol-­4,5-­ bisphosphate 3-kinase (PI3K)-Akt signaling cascade of phosphatase and tensin

Role of Gut Microbiome in Colorectal Cancer

155

homolog (PTEN) and PI3K catalytic subunit alpha (PI3KCA) (Danielsen et  al. 2015). The tumors then experience mutation of transforming growth factor beta (TGF-β) signaling with activation of TGF-β receptor 2 (TGFBR2) and the tumors frequently acquire genomic instability (Bellam and Pasche 2010). Lastly, mutation in tumor protein p53 (TP53) is associated with later stages of cellular transformation and with invasive characteristics of adenocarcinomas (Li et al. 2015). A number of genetic and environmental factors contribute to the initiation and progression of CRC, including hereditary elements, familial history, inflammation, and microbiome. The incidence of CRC is generally classified as sporadic, hereditary, familial, and inflammatory bowel disease (IBD)-related CRC (Fig. 3). Genetic disorders of familial adenomatous polyposis (FAP), mutY homolog (MYH)associated polyposis (MAP), and Lynch syndrome (hereditary nonpolyposis colorectal cancer [HNPCC]) are the most common of the heredity CRC.  These genetic mutations are inherited in an autosomal fashion and associated with a very high risk of developing colon cancer. FAP, MAP, and Lynch syndrome together account for approximately 5–6% of CRC cases (Lynch and de la Chapelle 2003). Classic FAP results from a germline mutation of autosomal dominant form in the APC gene. The incidence of FAP at birth is about one in 8300 in males and females, and accounts for less than 1% of CRC cases (Half et al. 2009). Germline mutations in one of several DNA mismatch repair (MMR) genes are responsible for Lynch syndrome (Lynch and Krush 1971). The four most commonly mutated DNA mismatch repair genes are mutL homolog 1 (MLH1), MutS Homolog 2 (MSH2), MSH6, or mismatch repair system component homolog 2 (PMS2). In a clinical study with 1058 participants who received CRC care, Yurgelun and colleagues reported that 9.9% of them carried one or more pathogenic mutations with 3.1% of them Lynch Syndrome (Yurgelun et al. 2017). In this study, 23 participants

Fig. 3  Types of CRC

156

X. Sun

(2.2%) inherited mutations in high-penetrance genes (5 APC, 5 biallelic MUTYH, 11 BRCA1/2, 2 PALB2, 1 CDKN2A, and 1 TP53), 15 of whom failed to show clinical histories of the underlying mutations. In addition, 3.6% of the participants had moderate-penetrance CRC risk gene mutations (19 monoallelic MUTYH, 17 APC I1307K, 2 CHEK2). IBD is regarded as one of the important risk factors for CRC. IBD is the third highest risk factor for CRC, behind only FAP and Lynch Syndrome (Kulaylat and Dayton 2010). It is well known that the extent, duration, and activity of chronic ulcerative colitis have a strong association with CRC (Jess et al. 2006). In fact, CRC is a serious complication of IBD and accounts for 10–15% of all deaths in IBD patients (Munkholm 2003). Pancolitis patients have a 5- to 15-fold increased risk of developing CRC compared to the expected incidence in the general population, whereas colitis limited to the left side is associated with approximately a 3-fold increased risk (Ekbom et al. 1990). Interestingly, in a Denmark cohort study between 1962 and 1987, only 13 cases of CRC were reported among 1160 patients with ulcerative colitis, followed up for 22,290 persons per year, yielding an annual risk of 0.06% (Winther et al. 2004). The 30-year cumulative CRC risk was 2.1%. The relatively low rate of CRC in these IBD patients may reflect the fact of controlled ulcerative colitis in the patients. In contrast to the risk of CRC comprehensively investigated in ulcerative colitis patients, the risk of CRC in Crohn’s disease patients remains less explored. As with the risk of CRC in ulcerative colitis, studies on risk of intestinal cancer in Crohn’s disease patients have revealed inconsistent results with a variation in reported relative risk estimates from 0.8% to 20% (Canavan et al. 2006). The risk of CRC cancer was significantly increased in Crohn’s disease patients with colonic involvement, nonstatistically increased in patients with ileocolonic Crohn’s disease, and not increased in Crohn’s disease patients with pure ileal disease. As many as 20–25% of CRC patients carry one or more genetic mutations of non-Lynch syndrome or FAP, have a family or personal history of CRC, or adenomatous polyps of the colon (Armelao and de Pretis 2014). Individuals having personal history of CRC or colorectal adenomatous polyps are at higher risk of developing CRC in the future. Among patients with resection of a single CRC, 1.5–3% patients develop metachronous primary cancers in the first 5 years postoperatively. In addition, individuals with a single affected first-degree relative (parent, sibling, or child) of CRC are at about twofold increased risk compared to the general population (Tuohy et al. 2014). In a study with a total of 2,327,327 individuals (10,556 CRC patients), risk of developing CRC is increased if two first-, or one first- and one or more first- or second-degree relatives on either side of the family are diagnosed with colon cancer, or if the index case is diagnosed below 50 years of age (Taylor et al. 2010). The majority of CRC diseases are sporadic ones ranging from 50% to 60%. Many factors are involved in sporadic CRC, such as abdominal radiation, obesity, diabetes, tobacco, alcohol, red and processed meat, physical activities, etc. The risk of secondary CRC is increased in adult patients who had childhood malignancy and who received abdominal radiation. In a study with a median follow-up of 22.8 years,

Role of Gut Microbiome in Colorectal Cancer

157

the risk of colorectal cancer was 4.2 standardized incidence ratios (Henderson et al. 2012). In addition to abdominal radiation, high dose of procarbazine and platinum drugs independently increase the risk of gastrointestinal neoplasm. Obesity is also a risk factor for CRC and obesity increases the likelihood of dying from CRC.  A meta-analysis of prospective studies found that the highest weight gain category, measured by weight/body mass index, compared with a reference category, was associated with increased risk of CRC (hazard ratio [HR] 1.16) (Karahalios et al. 2015). Diabetes mellitus is associated with an elevated risk of CRC at 20–38% higher compared to nondiabetics (Yuhara et al. 2011). Cigarette smoking has been associated with increased incidence and mortality (HR 1.25) from CRC compared to nonsmokers (Botteri et al. 2008). In addition, alcohol consumption is associated with an increased risk of CRC. In a meta-analysis study, risk of CRC is increased for heavy (≥4 drinks per day) and moderate drinkers (2–3 drinks per day), but not light drinkers (≤1 drink per day) compared with never drinkers (Fedirko et  al. 2011). In 2015, the World Health Organization’s International Agency for Research on Cancer conducted a meta-analysis study on the association of intake of red and processed meat with CRC development (Bouvard et al. 2015). In the study, a significant dose response between meat consumption and CRC risk was observed with a 17% increased risk if consuming 100 g red meat per day, and 18% increase in risk if consuming 50 g processed meat per day. Finally, regular physical activity, either occupational or leisure time, is associated with protection against CRC. In a meta-­ analysis study, the risk of proximal and distal colon cancer is 26–27% lower among the most physically active people compared with the least active people (Boyle et al. 2012). The mechanism underlying the protective association of physical activity remains elusive and more intervention trials of physical activity against CRC are much needed.

3  Tumor-Associated Microbiome A complex community of trillions of microbes resides in the GI tract, including bacteria, archaea, virus, and eukarya. These microbes (microbiota) along with their metabolic activities and products are often referred to as the microbiome (Sun and Jia 2018). The healthy adult human microbiota consists of thousands of prokaryotic species and 12 different phyla, and 93.5% of phyla are Bacteroidetes, Firmicutes, Proteobacteria, and Actinobacteria (Hugon et  al. 2015) at relative abundance of 36–43%, 32–48%, 3–7%, and 1–7%, respectively (Koliada et  al. 2017; Mendez-­ Salazar et al. 2018). Various clinical studies have demonstrated microbiota composition changes in CRC patients. Based on a clustering method using Pearson correlation coefficients of relative abundance of operational taxonomic units in mucosal microbiota, the abundance of Bacteroidetes Cluster 1 (e.g., genus Barnesiella) and Firmicutes Cluster 1 (e.g., Blautia) was decreased in CRC mucosa, whereas the abundance of Bacteroidetes Cluster 2 (e.g., Parasutterella), Firmicutes Cluster 2 (e.g., Faecalibacterium), Pathogen Cluster (e.g., Peptostreptococcus), and

158

X. Sun

Prevotella Cluster (e.g., Clostridium_sensu_stricto) was increased in CRC mucosa (Flemer et al. 2017). There is a fungal dysbiosis in colon polyps and CRC, showing as decreased diversity in polyp patients and an increased Ascomycota/Basidiomycota ratio, and an increased proportion of opportunistic fungi Trichosporon and Malassezia (Gao et al. 2017). In another study, Hibberd and colleagues reported that tumor microbiota was associated with increased microbial diversity and enrichment of several taxa including Fusobacterium, Selenomonas, and Peptostreptococcus compared with the control microbiota (Hibberd et al. 2017). Hence, specific members of microbiota appear more important in CRC development compared to microbiota diversity. Specific members of microbiota are recently found to be associated with CRC. A meta-analysis of fecal metagenomes identified a core set of 29 species in significant association with CRC, including Fusobacterium nucleatum s. animalis, Parvimonas micra, Gemella morbillorum, Peptostreptococcus stomatis, unknown Dialister, unknown Porphyromonas, Solobacterium moorei, Clostridium symbiosum, Porphyromonas uenonis, unknown Clostridiales, Hungatella hathewayi, Prevotella intermedia, Porphyromonas somerae, Porphyromonas asaccharolytica, Fusobacterium nucleatum s. nucleatum, Parvimonas sp., Prevotella nigrescens, unknown Porphyromonas, Ruminococcus torques, Fusobacterium nucleatum s. vincentii, Fusobacterium sp. oral taxon 370, unknown Peptostreptococcaceae, Anaerococcus obesiensis/vaginalis, unknown Anaerotruncus, Porphyromonas uenonis, unknown Clostridiales, unknown Porphyromonas, Clostridium bolteae/ clostridioforme, Subdoligranulum sp. (Wirbel et  al. 2019). Fusobacterium is enriched in the microbiota of colorectal carcinoma (Kostic et al. 2012). The microbiota of CRC patients show a lower relative abundance of Clostridia and increased carriage of Fusobacterium and Porphyromonas compared to control subjects (Ahn et al. 2013). F. nucleatum abundance is increased in tumor tissue of both high-grade dysplasia and established CRC, whereas patients with low F. nucleatum levels are associated with overall longer survival time (Flanagan et  al. 2014). Moderate to high levels of relative abundance of F. nucleatum are associated with poorer survival in CRC patients (Mima et al. 2016). F. nucleatum is a gram-negative anaerobe typically implicated in periodontal disease. Several mechanisms of F. nucleatum in the pathogenesis of CRC have been proposed, including bacterial attachment, invasion of host cells, and modulation of pro- or anti-inflammatory response. F. nucleatum virulence factor FadA facilitates attachment and invasion of intestinal epithelial cells, and FadA differentially regulates inflammatory and oncogenic responses through binding to E-cadherin and activating β-catenin signaling (Rubinstein et  al. 2013). F. nucleatum potentiates intestinal tumorigenesis and modulates the tumor-immune microenvironment without exacerbating colitis, enteritis, or inflammation-associated intestinal carcinogenesis (Kostic et  al. 2013). Fap2 protein from F. nucleatum interacts with T-cell immunoreceptor with Ig and ITIM domains (TIGIT) on NK and T cells, leading to the inhibition of NK cell cytotoxicity to tumors and tumor-infiltrating lymphocyte activation (Gur et al. 2015). Diets promoting intestinal inflammation based on an empiric dietary inflammatory pattern (EDIP) score are associated with increased

Role of Gut Microbiome in Colorectal Cancer

159

possibility of F nucleatum-positive colorectal carcinomas, but not carcinomas without the bacterium (Liu et al. 2018). Sulfidogenic bacteria such as F. nucleatum produce hydrogen sulfide which is a genotoxic compound that has been shown to damage DNA, leading to genomic or chromosomal instability (Attene-Ramos et al. 2006); however, the direct association between F. nucleatum, hydrogen sulfide, and CRC initiation and progression remains unclear. APCmin/+ mice infected with F nucleatum developed more colorectal tumors and lived shorter compared with control mice given PBS (Yang et al. 2017). Consistent with tumor development, several inflammatory factors of IL17F, IL21, IL22, and MIP3A are increased in serum from mice infected with F. nucleatum. Bacteroides fragilis is a commensal anaerobic bacterium residing in the human intestine. There are two molecular subtypes of nontoxigenic and enterotoxigenic B. fragilis. The enterotoxigenic strain Enterotoxigenic B. fragilis (ETBF) expresses toxin BFT (gene bft), and induces diarrheal illness (Sears 2009). BFT binds to membrane-­associated E-cadherin, triggers beta-catenin nuclear localization, activates c-Myc, and induces cell proliferation in human colonic epithelial HT19 cells (Wu et al. 2003). The enterotoxin gene (bft) is detected by PCR in 38% of the stool isolates from CRC cancer patients compared with 12% of the isolates from the control group (Toprak et al. 2006). ETBF induces immune cell infiltration of an IL-17-­ driven myelopoiesis in favor of generation of protumoral monocytic MDSCs and exacerbates colon tumorigenesis in MinApc+/− mice (Thiele Orberg et al. 2017). Commensal bacterium E. coli is often associated with CRC. E. coli comprises a group of gut bacteria and some strains carry pks island and colibactin which have oncogenic potential and the possibility to cause intestinal inflammation (Cuevas-­ Ramos et al. 2010). CRC tumor tissues carry increased levels of mucosa-associated and -internalized E. coli compared with normal tissue (Bonnet et al. 2014). Poor prognostic factors for colon cancer are associated with colonization of mucosa by E. coli. Animal CRC model using mono-colonized Il10−/− mice shows that pks is indispensable for colonic tumor development (Arthur et  al. 2012). Colibactin-­ expressing E. coli enhances tumor growth in both xenograft and AOM/DSS models, and the tumor growth is sustained by cellular senescence (a direct consequence of small ubiquitin-like modifier-conjugated p53 accumulation) and is accompanied by the production of hepatocyte growth factor (Cougnoux et al. 2014). In a metagenomic study, a number of Bacteroides and Parabacteroides species, along with Alistipes putredinis, Bilophila wadsworthia, Lachnospiraceae bacterium, and E. coli are enriched in carcinoma samples compared with both healthy and advanced adenoma samples (Feng et al. 2015). It remains largely unclear how most of the tumor-associated bacteria promote intestinal tumorigenesis, although a number of virulence factors have been identified. Recently, the role of microbiota on intestinal metabolomics is gaining traction. Dietary carbohydrate utilization is dominant in a healthy gut microbiome, while amino acid degradation is prominent in CRC microbiome (Zeller et al. 2014). The increased capacity for amino acid degradation is mostly mediated by CRC-­ associated Clostridiales (Wirbel et  al. 2019). Concentrations of amino acids by GC-MS profiling are higher in stool samples from CRC patients, while poly and

160

X. Sun

monounsaturated fatty acids and ursodeoxycholic acid are higher in stool samples from healthy adults (Weir et al. 2013). The amino acid metabolism in CRC metabolome is consistent with established CRC dietary risk factors of consuming red and processed meat consumption and low fiber intake (Aykan 2015). Meta-analysis of the metagenome on microbiome functional potential finds that CRC is associated with microbial gluconeogenesis and the putrefaction and fermentation pathways, whereas the stachyose and starch degradation pathways are associated with healthy controls (Thomas et  al. 2019). In addition, pooled analysis of raw metagenomes identifies increased abundance of the choline trimethylamine-lyase gene in CRC, suggesting increased choline metabolism.

4  Microbiome Against CRC Currently, the majority of microbiome and CRC researches focus on identifying CRC-genic/associated bacteria in the above-mentioned literatures. The main composition of microbiota is, in fact, neutral or possibly protective. For instance, only 29 CRC-associated bacteria have been found (Wirbel et al. 2019) compared to thousands of bacteria in a colon microbiota. Indeed, microbiota utilizing carbohydrate (Wirbel et al. 2019) or with stachyose and starch degradation (Thomas et al. 2019) are enriched in healthy control subjects compared to those in CRC patients. Bacteroides genus possesses very broad saccharolytic potential and some strains are able to metabolize dozens of different complex glycans (Salyers et al. 1977). High proportions of Firmicutes are recovered from human colonic bacteria attached to wheat bran, resistant starch, and mucin in a fermentor system (Leitch et al. 2007). Ruminococcus sp., Clostridium sp., Eubacterium sp., and Bacteroides sp. from human feces have been identified with cellulolytic capacity (Chassard et al. 2010; Wedekind et  al. 1988). Faecalibacterium prausnitzii, Eubacterium rectale, and Ruminococcus bromii have been found to be involved in resistant starch metabolism (Cockburn et al. 2015; Khan et al. 2012; Ze et al. 2012). It remains elusive that the phenome of the enriched carbohydrate-metabolizing bacteria in healthy individual colon is an association or a “cause-result.” The microbiota from CRC patients administered probiotics of Bifidobacterium lactis Bl-04 and Lactobacillus acidophilus NCFM showed increased abundance of butyrate-­ producing bacteria, especially Faecalibacterium and Clostridiales spp., while CRC-­ associated genera such as Fusobacterium and Peptostreptococcus tend to be reduced in the fecal microbiota (Hibberd et  al. 2017). The results suggest that beneficial microbiota may promote protection against CRC.  A clinical study found that Faecalibacterium prausnitzii and Roseburia hominis, butyrate-producing bacteria of the Firmicutes phylum, are at low abundance in ulcerative colitis patients (Machiels et al. 2014). Lower levels of total F. prausnitzii are found in subjects with Crohn’s disease, ulcerative colitis, and CRC (Lopez-Siles et al. 2016). F. prausnitzii strain A2-165 elicits high amounts of IL-10 secretion, upregulates ovalbumin-­ specific T-cell proliferation, and reduces the number of IFN-γ-positive T cells to

Role of Gut Microbiome in Colorectal Cancer

161

yield anti-inflammatory effects (Rossi et  al. 2016). However, it requires active investigation to answer whether P. prausnitzii is a very promising beneficial gut microbiota against inflammatory diseases and CRC. To increase or maintain beneficial microbiota population, prebiotic is often used. In a study with elderly patients, ingesting a probiotic mixture of Bifidobacterium bifidum and B. lactis, including prebiotic of inulin or fructo-oligosaccharides, enhances the survival of the probiotic bifidobacteria and increases numbers of native bifidobacterial populations (Bartosch et al. 2005).

5  Conclusion As one of the prevalent neoplasm diseases, CRC poses a severe threat to the well-­ being of millions around the world. Hereditary elements, familial history, inflammation, and microbiome are among the risk factors contributing to CRC development on intestinal epithelial cell genetic instability. Accumulating knowledge indicates the association of increased bacterial members (dysbiosis) in CRC patients. The dysbiosis microbiota express virulence factors, disrupt host cellular genetic stability, and/or exacerbate intestinal inflammation, resulting in tumor initiation and progression. Increasing investigations have found that beneficial microbiota act against the detrimental actions of dysbiosis. More research is needed to discover additional beneficial microbiota and their metabolites against intestinal inflammation and CRC. Conflict of Interest  The author declares no conflict of interest. Grant Support  This research was supported by grants of Arkansas Biosciences Institute, USDA National Institute of Food and Agriculture (NIFA) Hatch project 1012366, USDA NIFA Hatch/Multi State project 1018699, USDA NIFA projects 2020-67016-31346 and 2019-69012-29905 to X. Sun. The funders had no role in study design, data collection, and analysis, decision to publish, or preparation of the chapter.

References Ahn, J., Sinha, R., Pei, Z., Dominianni, C., Wu, J., Shi, J., Goedert, J. J., Hayes, R. B., & Yang, L. (2013). Human gut microbiome and risk for colorectal cancer. Journal of the National Cancer Institute, 105, 1907–1911. Armelao, F., & de Pretis, G. (2014). Familial colorectal cancer: a review. World Journal of Gastroenterology, 20, 9292–9298. Arthur, J.  C., Perez-Chanona, E., Muhlbauer, M., Tomkovich, S., Uronis, J.  M., Fan, T.  J., Campbell, B. J., Abujamel, T., Dogan, B., Rogers, A. B., et al. (2012). Intestinal inflammation targets cancer-inducing activity of the microbiota. Science, 338, 120–123.

162

X. Sun

Attene-Ramos, M. S., Wagner, E. D., Plewa, M. J., & Gaskins, H. R. (2006). Evidence that hydrogen sulfide is a genotoxic agent. Molecular Cancer Research, 4, 9–14. Aykan, N. F. (2015). Red Meat and Colorectal Cancer. Oncology Reviews, 9, 288. Bartosch, S., Woodmansey, E. J., Paterson, J. C., McMurdo, M. E., & Macfarlane, G. T. (2005). Microbiological effects of consuming a synbiotic containing Bifidobacterium bifidum, Bifidobacterium lactis, and oligofructose in elderly persons, determined by real-time polymerase chain reaction and counting of viable bacteria. Clinical Infectious Diseases : An Official Publication of the Infectious Diseases Society of America, 40, 28–37. Bellam, N., & Pasche, B. (2010). Tgf-beta signaling alterations and colon cancer. Cancer Treatment and Research, 155, 85–103. Bonnet, M., Buc, E., Sauvanet, P., Darcha, C., Dubois, D., Pereira, B., Dechelotte, P., Bonnet, R., Pezet, D., & Darfeuille-Michaud, A. (2014). Colonization of the human gut by E. coli and colorectal cancer risk. Clinical Cancer Research, 20, 859–867. Botteri, E., Iodice, S., Bagnardi, V., Raimondi, S., Lowenfels, A. B., & Maisonneuve, P. (2008). Smoking and colorectal cancer: a meta-analysis. JAMA, 300, 2765–2778. Bouvard, V., Loomis, D., Guyton, K. Z., Grosse, Y., Ghissassi, F. E., Benbrahim-Tallaa, L., Guha, N., Mattock, H., Straif, K., & International Agency for Research on Cancer Monograph Working, G. (2015). Carcinogenicity of consumption of red and processed meat. The Lancet Oncology, 16, 1599–1600. Boyle, T., Keegel, T., Bull, F., Heyworth, J., & Fritschi, L. (2012). Physical activity and risks of proximal and distal colon cancers: a systematic review and meta-analysis. Journal of the National Cancer Institute, 104, 1548–1561. Canavan, C., Abrams, K. R., & Mayberry, J. (2006). Meta-analysis: colorectal and small bowel cancer risk in patients with Crohn's disease. Alimentary Pharmacology & Therapeutics, 23, 1097–1104. CDC. (2019). Changes over time: All types of cancer (Centers for Disease Control and Prevention. https://gis.cdc.gov/Cancer/USCS/DataViz.html). Chassard, C., Delmas, E., Robert, C., & Bernalier-Donadille, A. (2010). The cellulose-degrading microbial community of the human gut varies according to the presence or absence of methanogens. FEMS Microbiology Ecology, 74, 205–213. Cockburn, D. W., Orlovsky, N. I., Foley, M. H., Kwiatkowski, K. J., Bahr, C. M., Maynard, M., Demeler, B., & Koropatkin, N. M. (2015). Molecular details of a starch utilization pathway in the human gut symbiont Eubacterium rectale. Molecular Microbiology, 95, 209–230. Colussi, D., Brandi, G., Bazzoli, F., & Ricciardiello, L. (2013). Molecular pathways involved in colorectal cancer: implications for disease behavior and prevention. International Journal of Molecular Sciences, 14, 16365–16385. Cougnoux, A., Dalmasso, G., Martinez, R., Buc, E., Delmas, J., Gibold, L., Sauvanet, P., Darcha, C., Dechelotte, P., Bonnet, M., et  al. (2014). Bacterial genotoxin colibactin promotes colon tumour growth by inducing a senescence-associated secretory phenotype. Gut, 63, 1932–1942. Cuevas-Ramos, G., Petit, C. R., Marcq, I., Boury, M., Oswald, E., & Nougayrede, J. P. (2010). Escherichia coli induces DNA damage in vivo and triggers genomic instability in mammalian cells. Proceedings of the National Academy of Sciences of the United States of America, 107, 11537–11542. Danielsen, S. A., Eide, P. W., Nesbakken, A., Guren, T., Leithe, E., & Lothe, R. A. (2015). Portrait of the PI3K/AKT pathway in colorectal cancer. Biochimica et Biophysica Acta, 1855, 104–121. Ekbom, A., Helmick, C., Zack, M., & Adami, H. O. (1990). Ulcerative colitis and colorectal cancer. A population-based study. The New England Journal of Medicine, 323, 1228–1233. Fedirko, V., Tramacere, I., Bagnardi, V., Rota, M., Scotti, L., Islami, F., Negri, E., Straif, K., Romieu, I., La Vecchia, C., et al. (2011). Alcohol drinking and colorectal cancer risk: an overall and dose-response meta-analysis of published studies. Annals of Oncology, 22, 1958–1972. Feng, Q., Liang, S., Jia, H., Stadlmayr, A., Tang, L., Lan, Z., Zhang, D., Xia, H., Xu, X., Jie, Z., et al. (2015). Gut microbiome development along the colorectal adenoma-carcinoma sequence. Nature Communications, 6, 6528.

Role of Gut Microbiome in Colorectal Cancer

163

Flanagan, L., Schmid, J., Ebert, M., Soucek, P., Kunicka, T., Liska, V., Bruha, J., Neary, P., Dezeeuw, N., Tommasino, M., et al. (2014). Fusobacterium nucleatum associates with stages of colorectal neoplasia development, colorectal cancer and disease outcome. European Journal of Clinical Microbiology & Infectious Diseases, 33, 1381–1390. Flemer, B., Lynch, D. B., Brown, J. M., Jeffery, I. B., Ryan, F. J., Claesson, M. J., O'Riordain, M., Shanahan, F., & O'Toole, P. W. (2017). Tumour-associated and non-tumour-associated microbiota in colorectal cancer. Gut, 66, 633–643. Gao, R., Kong, C., Li, H., Huang, L., Qu, X., Qin, N., & Qin, H. (2017). Dysbiosis signature of mycobiota in colon polyp and colorectal cancer. European Journal of Clinical Microbiology & Infectious Diseases, 36, 2457–2468. Gur, C., Ibrahim, Y., Isaacson, B., Yamin, R., Abed, J., Gamliel, M., Enk, J., Bar-On, Y., Stanietsky-Kaynan, N., Coppenhagen-Glazer, S., et al. (2015). Binding of the Fap2 protein of Fusobacterium nucleatum to human inhibitory receptor TIGIT protects tumors from immune cell attack. Immunity, 42, 344–355. Half, E., Bercovich, D., & Rozen, P. (2009). Familial adenomatous polyposis. Orphanet Journal of Rare Diseases, 4, 22. Helander, H. F., & Fandriks, L. (2014). Surface area of the digestive tract - revisited. Scandinavian Journal of Gastroenterology, 49, 681–689. Henderson, T. O., Oeffinger, K. C., Whitton, J., Leisenring, W., Neglia, J., Meadows, A., Crotty, C., Rubin, D. T., Diller, L., Inskip, P., et al. (2012). Secondary gastrointestinal cancer in childhood cancer survivors: a cohort study. Annals of Internal Medicine, 156, 757–766, W-260. Hibberd, A. A., Lyra, A., Ouwehand, A. C., Rolny, P., Lindegren, H., Cedgard, L., & Wettergren, Y. (2017). Intestinal microbiota is altered in patients with colon cancer and modified by probiotic intervention. BMJ Open Gastroenterology, 4, e000145. Hugon, P., Dufour, J. C., Colson, P., Fournier, P. E., Sallah, K., & Raoult, D. (2015). A comprehensive repertoire of prokaryotic species identified in human beings. The Lancet Infectious Diseases, 15, 1211–1219. Jess, T., Loftus, E. V., Jr., Velayos, F. S., Harmsen, W. S., Zinsmeister, A. R., Smyrk, T. C., Schleck, C. D., Tremaine, W. J., Melton, L. J., 3rd, Munkholm, P., et al. (2006). Risk of intestinal cancer in inflammatory bowel disease: a population-based study from olmsted county, Minnesota. Gastroenterology, 130, 1039–1046. Jones, S., Chen, W. D., Parmigiani, G., Diehl, F., Beerenwinkel, N., Antal, T., Traulsen, A., Nowak, M.  A., Siegel, C., Velculescu, V.  E., et  al. (2008). Comparative lesion sequencing provides insights into tumor evolution. Proceedings of the National Academy of Sciences of the United States of America, 105, 4283–4288. Karahalios, A., English, D. R., & Simpson, J. A. (2015). Weight change and risk of colorectal cancer: a systematic review and meta-analysis. American Journal of Epidemiology, 181, 832–845. Khan, M. T., Duncan, S. H., Stams, A. J., van Dijl, J. M., Flint, H. J., & Harmsen, H. J. (2012). The gut anaerobe Faecalibacterium prausnitzii uses an extracellular electron shuttle to grow at oxic-anoxic interphases. The ISME Journal, 6, 1578–1585. Koliada, A., Syzenko, G., Moseiko, V., Budovska, L., Puchkov, K., Perederiy, V., Gavalko, Y., Dorofeyev, A., Romanenko, M., Tkach, S., et al. (2017). Association between body mass index and Firmicutes/Bacteroidetes ratio in an adult Ukrainian population. BMC Microbiology, 17, 120. Kostic, A. D., Gevers, D., Pedamallu, C. S., Michaud, M., Duke, F., Earl, A. M., Ojesina, A. I., Jung, J., Bass, A.  J., Tabernero, J., et  al. (2012). Genomic analysis identifies association of Fusobacterium with colorectal carcinoma. Genome Research, 22, 292–298. Kostic, A.  D., Chun, E., Robertson, L., Glickman, J.  N., Gallini, C.  A., Michaud, M., Clancy, T. E., Chung, D. C., Lochhead, P., Hold, G. L., et al. (2013). Fusobacterium nucleatum potentiates intestinal tumorigenesis and modulates the tumor-immune microenvironment. Cell Host & Microbe, 14, 207–215. Kulaylat, M.  N., & Dayton, M.  T. (2010). Ulcerative colitis and cancer. Journal of Surgical Oncology, 101, 706–712.

164

X. Sun

Leitch, E. C., Walker, A. W., Duncan, S. H., Holtrop, G., & Flint, H. J. (2007). Selective colonization of insoluble substrates by human faecal bacteria. Environmental Microbiology, 9, 667–679. Li, X.  L., Zhou, J., Chen, Z.  R., & Chng, W.  J. (2015). P53 mutations in colorectal cancer  molecular pathogenesis and pharmacological reactivation. World Journal of Gastroenterology, 21, 84–93. Liu, L., Tabung, F.  K., Zhang, X., Nowak, J.  A., Qian, Z.  R., Hamada, T., Nevo, D., Bullman, S., Mima, K., Kosumi, K., et al. (2018). Diets That Promote Colon Inflammation Associate With Risk of Colorectal Carcinomas That Contain Fusobacterium nucleatum. Clinical Gastroenterology and Hepatology, 16(1622–1631), e1623. Lopez-Siles, M., Martinez-Medina, M., Suris-Valls, R., Aldeguer, X., Sabat-Mir, M., Duncan, S. H., Flint, H. J., & Garcia-Gil, L. J. (2016). Changes in the Abundance of Faecalibacterium prausnitzii Phylogroups I and II in the Intestinal Mucosa of Inflammatory Bowel Disease and Patients with Colorectal Cancer. Inflammatory Bowel Diseases, 22, 28–41. Lynch, H. T., & de la Chapelle, A. (2003). Hereditary colorectal cancer. The New England Journal of Medicine, 348, 919–932. Lynch, H.  T., & Krush, A.  J. (1971). Cancer family "G" revisited: 1895-1970. Cancer, 27, 1505–1511. Machiels, K., Joossens, M., Sabino, J., De Preter, V., Arijs, I., Eeckhaut, V., Ballet, V., Claes, K., Van Immerseel, F., Verbeke, K., et  al. (2014). A decrease of the butyrate-producing species Roseburia hominis and Faecalibacterium prausnitzii defines dysbiosis in patients with ulcerative colitis. Gut, 63, 1275–1283. Mendez-Salazar, E. O., Ortiz-Lopez, M. G., Granados-Silvestre, M. L. A., Palacios-Gonzalez, B., & Menjivar, M. (2018). Altered Gut Microbiota and Compositional Changes in Firmicutes and Proteobacteria in Mexican Undernourished and Obese Children. Frontiers in Microbiology, 9, 2494. Mima, K., Nishihara, R., Qian, Z. R., Cao, Y., Sukawa, Y., Nowak, J. A., Yang, J., Dou, R., Masugi, Y., Song, M., et al. (2016). Fusobacterium nucleatum in colorectal carcinoma tissue and patient prognosis. Gut, 65, 1973–1980. Munkholm, P. (2003). Review article: the incidence and prevalence of colorectal cancer in inflammatory bowel disease. Alimentary Pharmacology & Therapeutics, 18(Suppl 2), 1–5. Rossi, O., van Berkel, L. A., Chain, F., Tanweer Khan, M., Taverne, N., Sokol, H., Duncan, S. H., Flint, H. J., Harmsen, H. J., Langella, P., et al. (2016). Faecalibacterium prausnitzii A2-165 has a high capacity to induce IL-10 in human and murine dendritic cells and modulates T cell responses. Scientific Reports, 6, 18507. Rubinstein, M.  R., Wang, X., Liu, W., Hao, Y., Cai, G., & Han, Y.  W. (2013). Fusobacterium nucleatum promotes colorectal carcinogenesis by modulating E-cadherin/beta-catenin signaling via its FadA adhesin. Cell Host & Microbe, 14, 195–206. Salyers, A. A., West, S. E., Vercellotti, J. R., & Wilkins, T. D. (1977). Fermentation of mucins and plant polysaccharides by anaerobic bacteria from the human colon. Applied and Environmental Microbiology, 34, 529–533. Sears, C.  L. (2009). Enterotoxigenic Bacteroides fragilis: a rogue among symbiotes. Clinical Microbiology Reviews, 22, 349–369, Table of Contents. Siegel, R. L., Miller, K. D., & Jemal, A. (2019). Cancer statistics, 2019. CA: a Cancer Journal for Clinicians, 69, 7–34. Sun, X., & Jia, Z. (2018). Microbiome modulates intestinal homeostasis against inflammatory diseases. Veterinary Immunology and Immunopathology, 205, 97–105. Taylor, D.  P., Burt, R.  W., Williams, M.  S., Haug, P.  J., & Cannon-Albright, L.  A. (2010). Population-based family history-specific risks for colorectal cancer: a constellation approach. Gastroenterology, 138, 877–885. Thiele Orberg, E., Fan, H., Tam, A. J., Dejea, C. M., Destefano Shields, C. E., Wu, S., Chung, L., Finard, B. B., Wu, X., Fathi, P., et al. (2017). The myeloid immune signature of enterotoxigenic Bacteroides fragilis-induced murine colon tumorigenesis. Mucosal Immunology, 10, 421–433.

Role of Gut Microbiome in Colorectal Cancer

165

Thomas, A. M., Manghi, P., Asnicar, F., Pasolli, E., Armanini, F., Zolfo, M., Beghini, F., Manara, S., Karcher, N., Pozzi, C., et al. (2019). Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation. Nature Medicine, 25, 667–678. Toprak, N. U., Yagci, A., Gulluoglu, B. M., Akin, M. L., Demirkalem, P., Celenk, T., & Soyletir, G. (2006). A possible role of Bacteroides fragilis enterotoxin in the aetiology of colorectal cancer. Clinical Microbiology and Infection : The Official Publication of the European Society of Clinical Microbiology and Infectious Diseases, 12, 782–786. Tuohy, T. M., Rowe, K. G., Mineau, G. P., Pimentel, R., Burt, R. W., & Samadder, N. J. (2014). Risk of colorectal cancer and adenomas in the families of patients with adenomas: a population-­ based study in Utah. Cancer, 120, 35–42. Wedekind, K.  J., Mansfield, H.  R., & Montgomery, L. (1988). Enumeration and isolation of cellulolytic and hemicellulolytic bacteria from human feces. Applied and Environmental Microbiology, 54, 1530–1535. Weir, T. L., Manter, D. K., Sheflin, A. M., Barnett, B. A., Heuberger, A. L., & Ryan, E. P. (2013). Stool microbiome and metabolome differences between colorectal cancer patients and healthy adults. PLoS One, 8, e70803. Winther, K. V., Jess, T., Langholz, E., Munkholm, P., & Binder, V. (2004). Long-term risk of cancer in ulcerative colitis: a population-based cohort study from Copenhagen County. Clinical Gastroenterology and Hepatology, 2, 1088–1095. Wirbel, J., Pyl, P. T., Kartal, E., Zych, K., Kashani, A., Milanese, A., Fleck, J. S., Voigt, A. Y., Palleja, A., Ponnudurai, R., et al. (2019). Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer. Nature Medicine, 25, 679–689. Wu, S., Morin, P. J., Maouyo, D., & Sears, C. L. (2003). Bacteroides fragilis enterotoxin induces c-Myc expression and cellular proliferation. Gastroenterology, 124, 392–400. Yang, Y., Weng, W., Peng, J., Hong, L., Yang, L., Toiyama, Y., Gao, R., Liu, M., Yin, M., Pan, C., et  al. (2017). Fusobacterium nucleatum Increases Proliferation of Colorectal Cancer Cells and Tumor Development in Mice by Activating Toll-Like Receptor 4 Signaling to Nuclear Factor-kappaB, and Up-regulating Expression of MicroRNA-21. Gastroenterology, 152(851–866), e824. Yuhara, H., Steinmaus, C., Cohen, S. E., Corley, D. A., Tei, Y., & Buffler, P. A. (2011). Is diabetes mellitus an independent risk factor for colon cancer and rectal cancer? The American Journal of Gastroenterology, 106, 1911–1921; quiz 1922. Yurgelun, M. B., Kulke, M. H., Fuchs, C. S., Allen, B. A., Uno, H., Hornick, J. L., Ukaegbu, C. I., Brais, L. K., McNamara, P. G., Mayer, R. J., et al. (2017). Cancer Susceptibility Gene Mutations in Individuals With Colorectal Cancer. Journal of Clinical Oncology, 35, 1086–1095. Ze, X., Duncan, S. H., Louis, P., & Flint, H. J. (2012). Ruminococcus bromii is a keystone species for the degradation of resistant starch in the human colon. The ISME Journal, 6, 1535–1543. Zeller, G., Tap, J., Voigt, A. Y., Sunagawa, S., Kultima, J. R., Costea, P. I., Amiot, A., Bohm, J., Brunetti, F., Habermann, N., et al. (2014). Potential of fecal microbiota for early-stage detection of colorectal cancer. Molecular Systems Biology, 10, 766.

Gut Microbiota and Risk for Atherosclerosis: Current Understanding of the Mechanisms Bidisha Dutta, Chitrine Biswas, Rakesh K. Arya, and Shaik O. Rahaman

1  Introduction The human gut is inhabited by a plethora of commensal and symbiont microorganisms essential for the normal functioning of the host (Aron-Wisnewsky et al. 2012; Bäckhed et al. 2004; Cani et al. 2012; Cox and Blaser 2013; den Besten et al. 2013; Le Chatelier et al. 2013; Nicholson et al. 2005; Tremaroli and Bäckhed 2012). The colonization of the gut by a consortium of bacteria, archaea, fungi, viruses, and other protozoans, collectively termed the gut microbiota, is the result of a coevolutionary process that has occurred over many million years (Aron-Wisnewsky et al. 2012; Bäckhed et al. 2004; Cani et al. 2012; Cox and Blaser 2013; den Besten et al. 2013; Le Chatelier et al. 2013; Nicholson et al. 2005; Tremaroli and Bäckhed 2012). These organisms derive nutrition from the host, help the host in the digestion of complex carbohydrates, fine-tune the immune system, maintain metabolic and energy homeostasis, provide protection against opportunist pathogens, and even aid in neurodevelopment (Aron-Wisnewsky et al. 2012; Bäckhed et al. 2004; Cani et al. 2012; Cox and Blaser 2013; den Besten et  al. 2013; Le Chatelier et  al. 2013; Nicholson et al. 2005; Tremaroli and Bäckhed 2012). Interestingly, the gut, which is sterile before birth, acquires the early colonizers through maternal physical contact at the time of delivery (Palmer et al. 2007; Dominguez-Bello et al. 2010). Out of the trillions of microorganisms the intestine harbors, most are obligate anaerobes whose composition varies along the digestive tract (Aron-Wisnewsky et al. 2012; Fouhy et al. 2012). The development of high throughput sequencing (HTS) studies and bioinformatic tools has been revolutionary in elucidating the interindividual differences in the composition of gut microbiota based on age, sex, genetic makeup, and environmental influences (Fouhy et  al. 2012; Li et  al. 2014; Parkhill 2013; Santiago et  al. 2014). Various state-of-the-art approaches such as screening for B. Dutta · C. Biswas · R. K. Arya · S. O. Rahaman (*) University of Maryland, Department of Nutrition and Food Science, College Park, MD, USA e-mail: [email protected] © Springer Nature Switzerland AG 2020 D. Biswas, S.O. Rahaman (eds.), Gut Microbiome and Its Impact on Health and Diseases, https://doi.org/10.1007/978-3-030-47384-6_8

167

168

B. Dutta et al.

metabolites derived from the microbiota, metatranscriptomics, and metaproteomics provide the means to harness large datasets to better understand the gut microbiome and its association with atherosclerosis (Nicholson et al. 2005; Gosalbes et al. 2011, 2012; Kolmeder et al. 2012). Results from HTS-based studies have established that the adult gut microbiota is dominated by the bacterial phyla Bacteroides and Firmicutes but includes other phyla such as Actinobacteria, Fusobacteria, Verrucomicrobia, and Proteobacteria. (Tremaroli and Bäckhed 2012; Eckburg et al. 2005). Dysbiosis, an imbalance in the proportions of bacterial groups in the microbiota, contributes to the pathogenesis of various diseases like irritable bowel syndrome, ulcerative colitis, metabolic syndrome, type-2 diabetes, obesity, hypertension, and cardiovascular diseases (CVDs) (Aron-Wisnewsky et al. 2012; Bäckhed et al. 2004; Cani et al. 2012; Cox and Blaser 2013; den Besten et al. 2013; Le Chatelier et al. 2013; Nicholson et al. 2005; Tremaroli and Bäckhed 2012). Atherosclerosis, a progressive chronic inflammatory disease, is the primary cause of cerebral and myocardial infarction, coronary artery disease, and loss of function of the extremities (Lusis 2000; Moore and Tabas 2011; Moore et al. 2013; McLaren et al. 2011; Collot-Teixeira et al. 2007; Falk et al. 2013). The pathogenic process consists of slowly progressing fibro-fatty lesion formation, aortic tissue inflammation, and luminal narrowing of the arteries (Lusis 2000; Moore and Tabas 2011; Moore et al. 2013; McLaren et al. 2011; Collot-Teixeira et al. 2007; Falk et al. 2013). The earliest recognizable injuries to the artery wall associated with atherosclerosis are endothelial dysfunction and structural alterations that result in the trapping of modified/oxidized lipoprotein particles in the artery (Lusis 2000; Moore and Tabas 2011; Moore et al. 2013; McLaren et al. 2011; Collot-Teixeira et al. 2007; Falk et al. 2013). The injured endothelium also expresses specific adhesion proteins such as vascular cell adhesion molecule (VCAM-1), intercellular adhesion molecule (ICAM-1), and selectin-E that facilitate transmigration of monocytes and T lymphocytes into the intimal layer of the artery under the influence of various cytokines (Lusis 2000; Moore and Tabas 2011; Moore et al. 2013; McLaren et al. 2011; Collot-Teixeira et al. 2007; Falk et al. 2013). As the process continues, the monocytes differentiate into tissue macrophages and upregulate the expression of scavenger receptors (SRs) like SR-A and CD36 (Lusis 2000; Moore and Tabas 2011; Moore et  al. 2013; McLaren et  al. 2011; Collot-Teixeira et  al. 2007; Falk et  al. 2013). The accelerated uptake of oxidized/modified lipoproteins by the macrophages, aided by scavenger receptors, leads to the generation of foam cells, a critical process in atherogenesis (Lusis 2000; Moore and Tabas 2011; Moore et al. 2013; McLaren et al. 2011; Collot-Teixeira et al. 2007; Falk et al. 2013). T lymphocytes and macrophages exacerbate the production of inflammatory cytokines, which in turn, activate smooth muscle cells to proliferate and to secrete extracellular matrix thus forming atherosclerotic plaque (Lusis 2000; Moore and Tabas 2011; Moore et  al. 2013; McLaren et  al. 2011; Collot-Teixeira et  al. 2007; Falk et  al. 2013). Vulnerable plaques formed by the degradation of smooth muscle cells undergo frequent rupture and lead to thrombus formation, increasing the risk of cerebral stroke and myocardial infarction (Lusis 2000; Moore and Tabas 2011; Moore et al. 2013; McLaren et al. 2011; Collot-Teixeira et al. 2007; Falk et al. 2013). Atherosclerosis

Gut Microbiota and Risk for Atherosclerosis: Current Understanding of the Mechanisms

169

is a disease of complex etiology involving both inflammatory and metabolic pathways that have recently been shown to be modulated by the gut microbiota. Microbiota-dependent development of atherosclerosis is complex, and involves inflammation induced by infection, microbial metabolites, and altered host lipid metabolism. Here, we discuss the data supporting the role of gut microbiota in atherogenesis and its associated risk factors.

2  Role of Gut Microbiota in Obesity and Lipid Metabolism Obesity is a consequence of an imbalance between energy expenditure and intake. The incidence of obesity and its associated disorders such as type-2 diabetes and atherosclerosis have increased epidemically worldwide over the last few decades (Ortega et  al. 2016; Gregor and Hotamisligil 2011; Kallus and Brandt 2012; Turnbaugh et al. 2006; Gómez-Ambrosi et al. 2011). Although sedentary lifestyle and increased food intake are implicated as the primary underlying cause of the disease, recent studies point to the intricate interplay between nutritional, physiological, genetic, social, and environmental factors (Ortega et al. 2016; Gregor and Hotamisligil 2011; Kallus and Brandt 2012; Turnbaugh et al. 2006; Gómez-Ambrosi et al. 2011). The advancement of molecular biologic techniques such as HTS, proteomics, and the use of gnotobiological models have tremendously contributed to our understanding of the role of gut microbiota in obesity and lipid metabolism (Aron-Wisnewsky et al. 2012; Bäckhed et al. 2004; Cani et al. 2012; Cox and Blaser 2013; den Besten et  al. 2013; Le Chatelier et  al. 2013; Nicholson et  al. 2005; Tremaroli and Bäckhed 2012; Gosalbes et al. 2011, 2012; Kolmeder et al. 2012). Recent reports show that gut microbiota plays a role in the pathogenesis of obesity by affecting energy homeostasis and inflammation (Turnbaugh et  al. 2006, 2009; Samuel et al. 2008). Compared with conventional mice, germ-free mice have less total body fat, gain less weight, and are protected against diet-induced insulin resistance (Turnbaugh et al. 2006; Piya et al. 2013). Transplantation of fecal material from conventional mice into the colon of germ-free mice triggers an increase in body fat, hepatic triglyceride content, and insulin resistance, suggesting a link between gut microbiota and obesity (Bäckhed et al. 2004). Intriguingly, the ratio of Firmicutes to Bacteroides shows a strong positive correlation with an obese phenotype independent of diet (Turnbaugh et al. 2006; Ley et al. 2005). In a comparison of the gut microbiota of lean mice and mice with diet-induced obesity, Turnbaugh et al. found an increase in abundance of Firmicutes associated with the diet-induced obesity (Turnbaugh et al. 2006). Furthermore, transplantation of fecal matter from co-twins discordant for obesity into germ-free mice showed that mice receiving a fecal transplant from the obese twin had a greater increase in body weight and amount of adiposity than mice receiving a transplant from the lean counterpart (Ridaura et  al. 2013). Altogether, the results of these studies suggest a complex relationship between the development of obesity and gut microbiota. Patients undergoing Roux-en-Y gastric bypass surgery, which is associated with gut microbial

170

B. Dutta et al.

composition changes, experience dramatic improvements in metabolic functions, further indicating a role of gut microbiota in obesity (Aron-Wisnewsky et al. 2012; Cani et al. 2012; Cox and Blaser 2013; Kallus and Brandt 2012; Zhang et al. 2009; Tremaroli et al. 2015; Lutz and Bueter 2014; Osto et al. 2013; Kugelberg 2013). Some scientists have focused on Akkermansia muciniphila, whose levels have been seen to decrease in obese and type 2 diabetic mice. Treatment with this species reverses obesity-related metabolic disorders, leading to the hypothesis that A. muciniphila can control gut barrier functions and inflammation in the pathophysiology of obesity (Everard et al. 2013). Separate studies have attributed these effects to the outer membrane protein Amuc_1100, which interacts with toll-like receptor 2, leading to high levels of interleukin-10 (IL-10) expression and improvement in gut barrier function (Plovier et al. 2017; Ottman et al. 2017). Several mechanisms linking gut microbiota and energy metabolism have been recognized. Gut microbiota is thought to downregulate the expression of fasting-­ induced adipose factor (FIAF), which is needed for the breakdown of lipoprotein containing triacylglycerol to free fatty acids that provide energy for muscle and adipose tissue (Bäckhed et al. 2004). As such, inhibition of FIAF promotes triglyceride deposition in adipocytes (Bäckhed et  al. 2004). Short-chain fatty acids (SCFAs), the primary compounds derived from nondigestible polysaccharides, are produced by the action of gut microbiota. SCFAs are a ligand for various G protein-­ coupled receptors (GPCR) such as GPR41, GPR43, and GPR109A, and are expressed in gut enteroendocrine cells. Upon SCFA binding, GPCR stimulates peptide YY9, which alters gut motility and facilitates nutrient absorption. A recent study showed that GPR41 null mice have more lean body mass and less fat compared to wild-type littermates (Samuel et al. 2008). However, contradictory results also showed that knockout of GPR41 increased the amount of body fat and decreased energy expenditure (Bellahcene et al. 2013). Mice deficient in GPR43 were obese, and overexpression of GPR43 resulted in lean counterparts (Bjursell et al. 2011). SCFAs are known to activate adenosine monophosphate (AMP)-activated protein kinase in liver and muscle tissues, which activates key factors in cholesterol, lipid, and glucose metabolism (den Besten et al. 2013). SCFAs can signal through peroxisome proliferator-activated receptors to modulate the balance between fatty acid synthesis and oxidation (Canfora et al. 2015). SCFAs also promote fatty acid oxidation and inhibit lipolysis, thereby decreasing the pool of free fatty acids (Canfora et al. 2017; Chaplin et al. 2015). Bile acids are generated in the liver; they aid in the digestion of dietary fats and vitamins, and maintain cholesterol homeostasis. Bacteria are capable of converting primary bile acids to secondary bile acids. Secondary bile acids are absorbed into the systemic circulation and modulate lipid and glucose metabolism through the nuclear receptor farsenoid X receptor (FXR) and G protein-coupled receptor, TGR5 (Kaska et al. 2016; Ryan et al. 2014). TGR5 signaling stimulates intestinal glucagon-­ like peptide 1 release improving liver and pancreatic function (Thomas et al. 2009). Obesity, characterized by low-grade inflammation, is modulated by the expression of proinflammatory cytokines and activation of signaling molecules such as nuclear factor-κB (NFκB), the master regulator of inflammatory cascades (Cani

Gut Microbiota and Risk for Atherosclerosis: Current Understanding of the Mechanisms

171

et al. 2012; Cox and Blaser 2013; Gregor and Hotamisligil 2011; Kallus and Brandt 2012). Lipopolysaccharides (LPS), a major component of the outer membrane of the gram-negative bacteria, are known to trigger these inflammatory pathways. Systemic LPS are found in high concentrations in obese individuals triggering a condition called metabolic endotoxemia. LPS cross the gastrointestinal track mucosa via leaky tight junctions or in dietary chylomicrons and reach tissues including liver and adipose tissues through systemic circulation (Cani et  al. 2007; Vreugdenhil et al. 2003; Neal et al. 2006). In the tissues, LPS bind to toll-like receptor 4 (TLR4) present on cell surfaces, which activates downstream signaling pathways, promoting expression of proinflammatory genes including nuclear factor NFκB and activator protein 1 (Neal et al. 2006; Vijay-Kumar et al. 2010). The conclusion suggested by these studies is that a high-fat diet alters the gut microbiota, increasing gut permeability and levels of chylomicron, and thus leading to an increase in systemic levels of LPS (Ghoshal et al. 2009). It has been shown that LPS infusion into genetically identical male mice for 4  weeks results in comparable weight gain to that observed in mice consuming a high-fat diet (Cani et al. 2007). CD14 null ob/ob mice are unable to activate the LPS-mediated pathway, are resistant to weight gain, and are insulin hypersensitive despite being fed the same diet as leptin-deficient ob/ob mice (Cani et  al. 2008). Furthermore, unlike a diet rich in fiber, a high fat and high carbohydrate diet activate the secretion of LPS, inducing the expression of TLR4, NFκB, and suppressors of cytokine signaling 3 (SOCS-3), all of which are involved in the regulation of inflammation and insulin secretion (Ghanim et  al. 2009). Thus, the evidence pertaining to relationships among gut microbiota, obesity, and lipid metabolism further strengthens the notion that obesity is a disease of multifactorial etiology, and highlights the need to optimize therapeutic strategies to manipulate the gut microbial ecology for the benefit of the host.

3  R  ole of Gut Microbiota in the Regulation of Blood Pressure Hypertension, which affects one-quarter of the population worldwide, is induced by genetic susceptibility and environmental factors; hypertension is also considered a significant risk factor for cardiovascular disease. With the elucidation of the role of gut microbiota in metabolic diseases, the role of gut microbiota in hypertension has also been under investigation (Tremaroli and Bäckhed 2012; Kapil et  al. 2013; Karbach et al. 2016; Karlsson et al. 2012; Yamashiro et al. 2017; Li et al. 2017; Yang et  al. 2015). The prevalence of bacteria from the genus Prevotella is elevated in patients with prehypertension and hypertension, whereas the largest component of gut microbiota in healthy subjects is Bacteroides (Li et al. 2017). Additionally, studies in spontaneously hypertensive rat models identified an increase in the ratio of Firmicutes to Bacteroides (Yang et al. 2015). Interestingly, transplantation of fecal microbial content from hypertensive donor animals induced hypertension in ­animals

172

B. Dutta et al.

that were previously normotensive (Durgan et al. 2016). Furthermore, the germ-free mice infused with angiotensin II (Ang II) were protected from hypertension and vascular dysfunction compared to conventionally raised mice (Karbach et al. 2016). Although the mechanisms relating gut microbial ecology with hypertension have not been elucidated completely, the critical roles of SCFA and oxidized/modified low-density lipoprotein (LDL) in the progression of hypertension are gaining prominence. SCFAs (such as acetate, propionate, and butyrate) are bacterial fermentation products of polysaccharides and dietary fibers, which play a role in maintaining homeostasis of the gut microbiome and host immunity (El Kaoutari et al. 2013; Koh et al. 2016; Miyamoto et al. 2016). Early studies have shown that dilation of rat-tail arteries with acetate and butyrate occurs in a concentration-dependent manner (Daugirdas and Nawab 1987; Nutting et al. 1991). In mice, it was shown that acetate and propionate reduce blood pressure (Marques et al. 2017; Pluznick et al. 2013). A study aimed at investigating the effect of chronic intake of acetate in drinking water showed that deoxycorticosterone acetate (DOCA)-treated mice had reduced left ventricular wall thickness and improved cardiac function compared to control mice (Marques et al. 2017). The role of metabolite-sensing GPCRs in hypertension and cardiovascular disease (CVD) has recently become a topic of interest (Pluznick et al. 2013; Tan et al. 2017). Metabolite sensing GPCRs bind metabolites like SCFA, medium chain fatty acids, and long chain fatty acids (e.g., omega 3 fatty acids). Of 12 metabolite-­ sensing GPCRs identified to date, at least three have been shown to bind SCFA (Tan et al. 2017). The GPCR, Olfr78, which is expressed in kidney and smooth muscle cells of small blood vessels, was identified as a receptor for acetate and propionate. Olfr78 was hypothesized to be involved in renin regulation. This result was consistent with the observation that lower amounts of renin were released from ex vivo renal juxtaglomerular cells from Olfr78-null mice compared to wild-type mice. Olfr78-deficient mice had lower plasma renin and slightly lower mean arterial pressure than wild-type mice. These observations, together with the fact that Olfr78 can induce production of cyclic AMP (cAMP) in response to SCFA, suggest that activation of OlfR78 causes renin release in juxtaglomerular cells by stimulating cAMP levels (Pluznick et al. 2013; Tan et al. 2017). Similar administration of propionate in mice lacking GPR41 does not promote a hypotensive effect. These findings indicate that propionate can increase the release of renin and increase blood pressure via Olfr78, despite lowering the blood pressure via GPR41 (Pluznick et al. 2013). Trimethylamine-n-oxide (TMAO), a metabolite of dietary choline and phosphatidylcholine, is associated with the development of atherosclerosis (Koeth et  al. 2013). Although there are no direct links between TMAO and blood pressure, a combination of TMAO infusion with low doses of Ang II prolonged the effects of hypertension (Ufnal et al. 2014). Interestingly, recently published data suggest that LPS have a role in the pathogenesis of hypertension. Metagenome sequencing of fecal samples shows that prehypertension and hypertension are associated with elevated LPS biosynthesis and export (Li et al. 2017). Nitrate and nitrite, the oxidation end products of nitric oxide metabolism, have recently been shown to be

Gut Microbiota and Risk for Atherosclerosis: Current Understanding of the Mechanisms

173

c­ onverted into nitric oxide (NO) (Petersson et  al. 2009; Sparacino-Watkins et  al. 2014; Lundberg and Govoni 2004). This nitrate–nitrite–nitric oxide pathway is involved in the pathogenesis of hypertension. NO is a lipophilic endogenously produced diffusible molecule that acts on smooth muscle cells to promote relaxation. The oral bacterial reduction of nitrate by a set of bacterial nitrate reductase enzymes can produce NO in humans (Petersson et al. 2009; Sparacino-Watkins et al. 2014; Lundberg and Govoni 2004). Depletion of oral bacterial nitrate reductases by chlorhexidine mouthwash resulted in a 90% decrease in oral nitrite levels and a 25% decrease in plasma levels, and was accompanied by a 2–3.5 mm increase in blood pressure (Kapil et al. 2013). Angiotensin-converting enzyme (ACE), which converts angiotensin I to angiotensin II, is thought to be an important target to reduce blood pressure. Sour milk contains two tripeptides (Val-Pro-Pro and Ile-Pro-Pro) that inhibit ACE. Rats fed sour milk fermented by a starter culture containing Lactobacillus helveticus demonstrated a significant decrease in systolic blood pressure (Koyama et al. 2014). While most of these promising studies have been performed in animal models, the differences in the gut microbial ecology between animals and humans necessitate more studies in humans and children as well as prospective clinical trials to establish a more definite relationship between hypertension and gut microbiota.

4  Role of Gut Microbiota in Type-2 Diabetes The prevalence of obesity and type-2 diabetes, the “twin epidemic,” has increased dramatically worldwide over the years. Emerging data indicate that the dysbiosis of the gut microbiota, inflammation, and consequent disruption of gut barrier functions are linked to the pathogenesis of obesity and type-2 diabetes (Gómez-Ambrosi et al. 2011; Everard et al. 2013; Wander et al. 2013; Qin et al. 2012; Karlsson et al. 2013). Comparison of the gut microbiota of healthy and diseased individuals using advanced sequencing technologies and metagenomic analyses has identified significant correlations among the gut microbiota, metabolic pathways, and type-2 diabetes (Qin et  al. 2012). In a Chinese study, the incidence of butyrate-producing Roseburia intestinalis and Faecalibacterium prausnitzii was lower in individuals with type-2 diabetes than in healthy controls (Qin et al. 2012). Quantitative polymerase chain reaction studies of fecal microbiota have shown a higher prevalence of Bifidobacteria species in healthy subjects than in individuals with type-2 diabetes (Wu et al. 2010). A Danish study of obese and nonobese subjects showed that low diversity in the gut microbiome directly correlated with the prevalence of obesity, fatty liver, insulin resistance, and low-grade inflammation (Le Chatelier et al. 2013). LPS are generated from the outer membrane of gram-negative bacteria, and have long been known to promote inflammatory processes. Systemic LPS are typically found in lower concentrations in healthy individuals but increase markedly in obese individuals, giving rise to metabolic endotoxemia (Cani et  al. 2007, 2012). The importance of metabolic endotoxemia in the development and progression of i­ nsulin

174

B. Dutta et al.

resistance is described in the seminal works of Cani et al. who showed that a highfat diet increased fat mass, body weight, and a low-grade inflammatory state in liver, fat, and muscle tissues through an LPS-elicited process (Cani et al. 2007, 2012). The role of the gut microbiota in the pathophysiology of this response has been further examined in mice chronically treated with broad-spectrum antibiotics. Mice fed a high-fat diet and treated with antibiotics showed decreased metabolic endotoxemia, decreased inflammation, and decreased insulin resistance (Cani et al. 2008). Shi et  al. showed that mice deficient in the LPS receptor, TLR4, were protected against insulin resistance induced by a high-fat diet (Shi et al. 2006). Numerous animal studies have confirmed both beneficial and harmful roles of gut microbial metabolites in obesity and type-2 diabetes. SCFAs, fermentation products of indigestible carbohydrates produced by the gut microbiota, affect adipose tissue, skeletal muscle, and pancreatic β-cell function. Type-2 diabetes is characterized by a decreased capacity to produce insulin in the face of insulin resistance due to the loss of β-cell function. It has been shown by receptor knockout experiments that SCFA can increase glucose-stimulated insulin secretion via signaling through the GPR43 receptor on pancreatic β-cells (McNelis et al. 2015). The SCFA-­ GPR41 signaling axis also plays a vital role in β-cell insulin secretion (Veprik et al. 2016). Succinate produced by gut microbiota has been shown to manifest a protective effect by decreasing the obese phenotype and improving insulin sensitivity (De Vadder et al. 2016). Other products of proteolytic fermentation such as p-cresol and branched-chain amino acids (BCAA) are also associated with development of insulin resistance (Koppe et al. 2013; Pedersen et al. 2016).

5  Role of Gut Microbiota in Inflammation The commensal bacteria are responsible for striking a balance between the pro- and anti-inflammatory mechanisms. In mice, proinflammatory T helper 1 and T helper 17 cells accumulate in the intestine in response to segmented filamentous bacteria (Gaboriau-Routhiau et al. 2009). In contrast, SCFAs can effectuate anti-­inflammatory responses by upregulating the generation of regulatory T (Treg) cells (Arpaia et al. 2013). Any discordance in the gut microbiota leads to “leaky gut,” characterized by disruption of gut permeability and microbial imbalance, which has been seen to precede inflammatory diseases. Recent research has produced compelling evidence supporting the role of gut microbiota in the pathogenesis of various inflammatory diseases (Sartor and Wu 2017; Sartor 2008; Senthong et al. 2016; Guarner 2008). Gut microbial diversity is altered in inflammatory bowel diseases (IBD) with depletion of SCFA producers like Eubacterium, Roseburia, and F. prausnitzii, which produce butyrate, a known inducer of Treg cell differentiation via the GPR43 receptor (Sartor and Wu 2017; Sartor 2008; Guarner 2008). Increased proportions of E. coli and B. fragilis are linked to IBD (Sartor and Wu 2017; Sartor 2008; Guarner 2008). In Crohn’s disease, fecal stream diversion promotes mucosal healing, whereas infusion of

Gut Microbiota and Risk for Atherosclerosis: Current Understanding of the Mechanisms

175

i­ ntestinal contents reactivates the disease (Sartor and Wu 2017; Sartor 2008; Guarner 2008). Other inflammatory diseases including multiple sclerosis, autoimmune encephalomyelitis, rheumatoid arthritis, and psoriasis are also linked to alterations in the gut microbiome (Wang and Kasper 2014; Ochoa-Repáraz et al. 2009; Colldahl 1965; Kohashi et  al. 1979; Valdimarsson et  al. 1995; Fry and Baker 2007). Intriguingly, obesity and insulin resistance are intertwined with low-grade systemic inflammation. Bacterial LPS, which reach a high concentration in obesity, mediate endotoxemia and may act as the triggering factor for inflammation leading to insulin resistance (Cani et al. 2007, 2008, 2012). Several other microbe-derived metabolites such as indole produced from tryptophan by the action of bacterial tryptophanase from Bacteroides thetaiotaomicron or Proteus vulgaris have also been implicated in affecting host immunity. It was shown that these metabolites are further processed into compounds such as 3-indoxyl sulfate and indole-3-propionate that interact with inflammation-eliciting processes, upregulating transcription of IL-6 and enzymes from the P450 superfamily complex (Venkatesh et al. 2014; Ramadoss et al. 2005).

6  Role of Gut Microbial Metabolites in Atherosclerosis Besides their contribution to dysbiosis-mediated inflammation, gut microbiota-­ derived metabolites also play a proatherogenic role in the development of CVD. Among the plethora of metabolites generated from the gut microbiota, the role of SCFAs and trimethylamine N-oxide (TMAO) has been extensively studied in relation to atherosclerosis and metabolic diseases (Brown and Hazen 2018; Li and Shimizu 2017). The proatherogenic metabolite TMAO is generated from microbial metabolism of dietary phosphatidylcholine. Trimethyl amine (TMA) lyase hydrolyzes phosphatidylcholine to TMA, which is further oxidized by flavin monooxygenase (FMO) in the liver, converting it to circulating TMAO (Wang et al. 2011; Lang et al. 1998). Knockdown of FMO3 in the liver results in decreased levels of TMAO in circulation, and stalls atherosclerosis through activation of macrophage reverse cholesterol transport (RCT) (Miao et  al. 2015; Shih et  al. 2015; Warrier et al. 2015). Increased levels of plasma phosphatidylcholine-related metabolites and TMAO are associated with increased risk of CVD, and correlate with poor prognosis (Tang et al. 2013, 2015). In this regard, a choline-rich diet administered to ApoE null mice induces aortic lesions (Wang et  al. 2011). Administration of broad-­ spectrum antibiotics reduces the number of macrophages in the atherosclerotic lesions and lipid-loaded macrophage foam cell formation. The level of plasma TMAO correlated with onset of atherosclerosis and size of atherosclerotic plaques (Wang et al. 2011). The emerging role of TMAO in atherosclerosis has prompted researchers to investigate the underlying mechanisms of its action in greater detail. In one study, ApoE null mice were given dietary choline supplements, and the expression of SR-A and CD36 was measured. Increased levels of CD36 and SR-A were seen in

176

B. Dutta et al.

the macrophages of the treated animals (Wang et al. 2011). Furthermore, TMAO was shown to suppress the expression of key bile acid synthetases, such as Cyp7a1 and Cyp27a1, and bile acid transporters including Oatp1, Oatp4, Mrp2, and NTCP, suggesting that TMAO promotes atherosclerosis by affecting bile metabolism (Koeth et  al. 2013). FMO3, the enzyme required for the synthesis of TMAO, is regulated by FXR, a nuclear receptor controlling bile metabolism. Injection of FXR ligands induces expression of FMO3 and TMAO (Bennett et  al. 2013), which is consistent with the finding that FXR-deficient ApoE null mice exhibit reduced atherosclerosis (Miyazaki-Anzai et  al. 2014; Hartman et  al. 2009). TMAO induces platelet activation by increasing the release of Ca2+ from intracellular stores, and is linked to the generation of unstable plaques and thrombosis (Zhu et al. 2016). Ma et al. suggest that TMAO promotes the development of endothelial dysfunction and monocyte adhesion by elevating the expression of molecules like VCAM-1, protein kinase C, and NFκB (Ma et  al. 2017). TMAO is thus an emerging atherogenic metabolite whose mode of action includes inhibition of cholesterol efflux, promotion of cholesterol influx, and disruption of bile metabolism. The dietary nutrient L-carnitine, which is found abundantly in red meat, has a structure similar to choline. In mammals, L-carnitine is produced from lysine, and aids in fatty acid transport across the mitochondrial membrane. L-carnitine is only catabolized by prokaryotes including gut microbiota, which are essential for conversion of L-carnitine to TMAO (Koeth et al. 2013). The proatherosclerotic activity of TMAO is a consequence of the suppression of reverse cholesterol transport, although the precise mechanisms remain unclear. Interestingly, an L-carnitine diet also causes modifications to gut microbiota resulting in increases in specific taxa, such as Prevotella, which are associated with high plasma TMAO levels. TMAO is a potential therapeutic target for the treatment of CVD; however, the elimination of TMAO might result in an accumulation of TMA and in the development of trimethylaminuria (Koeth et al. 2013; Cashman et al. 2003). Also, there has been increasing debate about the role of TMAO and choline in CVD as conflicting evidence emerges. In one study, there was no clear correlation between dietary choline and betaine intake and risk of CVD (Nagata et al. 2015). In another study, L-carnitine administration in ApoE null mice significantly increased circulating TMAO, but this increase surprisingly correlated with a decrease in aortic lesion size. (Collins et al. 2016). Several large population studies involving several countries have reported inconsistent associations between choline and betaine intake and the pathogenesis of CVD (Bidulescu et al. 2007; Dalmeijer et al. 2008).

7  Therapeutic Manipulation of the Gut Microbiota Because of the strength of the evidence that the gut microbiota contribute to development of CVD, there is interest in therapeutic manipulation of the microbiota. Therapeutic manipulation has been achieved through diet modification, use of prebiotics, probiotics and antibiotics, fecal microbial transfer, and the use of small

Gut Microbiota and Risk for Atherosclerosis: Current Understanding of the Mechanisms

177

molecules. All of these therapies aim to rebalance the dysbiotic microbial community by enhancing representation of specific bacterial strains that confer a health benefit to the host. Prebiotics are plant-derived ingredients that can stimulate the growth of specific bacterial species. Prebiotics contribute to the production of SCFAs, stimulation of the immune system, production of vitamin B, and protection against the invasion of commensal and pathogens (Roberfroid et al. 2010). The most commonly studied prebiotics include inulin-type fructans, galactooligosaccharides, and lactose. These products stimulate the growth of Bifidobacteria and Lactobacilli causing significant changes in the gut microbial population (Roberfroid et al. 2010). Mechanistically, prebiotics confer their protective roles in cardiovascular diseases and related metabolic diseases by lowering serum lipid and cholesterol levels (Ferrier et al. 2002). Nania et al. reported that long chain inulin inhibited the formation of atherosclerotic plaques in ApoE null mice models (Rault-Nania et al. 2006), whereas more recent studies showed that inulin-type fructan administration improved endothelial function, and exerted an atheroprotective role by production of butyrate (Watzl et  al. 2005; Catry et al. 2018). Additionally, mannan oligosaccharide supplement, another prebiotic, lowered plasma cholesterol levels and reduced atherosclerotic plaque formation in mice fed a high-cholesterol diet (Hoving et al. 2018). Furthermore, Cani et al. showed that mice on a high carbohydrate diet supplemented with oligofructose exhibited shifts in the intestinal flora dominated by Bifidobacteria and Lactobacilli, improved connections between tight junctions, gut permeability, and lower systemic endotoxemia compared to control mice fed a high-fat diet without the supplements (Cani et al. 2012). Population studies have also shown a lower risk of obesity and hypertension with increased consumption of dietary fiber (Lairon et al. 2005). Probiotics are “microbial feed supplements” that show numerous beneficial effects on host metabolism when provided in adequate amounts (Sanders 2008; Ettinger et al. 2014). Commonly used probiotics are Lactobacillus, Bifidobacterium, and Streptococcus thermophilus. Consumption of a dietary product mixture including Enterococcus faecium and two strains of Streptococcus faecium over 8 weeks showed antihypertensive effects (Agerholm-Larsen et  al. 2000). In a study by Nyugen et al., the ingestion of L. plantarum PH04 by hypercholesterolemic mice reduced total serum cholesterol and triglyceride levels (Nguyen et  al. 2007). In another randomized clinical trial, it was found that L. plantarum CECT 7527, 7528, and 7529 improved plasma levels of cholesterol and prevented the formation of atherosclerotic plaques (Fuentes et  al. 2013). Administration of probiotic “dahi” (Indian yogurt) was shown to significantly delay glucose intolerance, hyperglycemia, and dyslipidemia and decreased oxidative stress (Yadav et al. 2007). Natural components from herbs have been found to have a protective role on CVD by modifying the gut microbiota. Berberine, an herb-derived chemical, was found to produce an anti-atherosclerotic effect by stimulating growth of Akkermansia sp. in ApoE null mice (Zhu et al. 2018). Chen et al. recently found that by remodeling the gut microbiota resveratrol attenuated TMAO-dependent atherosclerosis by decreasing TMAO levels and increasing hepatic bile acid neo-synthesis (Chen et al. 2016).

178

B. Dutta et al.

8  Conclusion Atherosclerosis is a multifactorial chronic inflammatory disease. It is, therefore, difficult to elucidate precise underlying mechanisms. However, recent findings have shown a link between the gut microbiota and the pathogenesis of numerous metabolic diseases, including atherosclerosis. Studies indicate that the microbiota might influence atherosclerosis through multiple mechanisms such as plaque development, activating the immune system, altering lipid and cholesterol metabolism, causing inflammation in the arterial wall, and production of bacterial metabolites. Experimental studies with gut microbiota transplantation and analysis of the composition of gut microbiota in humans and mice indicate that alteration of the abundance of specific gut microbial strains is associated with atherogenesis. Recent studies in various animal models have reported successful therapeutic manipulation of atherosclerosis development using prebiotics, probiotics, antibiotics, and small molecules targeting the gut microbiota. However, there is still a long way to go before we see routine application of gut microbiota-targeted therapy for CVD in the clinic. We are at the stage where large prospective clinical trials are warranted to establish definitive relationships between dysbiosis and atherosclerosis. In addition, it is essential to identify key bacterial taxa and metabolites associated with the disease before deploying therapeutics targeting the gut microbiome.

References Agerholm-Larsen, L., Raben, A., Haulrik, N., Hansen, A. S., Manders, M., & Astrup, A. (2000). Effect of 8-week intake of probiotic milk products on risk factors for cardiovascular diseases. European Journal of Clinical Nutrition, 54(4), 288–297. Aron-Wisnewsky, J., Doré, J., & Clement, K. (2012). The importance of the gut microbiota after bariatric surgery. Nature Reviews. Gastroenterology & Hepatology, 9(10), 590–598. Arpaia, N., Campbell, C., Fan, X., Dikiy, S., van der Veeken, J., de Roos, P., Liu, H., Cross, J. R., Pfeffer, K., Coffer, P. J., & Rudensky, A. Y. (2013). Metabolites produced by commensal bacteria promote peripheral regulatory T-cell generation. Nature, 504(7480), 451–455. Bäckhed, F., Ding, H., Wang, T., Hooper, L.  V., Koh, G.  Y., Nagy, A., Semenkovich, C.  F., & Gordon, J. I. (2004). The gut microbiota as an environmental factor that regulates fat storage. Proceedings of the National Academy of Sciences of the United States of America, 101(44), 15718–15723. Bellahcene, M., O'Dowd, J. F., Wargent, E. T., Zaibi, M. S., Hislop, D. C., Ngala, R. A., Smith, D.  M., Cawthorne, M.  A., Stocker, C.  J., & Arch, J.  R. (2013). Male mice that lack the G-protein-coupled receptor GPR41 have low energy expenditure and increased body fat content. The British Journal of Nutrition, 109(10), 1755–1764. Bennett, B.  J., de Aguiar Vallim, T.  Q., Wang, Z., Shih, D.  M., Meng, Y., Gregory, J., Allayee, H., Lee, R., Graham, M., Crooke, R., Edwards, P.  A., Hazen, S.  L., & Lusis, A.  J. (2013). Trimethylamine-N-oxide, a metabolite associated with atherosclerosis, exhibits complex genetic and dietary regulation. Cell Metabolism, 17(1), 49–60. Bidulescu, A., Chambless, L. E., Siega-Riz, A. M., Zeisel, S. H., & Heiss, G. (2007). Usual choline and betaine dietary intake and incident coronary heart disease: the Atherosclerosis Risk in Communities (ARIC) study. BMC Cardiovascular Disorders, 7, 20.

Gut Microbiota and Risk for Atherosclerosis: Current Understanding of the Mechanisms

179

Bjursell, M., Admyre, T., Göransson, M., Marley, A. E., Smith, D. M., Oscarsson, J., & Bohlooly-Y, M. (2011). Improved glucose control and reduced body fat mass in free fatty acid receptor 2-deficient mice fed a high-fat diet. American Journal of Physiology. Endocrinology and Metabolism, 300(1), E211–E220. Brown, J.  M., & Hazen, S.  L. (2018). Microbial modulation of cardiovascular disease. Nature Reviews. Microbiology, 16(3), 171–181. Canfora, E. E., Jocken, J. W., & Blaak, E. E. (2015). Short-chain fatty acids in control of body weight and insulin sensitivity. Nature Reviews. Endocrinology, 11(10), 577–591. Canfora, E. E., van der Beek, C. M., Jocken, J. W. E., Goossens, G. H., Holst, J. J., Olde Damink, S. W. M., Lenaerts, K., Dejong, C. H. C., & Blaak, E. E. (2017). Colonic infusions of short-­ chain fatty acid mixtures promote energy metabolism in overweight/obese men: a randomized crossover trial. Scientific Reports, 7(1), 2360. Cani, P. D., Amar, J., Iglesias, M. A., Poggi, M., Knauf, C., Bastelica, D., Neyrinck, A. M., Fava, F., Tuohy, K.  M., Chabo, C., Waget, A., Delmée, E., Cousin, B., Sulpice, T., Chamontin, B., Ferrières, J., Tanti, J. F., Gibson, G. R., Casteilla, L., Delzenne, N. M., Alessi, M. C., & Burcelin, R. (2007). Metabolic endotoxemia initiates obesity and insulin resistance. Diabetes, 56(7), 1761–1172. Cani, P. D., Bibiloni, R., Knauf, C., Waget, A., Neyrinck, A. M., Delzenne, N. M., & Burcelin, R. (2008). Changes in gut microbiota control metabolic endotoxemia-induced inflammation in high-fat diet-induced obesity and diabetes in mice. Diabetes, 57(6), 1470–1481. Cani, P. D., 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. Cashman, J.  R., Camp, K., Fakharzadeh, S.  S., Fennessey, P.  V., Hines, R.  N., Mamer, O.  A., Mitchell, S.  C., Nguyen, G.  P., Schlenk, D., Smith, R.  L., Tjoa, S.  S., Williams, D.  E., & Yannicelli, S. (2003). Biochemical and clinical aspects of the human flavin-containing monooxygenase form 3 (FMO3) related to trimethylaminuria. Current Drug Metabolism, 4(2), 151–170. Catry, E., Bindels, L. B., Tailleux, A., Lestavel, S., Neyrinck, A. M., Goossens, J. F., Lobysheva, I., Plovier, H., Essaghir, A., Demoulin, J. B., Bouzin, C., Pachikian, B. D., Cani, P. D., Staels, B., Dessy, C., & Delzenne, N. M. (2018). Targeting the gut microbiota with inulin-type fructans: preclinical demonstration of a novel approach in the management of endothelial dysfunction. Gut, 67(2), 271–283. Chaplin, A., Parra, P., Serra, F., & Palou, A. (2015). Conjugated linoleic acid supplementation under a high-fat diet modulates stomach protein expression and intestinal microbiota in adult mice. PLoS One, 10(4), e0125091. Chen, M. L., Yi, L., Zhang, Y., Zhou, X., Ran, L., Yang, J., Zhu, J. D., Zhang, Q. Y., & Mi, M. T. (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. Colldahl, H. (1965). The intestinal flora in patients with bronchial asthma and rheumatoid arthritis. Acta Allergol, 20, 94–104. Collins, H. L., Drazul-Schrader, D., Sulpizio, A. C., Koster, P. D., Williamson, Y., Adelman, S. J., Owen, K., Sanli, T., & Bellamine, A. (2016). L-Carnitine intake and high trimethylamine N-oxide plasma levels correlate with low aortic lesions in ApoE(−/−) transgenic mice expressing CETP. Atherosclerosis, 244, 29–37. Collot-Teixeira, S., Martin, J., McDermott-Roe, C., Poston, R., & McGregor, J. L. (2007). CD36 and macrophages in atherosclerosis. Cardiovascular Research, 75, 468–477. Cox, L. M., & Blaser, M. J. (2013). Pathways in microbe-induced obesity. Cell Metabolism, 17(6), 883–894. Dalmeijer, G.  W., Olthof, M.  R., Verhoef, P., Bots, M.  L., & van der Schouw, Y.  T. (2008). Prospective study on dietary intakes of folate, betaine, and choline and cardiovascular disease risk in women. European Journal of Clinical Nutrition, 62(3), 386–394.

180

B. Dutta et al.

Daugirdas, J. T., & Nawab, Z. M. (1987). Acetate relaxation of isolated vascular smooth muscle. Kidney International, 32(1), 39–46. De Vadder, F., Kovatcheva-Datchary, P., Zitoun, C., Duchampt, A., Bäckhed, F., & Mithieux, G. (2016). Microbiota-produced succinate improves glucose homeostasis via intestinal gluconeogenesis. Cell Metabolism, 24(1), 151–157. den Besten, G., van Eunen, K., Groen, A.  K., Venema, K., Reijngoud, D.  J., & Bakker, B.  M. (2013). The role of short-chain fatty acids in the interplay between diet, gut microbiota, and host energy metabolism. Journal of Lipid Research, 54(9), 2325–2340. Dominguez-Bello, M. G., Costello, E. K., Contreras, M., Magris, M., Hidalgo, G., Fierer, N., & Knight, R. (2010). Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proceedings of the National Academy of Sciences of the United States of America, 107, 11971–11975. Durgan, D. J., Ganesh, B. P., Cope, J. L., Ajami, N. J., Phillips, S. C., Petrosino, J. F., Hollister, E.  B., & Bryan, R.  M., Jr. (2016). Role of the gut microbiome in obstructive sleep Apnea-­ induced hypertension. Hypertension, 67(2), 469–474. Eckburg, P. B., Bik, E. M., Bernstein, C. N., Purdom, E., Dethlefsen, L., Sargent, M., Gill, S. R., Nelson, K.  E., & Relman, D.  A. (2005). Diversity of the human intestinal microbial flora. Science, 308(5728), 1635–1638. El Kaoutari, A., Armougom, F., Gordon, J. I., Raoult, D., & Henrissat, B. (2013). The abundance and variety of carbohydrate-active enzymes in the human gut microbiota. Nature Reviews. Microbiology, 11(7), 497–504. Ettinger, G., MacDonald, K., Reid, G., & Burton, J. P. (2014). The influence of the human microbiome and probiotics on cardiovascular health. Gut Microbes, 5(6), 719–728. Everard, A., Belzer, C., Geurts, L., Ouwerkerk, J. P., Druart, C., Bindels, L. B., Guiot, Y., Derrien, M., Muccioli, G. G., Delzenne, N. M., de Vos, W. M., & Cani, P. D. (2013). Cross-talk between Akkermansia muciniphila and intestinal epithelium controls diet-induced obesity. Proceedings of the National Academy of Sciences of the United States of America, 110(22), 9066–9071. Falk, E., Nakano, M., Bentzon, J. F., Finn, A. V., & Virmani, R. (2013). Update on acute coronary syndromes: The pathologists’ view. European Heart Journal, 34, 719–728. Ferrier, K. E., Muhlmann, M. H., Baguet, J. P., Cameron, J. D., Jennings, G. L., Dart, A. M., & Kingwell, B. A. (2002). Intensive cholesterol reduction lowers blood pressure and large artery stiffness in isolated systolic hypertension. Journal of the American College of Cardiology, 39(6), 1020–1005. Fouhy, F., Ross, R.  P., Fitzgerald, G.  F., Stanton, C., & Cotter, P.  D. (2012). Composition of the early intestinal microbiota: knowledge, knowledge gaps and the use of high-throughput sequencing to address these gaps. Gut Microbes, 3(3), 203–220. Fry, L., & Baker, B. S. (2007). Triggering psoriasis: the role of infections and medications. Clinics in Dermatology, 25(6), 606–615. Fuentes, M.  C., Lajo, T., Carrión, J.  M., & Cuñé, J. (2013). Cholesterol-lowering efficacy of Lactobacillus plantarum CECT 7527, 7528 and 7529  in hypercholesterolaemic adults. The British Journal of Nutrition, 109(10), 1866–1872. Gaboriau-Routhiau, V., Rakotobe, S., Lécuyer, E., Mulder, I., Lan, A., Bridonneau, C., Rochet, V., Pisi, A., De Paepe, M., Brandi, G., Eberl, G., Snel, J., Kelly, D., & Cerf-Bensussan, N. (2009). The key role of segmented filamentous bacteria in the coordinated maturation of gut helper T cell responses. Immunity, 31(4), 677–689. Ghanim, H., Abuaysheh, S., Sia, C. L., Korzeniewski, K., Chaudhuri, A., Fernandez-Real, J. M., & Dandona, P. (2009). Increase in plasma endotoxin concentrations and the expression of Toll-­ like receptors and suppressor of cytokine signaling-3  in mononuclear cells after a high-fat, high-carbohydrate meal: implications for insulin resistance. Diabetes Care, 32(12), 2281–2287. Ghoshal, S., Witta, J., Zhong, J., de Villiers, W., & Eckhardt, E. (2009). Chylomicrons promote intestinal absorption of lipopolysaccharides. Journal of Lipid Research, 50(1), 90–97. Gómez-Ambrosi, J., Silva, C., Galofré, J.  C., Escalada, J., Santos, S., Gil, M.  J., Valentí, V., Rotellar, F., Ramírez, B., Salvador, J., & Frühbeck, G. (2011). Body adiposity and type 2

Gut Microbiota and Risk for Atherosclerosis: Current Understanding of the Mechanisms

181

diabetes: increased risk with a high body fat percentage even having a normal BMI. Obesity, 19(7), 1439–1444. Gosalbes, M. J., Durbán, A., Pignatelli, M., Abellan, J. J., Jiménez-Hernández, N., Pérez-Cobas, A. E., Latorre, A., & Moya, A. (2011). Metatranscriptomic approach to analyze the functional human gut microbiota. PLoS One, 6(3), e17447. Gosalbes, M. J., Abellan, J. J., Durbán, A., Pérez-Cobas, A. E., Latorre, A., & Moya, A. (2012). Metagenomics of human microbiome: beyond 16s rDNA. Clinical Microbiology and Infection, 18(Suppl 4), 47–49. Gregor, M. F., & Hotamisligil, G. S. (2011). Inflammatory mechanisms in obesity. Annual Review of Immunology, 29, 415–445. Guarner, F. (2008). What is the role of the enteric commensal flora in IBD? Inflammatory Bowel Diseases, 14(Suppl 2), S83–S84. Hartman, H. B., Gardell, S. J., Petucci, C. J., Wang, S., Krueger, J. A., & Evans, M. J. (2009). Activation of farnesoid X receptor prevents atherosclerotic lesion formation in LDLR−/− and apoE−/− mice. Journal of Lipid Research, 50(6), 1090–1100. Hoving, L. R., Katiraei, S., Heijink, M., Pronk, A., van der Wee-Pals, L., Streefland, T., Giera, M., Willems van Dijk, K., & van Harmelen, V. (2018). Dietary Mannan oligosaccharides modulate gut microbiota, increase fecal bile acid excretion, and decrease plasma cholesterol and atherosclerosis development. Molecular Nutrition & Food Research, 62(10), e1700942. Kallus, S. J., & Brandt, L. J. (2012). The intestinal microbiota and obesity. Journal of Clinical Gastroenterology, 46(1), 16–24. Kapil, V., Haydar, S.  M., Pearl, V., Lundberg, J.  O., Weitzberg, E., & Ahluwalia, A. (2013). Physiological role for nitrate-reducing oral bacteria in blood pressure control. Free Radical Biology & Medicine, 55, 93–100. Karbach, S. H., Schönfelder, T., Brandão, I., Wilms, E., Hörmann, N., Jäckel, S., Schüler, R., Finger, S., Knorr, M., Lagrange, J., Brandt, M., Waisman, A., Kossmann, S., Schäfer, K., Münzel, T., Reinhardt, C., & Wenzel, P. (2016). Gut microbiota promote Angiotensin II-induced arterial hypertension and vascular dysfunction. Journal of the American Heart Association, 5(9), e003698. Karlsson, F. H., Fåk, F., Nookaew, I., Tremaroli, V., Fagerberg, B., Petranovic, D., Bäckhed, F., & Nielsen, J. (2012). Symptomatic atherosclerosis is associated with an altered gut metagenome. Nature Communications, 3, 1245. Karlsson, F. H., Tremaroli, V., Nookaew, I., Bergström, G., Behre, C. J., Fagerberg, B., Nielsen, J., & Bäckhed, F. (2013). Gut metagenome in European women with normal, impaired and diabetic glucose control. Nature, 498(7452), 99–103. Kaska, L., Sledzinski, T., Chomiczewska, A., Dettlaff-Pokora, A., & Swierczynski, J. (2016). Improved glucose metabolism following bariatric surgery is associated with increased circulating bile acid concentrations and remodeling of the gut microbiome. World Journal of Gastroenterology, 22(39), 8698–8719. Koeth, R. A., Wang, Z., Levison, B. S., Buffa, J. A., Org, E., Sheehy, B. T., Britt, E. B., Fu, X., Wu, Y., Li, L., Smith, J. D., DiDonato, J. A., Chen, J., Li, H., Wu, G. D., Lewis, J. D., Warrier, M., Brown, J. M., Krauss, R. M., Tang, W. H., Bushman, F. D., Lusis, A. J., & Hazen, S. L. (2013). Intestinal microbiota metabolism of L-carnitine, a nutrient in red meat, promotes atherosclerosis. Nature Medicine, 19(5), 576–585. Koh, A., De Vadder, F., Kovatcheva-Datchary, P., & Bäckhed, F. (2016). From dietary fiber to host physiology: short-chain fatty acids as key bacterial metabolites. Cell, 165(6), 1332–1345. Kohashi, O., Kuwata, J., Umehara, K., Uemura, F., Takahashi, T., & Ozawa, A. (1979). Susceptibility to adjuvant-induced arthritis among germfree, specific-pathogen-free, and conventional rats. Infection and Immunity, 26(3), 791–794. Kolmeder, C. A., de Been, M., Nikkilä, J., Ritamo, I., Mättö, J., Valmu, L., Salojärvi, J., Palva, A., Salonen, A., & de Vos, W. M. (2012). Comparative metaproteomics and diversity analysis of human intestinal microbiota testifies for its temporal stability and expression of core functions. PLoS One, 7(1), e29913.

182

B. Dutta et al.

Koppe, L., Pillon, N.  J., Vella, R.  E., Croze, M.  L., Pelletier, C.  C., Chambert, S., Massy, Z., Glorieux, G., Vanholder, R., Dugenet, Y., Soula, H. A., Fouque, D., & Soulage, C. O. (2013). p-Cresyl sulfate promotes insulin resistance associated with CKD. Journal of the American Society of Nephrology, 24(1), 88–99. Koyama, M., Hattori, S., Amano, Y., Watanabe, M., & Nakamura, K. (2014). Blood pressure-­ lowering peptides from neo-fermented buckwheat sprouts: a new approach to estimating ACE-­ inhibitory activity. PLoS One, 9(9), e105802. Kugelberg, E. (2013). Surgery: Altered gut microbiota trigger weight loss. Nature Reviews. Endocrinology, 9(6), 314. Lairon, D., Arnault, N., Bertrais, S., Planells, R., Clero, E., Hercberg, S., & Boutron-Ruault, M. C. (2005). Dietary fiber intake and risk factors for cardiovascular disease in French adults. The American Journal of Clinical Nutrition, 82(6), 1185–1194. Lang, D. H., Yeung, C. K., Peter, R. M., Ibarra, C., Gasser, R., Itagaki, K., Philpot, R. M., & Rettie, A. E. (1998). Isoform specificity of trimethylamine N-oxygenation by human flavin-­containing monooxygenase (FMO) and P450 enzymes: selective catalysis by FMO3. Biochemical Pharmacology, 56(8), 1005–1012. Le Chatelier, E., Nielsen, T., Qin, J., Prifti, E., Hildebrand, F., Falony, G., Almeida, M., Arumugam, M., Batto, J.  M., Kennedy, S., Leonard, P., Li, J., Burgdorf, K., Grarup, N., Jørgensen, T., Brandslund, I., Nielsen, H. B., Juncker, A. S., Bertalan, M., Levenez, F., Pons, N., Rasmussen, S., Sunagawa, S., Tap, J., Tims, S., Zoetendal, E.  G., Brunak, S., Clément, K., Doré, J., Kleerebezem, M., Kristiansen, K., Renault, P., Sicheritz-Ponten, T., de Vos, W.  M., Zucker, J. D., Raes, J., Hansen, T., MetaHIT consortium, Bork, P., Wang, J., Ehrlich, S. D., & Pedersen, O. (2013). Richness of human gut microbiome correlates with metabolic markers. Nature, 500(7464), 541–546. Ley, R. E., Bäckhed, F., Turnbaugh, P., Lozupone, C. A., Knight, R. D., & Gordon, J. I. (2005). Obesity alters gut microbial ecology. Proceedings of the National Academy of Sciences of the United States of America, 102(31), 11070–11705. Li, X., & Shimizu, Y. (2017). Kimura I Gut microbial metabolite short-chain fatty acids and obesity. Bioscience of Microbiota, Food and Health, 36(4), 135–140. Li, J., Jia, H., Cai, X., Zhong, H., Feng, Q., Sunagawa, S., Arumugam, M., Kultima, J. R., Prifti, E., Nielsen, T., Juncker, A. S., Manichanh, C., Chen, B., Zhang, W., Levenez, F., Wang, J., Xu, X., Xiao, L., Liang, S., Zhang, D., Zhang, Z., Chen, W., Zhao, H., Al-Aama, J. Y., Edris, S., Yang, H., Wang, J., Hansen, T., Nielsen, H. B., Brunak, S., Kristiansen, K., Guarner, F., Pedersen, O., Doré, J., Ehrlich, S. D., MetaHIT Consortium, Bork, P., & Wang, J. (2014). An integrated catalog of reference genes in the human gut microbiome. Nature Biotechnology, 32(8), 834–841. Li, J., Zhao, F., Wang, Y., Chen, J., Tao, J., Tian, G., Wu, S., Liu, W., Cui, Q., Geng, B., Zhang, W., Weldon, R., Auguste, K., Yang, L., Liu, X., Chen, L., Yang, X., Zhu, B., & Cai, J. (2017). Gut microbiota dysbiosis contributes to the development of hypertension. Microbiome, 5(1), 14. Lundberg, J. O., & Govoni, M. (2004). Inorganic nitrate is a possible source for systemic generation of nitric oxide. Free Radical Biology & Medicine, 37(3), 395–400. Lusis, A. J. (2000). Atherosclerosis. Nature, 407, 233–241. Lutz, T.  A., & Bueter, M. (2014). Physiological mechanisms behind Roux-en-Y gastric bypass surgery. Digestive Surgery, 31(1), 13–24. Ma, G., Pan, B., Chen, Y., Guo, C., Zhao, M., Zheng, L., & Chen, B. (2017). Trimethylamine N-oxide in atherogenesis: impairing endothelial self-repair capacity and enhancing monocyte adhesion. Bioscience Reports, 37(2), BSR20160244. Marques, F. Z., Nelson, E., Chu, P. Y., Horlock, D., Fiedler, A., Ziemann, M., Tan, J. K., Kuruppu, S., Rajapakse, N. W., El-Osta, A., Mackay, C. R., & Kaye, D. M. (2017). High-fiber diet and acetate supplementation change the gut microbiota and prevent the development of hypertension and heart failure in hypertensive mice. Circulation, 135(10), 964–977. McLaren, J. E., Michael, D. R., Ashlin, T. G., & Ramji, D. P. (2011). Cytokines, macrophage lipid metabolism and foam cells: Implications for cardiovascular disease therapy. Progress in Lipid Research, 50, 331–347.

Gut Microbiota and Risk for Atherosclerosis: Current Understanding of the Mechanisms

183

McNelis, J. C., Lee, Y. S., Mayoral, R., van der Kant, R., Johnson, A. M., Wollam, J., & Olefsky, J. M. (2015). GPR43 potentiates β-Cell function in obesity. Diabetes, 64(9), 3203–3217. Miao, J., Ling, A.  V., Manthena, P.  V., Gearing, M.  E., Graham, M.  J., Crooke, R.  M., Croce, K.  J., Esquejo, R.  M., Clish, C.  B., Morbid Obesity Study Group, Vicent, D., & Biddinger, S. B. (2015). Flavin-containing monooxygenase 3 as a potential player in diabetes-associated atherosclerosis. Nature Communications, 6, 6498. Miyamoto, J., Kasubuchi, M., Nakajima, A., Irie, J., Itoh, H., & Kimura, I. (2016). The role of short-chain fatty acid on blood pressure regulation. Current Opinion in Nephrology and Hypertension, 25(5), 379–383. Miyazaki-Anzai, S., Masuda, M., Levi, M., Keenan, A. L., & Miyazaki, M. (2014). Dual activation of the bile acid nuclear receptor FXR and G-protein-coupled receptor TGR5 protects mice against atherosclerosis. PLoS One, 9(9), e108270. Moore, K. J., & Tabas, I. (2011). The cellular biology of macrophages in atherosclerosis. Cell, 145, 341–355. Moore, K. J., Sheedy, F. J., & Fisher, E. A. (2013). Macrophages in atherosclerosis: a dynamic balance. Nature Reviews. Immunology, 13(10), 709–721. Nagata, C., Wada, K., Tamura, T., Konishi, K., Kawachi, T., Tsuji, M., & Nakamura, K. (2015). Choline and Betaine intakes are not associated with cardiovascular disease mortality risk in Japanese men and women. The Journal of Nutrition, 145(8), 1787–1792. Neal, M. D., Leaphart, C., Levy, R., Prince, J., Billiar, T. R., Watkins, S., Li, J., Cetin, S., Ford, H., Schreiber, A., & Hackam, D. J. (2006). Enterocyte TLR4 mediates phagocytosis and translocation of bacteria across the intestinal barrier. Journal of Immunology, 176(5), 3070–3079. Nguyen, T.  D., Kang, J.  H., & Lee, M.  S. (2007). Characterization of Lactobacillus plantarum PH04, a potential probiotic bacterium with cholesterol-lowering effects. International Journal of Food Microbiology, 113(3), 358–361. Nicholson, J. K., Holmes, E., & Wilson, I. D. (2005). Gut microorganisms, mammalian metabolism and personalized health care. Nature Reviews. Microbiology, 3(5), 431–438. Nutting, C. W., Islam, S., & Daugirdas, J. T. (1991). Vasorelaxant effects of short chain fatty acid salts in rat caudal artery. The American Journal of Physiology, 261(2 Pt 2), H561–H567. Ochoa-Repáraz, J., Mielcarz, D.  W., Ditrio, L.  E., Burroughs, A.  R., Foureau, D.  M., Haque-­ Begum, S., & Kasper, L. H. (2009). Role of gut commensal microflora in the development of experimental autoimmune encephalomyelitis. Journal of Immunology, 183(10), 6041–6050. Ortega, F. B., Lavie, C. J., & Blair, S. N. (2016). Obesity and cardiovascular disease. Circulation Research, 118(11), 1752–1770. Osto, M., Abegg, K., Bueter, M., le Roux, C. W., Cani, P. D., & Lutz, T. A. (2013). Roux-en-Y gastric bypass surgery in rats alters gut microbiota profile along the intestine. Physiology & Behavior, 119, 92–96. Ottman, N., Reunanen, J., Meijerink, M., Pietilä, T. E., Kainulainen, V., Klievink, J., Huuskonen, L., Aalvink, S., Skurnik, M., Boeren, S., Satokari, R., Mercenier, A., Palva, A., Smidt, H., de Vos, W. M., & Belzer, C. (2017). Pili-like proteins of Akkermansia muciniphila modulate host immune responses and gut barrier function. PLoS One, 12(3), e0173004. Palmer, C., Bik, E. M., DiGiulio, D. B., Relman, D. A., & Brown, P. O. (2007). Development of the Human infant intestinal microbiota. PLoS Biology, 5, e177. Parkhill, J. (2013). What has high-throughput sequencing ever done for us? Nature Reviews. Microbiology, 11(10), 664–665. Pedersen, H. K., Gudmundsdottir, V., Nielsen, H. B., Hyotylainen, T., Nielsen, T., Jensen, B. A., Forslund, K., Hildebrand, F., Prifti, E., Falony, G., Le Chatelier, E., Levenez, F., Doré, J., Mattila, I., Plichta, D.  R., Pöhö, P., Hellgren, L.  I., Arumugam, M., Sunagawa, S., Vieira-­ Silva, S., Jørgensen, T., Holm, J. B., Trošt, K., MetaHIT Consortium, Kristiansen, K., Brix, S., Raes, J., Wang, J., Hansen, T., Bork, P., Brunak, S., Oresic, M., Ehrlich, S. D., & Pedersen, O. (2016). Human gut microbes impact host serum metabolome and insulin sensitivity. Nature, 535(7612), 376–381.

184

B. Dutta et al.

Petersson, J., Carlström, M., Schreiber, O., Phillipson, M., Christoffersson, G., Jägare, A., Roos, S., Jansson, E. A., Persson, A. E., Lundberg, J. O., & Holm, L. (2009). Gastroprotective and blood pressure lowering effects of dietary nitrate are abolished by an antiseptic mouthwash. Free Radical Biology & Medicine, 46(8), 1068–1675. Piya, M. K., McTernan, P. G., & Kumar, S. (2013). Adipokine inflammation and insulin resistance: the role of glucose, lipids and endotoxin. The Journal of Endocrinology, 216(1), T1–T15. Plovier, H., Everard, A., Druart, C., Depommier, C., Van Hul, M., Geurts, L., Chilloux, J., Ottman, N., Duparc, T., Lichtenstein, L., Myridakis, A., Delzenne, N. M., Klievink, J., Bhattacharjee, A., van der Ark, K.  C., Aalvink, S., Martinez, L.  O., Dumas, M.  E., Maiter, D., Loumaye, A., Hermans, M. P., Thissen, J. P., Belzer, C., de Vos, W. M., & Cani, P. D. (2017). A purified membrane protein from Akkermansia muciniphila or the pasteurized bacterium improves metabolism in obese and diabetic mice. Nature Medicine, 23(1), 107–113. Pluznick, J. L., Protzko, R. J., Gevorgyan, H., Peterlin, Z., Sipos, A., Han, J., Brunet, I., Wan, L. X., Rey, F., Wang, T., Firestein, S. J., Yanagisawa, M., Gordon, J. I., Eichmann, A., Peti-Peterdi, J., & Caplan, M. J. (2013). Olfactory receptor responding to gut microbiota-derived signals plays a role in renin secretion and blood pressure regulation. Proceedings of the National Academy of Sciences of the United States of America, 110(11), 4410–4415. Qin, J., Li, Y., Cai, Z., Li, S., Zhu, J., Zhang, F., Liang, S., Zhang, W., Guan, Y., Shen, D., Peng, Y., Zhang, D., Jie, Z., Wu, W., Qin, Y., Xue, W., Li, J., Han, L., Lu, D., Wu, P., Dai, Y., Sun, X., Li, Z., Tang, A., Zhong, S., Li, X., Chen, W., Xu, R., Wang, M., Feng, Q., Gong, M., Yu, J., Zhang, Y., Zhang, M., Hansen, T., Sanchez, G., Raes, J., Falony, G., Okuda, S., Almeida, M., LeChatelier, E., Renault, P., Pons, N., Batto, J. M., Zhang, Z., Chen, H., Yang, R., Zheng, W., Li, S., Yang, H., Wang, J., Ehrlich, S. D., Nielsen, R., Pedersen, O., Kristiansen, K., & Wang, J. (2012). A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature, 490(7418), 55–60. Ramadoss, P., Marcus, C., & Perdew, G. H. (2005). Role of the aryl hydrocarbon receptor in drug metabolism. Expert Opinion on Drug Metabolism & Toxicology, 1(1), 9–21. Rault-Nania, M. H., Gueux, E., Demougeot, C., Demigné, C., Rock, E., & Mazur, A. (2006). Inulin attenuates atherosclerosis in apolipoprotein E-deficient mice. The British Journal of Nutrition, 96(5), 840–844. Ridaura, V. K., Faith, J. J., Rey, F. E., Cheng, J., Duncan, A. E., Kau, A. L., Griffin, N. W., Lombard, V., Henrissat, B., Bain, J. R., Muehlbauer, M. J., Ilkayeva, O., Semenkovich, C. F., Funai, K., Hayashi, D. K., Lyle, B. J., Martini, M. C., Ursell, L. K., Clemente, J. C., Van Treuren, W., Walters, W. A., Knight, R., Newgard, C. B., Heath, A. C., & Gordon, J. I. (2013). Gut microbiota from twins discordant for obesity modulate metabolism in mice. Science, 341(6150), 1241214. Roberfroid, M., Gibson, G. R., Hoyles, L., McCartney, A. L., Rastall, R., Rowland, I., Wolvers, D., Watzl, B., Szajewska, H., Stahl, B., Guarner, F., Respondek, F., Whelan, K., Coxam, V., Davicco, M. J., Léotoing, L., Wittrant, Y., Delzenne, N. M., Cani, P. D., Neyrinck, A. M., & Meheust, A. (2010). Prebiotic effects: metabolic and health benefits. The British Journal of Nutrition, 104(Suppl 2), S1–63. Ryan, K. K., Tremaroli, V., Clemmensen, C., Kovatcheva-Datchary, P., Myronovych, A., Karns, R., Wilson-Pérez, H. E., Sandoval, D. A., Kohli, R., Bäckhed, F., & Seeley, R. J. (2014). FXR is a molecular target for the effects of vertical sleeve gastrectomy. Nature, 509(7499), 183–188. Samuel, B. S., Shaito, A., Motoike, T., Rey, F. E., Backhed, F., Manchester, J. K., Hammer, R. E., Williams, S. C., Crowley, J., Yanagisawa, M., & Gordon, J. I. (2008). Effects of the gut microbiota on host adiposity are modulated by the short-chain fatty-acid binding G protein-coupled receptor, Gpr41. Proceedings of the National Academy of Sciences of the United States of America, 105(43), 16767–16772. Sanders, M.  E. (2008). Probiotics: definition, sources, selection, and uses. Clinical Infectious Diseases, 46(Suppl 2), S58–61; discussion S144–51. Santiago, A., Panda, S., Mengels, G., Martinez, X., Azpiroz, F., Dore, J., Guarner, F., & Manichanh, C. (2014). Processing faecal samples: a step forward for standards in microbial community analysis. BMC Microbiology, 14, 112.

Gut Microbiota and Risk for Atherosclerosis: Current Understanding of the Mechanisms

185

Sartor, R.  B. (2008). Microbial influences in inflammatory bowel diseases. Gastroenterology, 134(2), 577–594. Sartor, R. B., & Wu, G. D. (2017). Roles for intestinal bacteria, viruses, and fungi in pathogenesis of inflammatory bowel diseases and therapeutic approaches. Gastroenterology, 152(2), 327–339. Senthong, V., Li, X. S., Hudec, T., Coughlin, J., Wu, Y., Levison, B., Wang, Z., Hazen, S. L., & Tang, W. H. (2016). Plasma Trimethylamine N-Oxide, a Gut Microbe-Generated Phosphatidylcholine Metabolite, Is Associated With Atherosclerotic Burden. Journal of the American College of Cardiology, 67(22), 2620–2628. Shi, H., Kokoeva, M. V., Inouye, K., Tzameli, I., Yin, H., & Flier, J. S. (2006). TLR4 links innate immunity and fatty acid-induced insulin resistance. The Journal of Clinical Investigation, 116(11), 3015–3025. Shih, D. M., Wang, Z., Lee, R., Meng, Y., Che, N., Charugundla, S., Qi, H., Wu, J., Pan, C., Brown, J. M., Vallim, T., Bennett, B. J., Graham, M., Hazen, S. L., & Lusis, A. J. (2015). Flavin containing monooxygenase 3 exerts broad effects on glucose and lipid metabolism and atherosclerosis. Journal of Lipid Research, 56(1), 22–37. Sparacino-Watkins, C., Stolz, J. F., & Basu, P. (2014). Nitrate and periplasmic nitrate reductases. Chemical Society Reviews, 43(2), 676–706. Tan, J.  K., McKenzie, C., Mariño, E., Macia, L., & Mackay, C.  R. (2017). Metabolite-sensing G protein-coupled receptors-facilitators of diet-related immune regulation. Annual Review of Immunology, 35, 371–402. Tang, W. H., Wang, Z., Levison, B. S., Koeth, R. A., Britt, E. B., Fu, X., Wu, Y., & Hazen, S. L. (2013). Intestinal microbial metabolism of phosphatidylcholine and cardiovascular risk. The New England Journal of Medicine, 368(17), 1575–1584. Tang, W. H., Wang, Z., Shrestha, K., Borowski, A. G., Wu, Y., Troughton, R. W., Klein, A. L., & Hazen, S.  L. (2015). Intestinal microbiota-dependent phosphatidylcholine metabolites, diastolic dysfunction, and adverse clinical outcomes in chronic systolic heart failure. Journal of Cardiac Failure, 21(2), 91–96. Thomas, C., Gioiello, A., Noriega, L., Strehle, A., Oury, J., Rizzo, G., Macchiarulo, A., Yamamoto, H., Mataki, C., Pruzanski, M., Pellicciari, R., Auwerx, J., & Schoonjans, K. (2009). TGR5-­ mediated bile acid sensing controls glucose homeostasis. Cell Metabolism, 10(3), 167–177. Tremaroli, V., & Bäckhed, F. (2012). Functional interactions between the gut microbiota and host metabolism. Nature, 489(7415), 242–249. Tremaroli, V., Karlsson, F., Werling, M., Ståhlman, M., Kovatcheva-Datchary, P., Olbers, T., Fändriks, L., le Roux, C. W., Nielsen, J., & Bäckhed, F. (2015). Roux-en-Y gastric bypass and vertical banded gastroplasty induce long-term changes on the human gut microbiome contributing to fat mass regulation. Cell Metabolism, 22(2), 228–238. Turnbaugh, P. J., Ley, R. E., Mahowald, M. A., Magrini, V., Mardis, E. R., & Gordon, J. I. (2006). An obesity-associated gut microbiome with increased capacity for energy harvest. Nature, 444(7122), 1027–1031. Turnbaugh, P.  J., Hamady, M., Yatsunenko, T., Cantarel, B.  L., Duncan, A., Ley, R.  E., Sogin, M. L., Jones, W. J., Roe, B. A., Affourtit, J. P., Egholm, M., Henrissat, B., Heath, A. C., Knight, R., & Gordon, J. I. (2009). A core gut microbiome in obese and lean twins. Nature, 457(7228), 480–484. Ufnal, M., Jazwiec, R., Dadlez, M., Drapala, A., Sikora, M., & Skrzypecki, J. (2014). Trimethylamine-N-oxide: a carnitine-derived metabolite that prolongs the hypertensive effect of angiotensin II in rats. The Canadian Journal of Cardiology, 30(12), 1700–1705. Valdimarsson, H., Baker, B.  S., Jónsdóttir, I., Powles, A., & Fry, L. (1995). Psoriasis: a T-cell-­ mediated autoimmune disease induced by streptococcal superantigens? Immunology Today, 16(3), 145–149. Venkatesh, M., Mukherjee, S., Wang, H., Li, H., Sun, K., Benechet, A.  P., Qiu, Z., Maher, L., Redinbo, M. R., Phillips, R. S., Fleet, J. C., Kortagere, S., Mukherjee, P., Fasano, A., Le Ven, J., Nicholson, J. K., Dumas, M. E., Khanna, K. M., & Mani, S. (2014). Symbiotic bacterial metabolites regulate gastrointestinal barrier function via the xenobiotic sensor PXR and Toll-­ like receptor 4. Immunity, 41(2), 296–310.

186

B. Dutta et al.

Veprik, A., Laufer, D., Weiss, S., Rubins, N., & Walker, M. D. (2016). GPR41 modulates insulin secretion and gene expression in pancreatic β-cells and modifies metabolic homeostasis in fed and fasting states. The FASEB Journal, 30(11), 3860–3869. Vijay-Kumar, M., Aitken, J.  D., Carvalho, F.  A., Cullender, T.  C., Mwangi, S., Srinivasan, S., Sitaraman, S. V., Knight, R., Ley, R. E., & Gewirtz, A. T. (2010). Metabolic syndrome and altered gut microbiota in mice lacking Toll-like receptor 5. Science, 328(5975), 228–231. Vreugdenhil, A. C., Rousseau, C. H., Hartung, T., Greve, J. W., van 't Veer, C., & Buurman, W. A. (2003). Lipopolysaccharide (LPS)-binding protein mediates LPS detoxification by chylomicrons. Journal of Immunology, 170(3), 1399–1405. Wander, P. L., Boyko, E. J., Leonetti, D. L., McNeely, M. J., Kahn, S. E., & Fujimoto, W. Y. (2013). Change in visceral adiposity independently predicts a greater risk of developing type 2 diabetes over 10 years in Japanese Americans. Diabetes Care, 36(2), 289–293. Wang, Y., & Kasper, L. H. (2014). The role of microbiome in central nervous system disorders. Brain, Behavior, and Immunity, 38, 1–12. Wang, Z., Klipfell, E., Bennett, B.  J., Koeth, R., Levison, B.  S., Dugar, B., Feldstein, A.  E., Britt, E. B., Fu, X., Chung, Y. M., Wu, Y., Schauer, P., Smith, J. D., Allayee, H., Tang, W. H., DiDonato, J. A., Lusis, A. J., & Hazen, S. L. (2011). Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease. Nature, 472(7341), 57–63. Warrier, M., Shih, D.  M., Burrows, A.  C., Ferguson, D., Gromovsky, A.  D., Brown, A.  L., Marshall, S., McDaniel, A., Schugar, R. C., Wang, Z., Sacks, J., Rong, X., Vallim, T. A., Chou, J., Ivanova, P. T., Myers, D. S., Brown, H. A., Lee, R. G., Crooke, R. M., Graham, M. J., Liu, X., Parini, P., Tontonoz, P., Lusis, A. J., Hazen, S. L., Temel, R. E., & Brown, J. M. (2015). The TMAO-generating enzyme flavin monooxygenase 3 is a central regulator of cholesterol balance. Cell Reports. pii: S2211-1247(14)01065-1. Watzl, B., Girrbach, S., & Roller, M. (2005). Inulin, oligofructose and immunomodulation. The British Journal of Nutrition, 93(Suppl 1), S49–S55. Wu, X., Ma, C., Han, L., Nawaz, M., Gao, F., Zhang, X., Yu, P., Zhao, C., Li, L., Zhou, A., Wang, J., Moore, J. E., Millar, B. C., & Xu, J. (2010). Molecular characterisation of the faecal microbiota in patients with type II diabetes. Current Microbiology, 61(1), 69–78. Yadav, H., Jain, S., & Sinha, P.  R. (2007). Antidiabetic effect of probiotic dahi containing Lactobacillus acidophilus and Lactobacillus casei in high fructose fed rats. Nutrition, 23(1), 62–68. Yamashiro, K., Tanaka, R., Urabe, T., Ueno, Y., Yamashiro, Y., Nomoto, K., Takahashi, T., Tsuji, H., Asahara, T., & Hattori, N. (2017). Gut dysbiosis is associated with metabolism and systemic inflammation in patients with ischemic stroke. PLoS One, 12(2), e0171521. Yang, T., Santisteban, M. M., Rodriguez, V., Li, E., Ahmari, N., Carvajal, J. M., Zadeh, M., Gong, M., Qi, Y., Zubcevic, J., Sahay, B., Pepine, C. J., Raizada, M. K., & Mohamadzadeh, M. (2015). Gut dysbiosis is linked to hypertension. Hypertension, 65(6), 1331–1340. Zhang, H., DiBaise, J.  K., Zuccolo, A., Kudrna, D., Braidotti, M., Yu, Y., Parameswaran, P., Crowell, M. D., Wing, R., Rittmann, B. E., & Krajmalnik-Brown, R. (2009). Human gut microbiota in obesity and after gastric bypass. Proceedings of the National Academy of Sciences of the United States of America, 106(7), 2365–2370. Zhu, W., Gregory, J. C., Org, E., Buffa, J. A., Gupta, N., Wang, Z., Li, L., Fu, X., Wu, Y., Mehrabian, M., Sartor, R. B., McIntyre, T. M., Silverstein, R. L., Tang, W. H. W., DiDonato, J. A., Brown, J. M., Lusis, A. J., & Hazen, S. L. (2016). Gut microbial metabolite TMAO enhances platelet hyperreactivity and thrombosis risk. Cell, 165(1), 111–124. Zhu, L., Zhang, D., Zhu, H., Zhu, J., Weng, S., Dong, L., Liu, T., Hu, Y., & Shen, X. (2018). Berberine treatment increases Akkermansia in the gut and improves high-fat diet-induced atherosclerosis in Apoe−/− mice. Atherosclerosis, 268, 117–126.

Gut Microbiome and Its Role in Enteric Infections with Microbial Pathogens Catherine Galleher, Kyah van Megesen, Audrey Resnicow, Josiah Manning, Lourdes Recalde, Kelly Hurtado, and William Garcia

1  Introduction Enteric infections are typically caused by enteric bacteria. Bacteria enter the human or animal body and travel to the intestines to cause acute enteric diseases. Some common examples of enteric bacteria are Escherichia coli, Vibrio cholerae, Shigella, and Salmonella enterica. The main route of entry is the mouth, since these are organisms most commonly found in contaminated food or water. When contaminated food is consumed, pathogenic organisms instantly gain access to the body and the process of invasion starts. Once the contaminated food reaches the stomach, the pH of the stomach increases as a result of digestion. When the pH in the stomach increases, some bacteria are able to survive and move on to the next part of the digestive tract, the small intestine. Fortunately, gastric juice is not the only barrier that pathogenic organisms have to overcome in order to colonize. Up to 70% of the body’s immune cells are found inside the small intestine, specifically in the ileum. These immune cells are clustered in masses called Peyer’s patches. The masses are lymphoid follicles and are considered the immune sensors of the intestines (Jung et al. 2010). They are recognized for their ability to transport luminal antigens and bacteria. The complex interactions between the Peyer’s patch cells, commensals, and pathogens induce the buildup of innate and adaptive immunity in the body.

Kyah van Megesen, Audrey Resnicow, Josiah Manning, Lourdes Recalde, Kelly Hurtado and William Garcia contributed equally with all other contributors. C. Galleher (*) · K. van Megesen · A. Resnicow · J. Manning · L. Recalde · K. Hurtado · W. Garcia Department of Animal and Avian Sciences, University of Maryland, College Park, MD, USA e-mail: [email protected] © Springer Nature Switzerland AG 2020 D. Biswas, S.O. Rahaman (eds.), Gut Microbiome and Its Impact on Health and Diseases, https://doi.org/10.1007/978-3-030-47384-6_9

187

188

C. Galleher et al.

Furthermore, pathogenic organisms need to overcome the so-called microbial barrier. Pathogenic organisms need to make space for themselves in the intestine to begin colonizing. The intestines are normally colonized by commensal bacteria with which the pathogenic organisms have to compete. According to Rolhion and Chassaing (2016), the microbial barrier “is the mechanism whereby the intestinal bacteria form a barrier to prevent incursion by new bacteria of other species or other strains of the same species. This notion is well exemplified by the range of infections resulting from the use of antibiotics, such as Clostridium difficile infection, as well as by the observation that many enteric pathogens induce stronger disease in mice under germ-free conditions (in the absence of an intestinal microbiota) or following antibiotic treatments.” As observed by Rolhion and Chassaing (2016), this is an effective protection mechanism of the lower intestinal tract. It protects the body from enteric bacterial invasions by housing beneficial bacteria that are better suited for survival in the intestines. Another protective mechanism of the digestive system is metabolites. There are many different kinds of metabolites with natural antibiotic effects. Some metabolites are efficient at destroying the cells of invading pathogens. Metabolites also work by creating competition between beneficial and pathogenic bacteria (Li et al. 2018). However, without a healthy microbial community, these types of metabolites might be absent allowing pathogenic organisms to survive due to the lack of competition from beneficial organisms that utilize metabolites. This can occur when the pH that is regulated by the normal microbiota is not within a proper range. When bacteria are not able to maintain an optimal pH, pathogens have a greater chance of surviving. For instance, as we move down the large intestine from beginning to end, we can observe an increase in pH. The first section of the large intestine, known as the ascending colon, has a pH of approximately 5.7. The middle section, also known as the transverse colon, has a pH of approximately 6.6. Lastly, the pH within the final section of the colon, called the descending colon, has a pH of about 7.0. When changes in pH occur, e.g., an increase of pH in the first section of the colon, pathogens may pass through without being compromised. Even with the slightest change of pH in this microbial barrier, there is a greater chance that more pathogens will be able to colonize and start competing with the beneficial microorganisms within the colon. Many factors such as diet, lifestyle, age, genetics, probiotic and antibiotic use, infection, acute and/or chronic conditions, geography, and the environment can have huge impacts on the diversity of the body’s microbiota (Singh et  al. 2015). These are just a few of the many contributing factors that play a role in enteric infection. Some of these factors will be further discussed throughout this chapter. This chapter will also explain the mechanisms that pathogenic organisms utilize to cause infections in the gut. In addition, this chapter details various protective mechanisms that the body performs during invasion and the role it plays when fighting to prevent the entry of enteric pathogens into the body.

Gut Microbiome and Its Role in Enteric Infections with Microbial Pathogens

189

2  V  arious Components of Gut Microbiome and Their Metabolites The gut microbiome contains trillions of bacteria, archaea, viruses, and eukaryotes that have a tremendous impact on the physiology and health of their host due to their role in metabolism and immune defense. The amount of microbes far outnumbers the cells of the human body, and the genes of those microbes are exponentially greater than that of human genes, demonstrating their importance in human health (Shreiner et al. 2015). The contents of the gut microbiome vary greatly across different individuals, but all humans are known to contain four major phyla: Bacteroidetes, Firmicutes, Actinobacteria, and Proteobacteria. Each phylum has unique characteristics and benefits, as well as detriments to the host. The role of phyla is briefly discussed below. Bacteria are a type of prokaryote with a cell membrane that contains ester bonds, a cell wall with peptidoglycan, and one RNA polymerase. There are two types of bacteria, gram negative and gram positive. Gram-negative bacteria have a thin, single-­layered peptidoglycan layer, an outer membrane, and high lipopolysaccharide (LPS) content; produce primarily endotoxins; and are generally more pathogenic to their host. The structural difference in their cell wall is what gives the bacteria their name. Gram-positive bacteria stain purple because of their thick layer of peptidoglycan, while the gram-negative bacteria stain pink because of their thinner wall retaining less of the stain. The differences between these two types of bacteria have clinical importance. The most clinically important difference between gram-negative and gram-­ positive bacteria is the presence of lipopolysaccharides. LPS are made of a hydrophobic lipid A or endotoxin, an oligosaccharide, and a polysaccharide. LPS is detected by the identification of lipid A by the plasma membrane protein, TLR4, which activates mediators of inflammation and adaptive immune response. This immune activation is what makes LPS clinically important. Because of this, researchers have targeted the enzymes that synthesize lipid A in the development of antibiotics in an attempt to prevent LPS synthesis and kill the bacteria as a result (Raetz and Whitfield 2002). LPS is present in gram-negative bacteria, which include Proteobacteria and Bacteroidetes in the human gut. Proteobacteria is a phylum consisting mostly of gram-negative bacteria and includes six classes with variable morphology and physiology. They have been found in the skin, oral cavity, vaginal tract, and most abundantly in the gastrointestinal tract. High amounts of Proteobacteria in the gut may be indicative of a dysbiosis, as it has been seen to be more abundant in patients with gut diseases, such as irritable bowel syndrome (Shin et al. 2015). Gram-negative bacteria such as E. coli and Salmonella can cause disease due to the presence of LPS, which causes an immune response in the body, but this does not mean all gram-negative bacteria are disease-causing. Bacteroidetes, for example, include some opportunistic pathogens but are accepted to be most beneficial to the human gut and are often used in probiotics.

190

C. Galleher et al.

Firmicutes and Bacteroidetes are the dominant phyla in the human gastrointestinal tract. Bacteroidetes make up more than half of the bacterial species present, mostly inhabiting the distal gut where they ferment undigested polysaccharides to produce short-chain fatty acids (Johnson et  al. 2017). Short-chain fatty acids (SCFAs) are essential to human health, as they are readily absorbed and used as an energy source by colonocytes, liver, muscle, and other tissues. They play a role in the body’s major metabolic functions, regulating cell growth, hormone secretion, and immune response, and they have been known to prevent major diseases such as colon cancer, irritable bowel disease, and diabetes (Vinolo et al. 2011). Firmicutes also produce SCFAs, but these are linked to obesity, as they are prevalent in high-­ fat, low-fiber western diets (Cornejo-Pareja et al. 2018). The benefits and detriments of Firmicutes demonstrate the importance of a balanced gut. Overproliferation of these bacteria has been linked to obesity, but a deficiency of Firmicutes could lead to decreased SCFA production, potentially resulting in disease. As the most prevalent bacterial phyla in the human gut, Firmicutes and Bacteroidetes are vital to human health, and thus, the balance of these bacteria is important. The last of the four major bacterial phyla in the human gut is Actinobacteria. Actinobacteria are predominantly gram-positive bacteria, more common in the oral cavity than the lower gut, and produce bioactive metabolites used in medicine and agriculture. For example, Bifidobacterium is a genus of Actinobacteria commonly used as a probiotic to promote a healthy gut. Streptomyces is another genus of actinobacteria. It is commonly used in natural antibiotics and is produced when the bacteria are deprived of nutrients and form spores. Actinobacteria also include some opportunistic pathogens. For example, while Streptomyces is used for medicine and is commonly found in a healthy human, an abundance of these bacteria can cause disease (Barka et  al. 2016). Although Streptomyces are generally beneficial to human health, their potential to cause disease demonstrates the importance of a balanced gut. Some phyla contain more pathogenic bacteria than others, but they all have potential harmful effects, such as LPS production, and beneficial effects, such as SCFA production. To maintain a healthy gut microbiome, one must balance the harmful and beneficial effects by promoting diversity of microbes. A higher diversity of microbes allows for increased immune function and resiliency against disease. The type of microbes that proliferate in the gut may be indicative of health or disease, as will be discussed throughout this chapter.

3  Dynamic of the Gut Microbiome It is found that the microbiome of humans varies between individuals and changes throughout life as we age and experience different physiological events. Between individuals, the gut microbiome tends to vary more in the relative abundances of taxa rather than in the number of present taxa (Flores et al. 2014). It has been shown that individuals with more diverse microbial communities have a more stable gut

Gut Microbiome and Its Role in Enteric Infections with Microbial Pathogens

191

microbiome (Flores et  al. 2014). As the mechanisms behind the variability and dynamics of the gut microbiome become clearer, it may be possible to customize treatments that aim at changing or stabilizing the gut microbiome in order to make them more effective for an individual person. The gut microbiome begins developing from birth. It has been shown that the mode of delivery and breastfeeding patterns are significant factors in the shaping of the gut microbiota for adulthood (Bäckhed et al. 2015). The gut microbiome matures a great deal during the first year of life through a regulated process. Studies have shown that the gut microbiome matures earlier when children are breastfed for a shorter period of time (Bäckhed et al. 2015). These children have a gut microbiome rich in Clostridium species, which is a dominant species seen in adults. In contrast, 1-year-olds who are still being breastfed have a gut microbiome dominated by Bifidobacterium and Lactobacillus. The gut microbiome is thought to be completely mature between the ages of three and five (Rodríguez et al. 2015). However, throughout the entire lifespan of an individual, the gut microbiome will change in response to many factors and can also influence health as it changes (such as when dysbiosis develops). A changing gut microbiome can be associated with infection, cancer, neurodegenerative diseases, cardiovascular diseases, and stress (Nagpal et al. 2018). During early childhood, the microbiome seems to be influenced by genetics and family environment. During adulthood, the microbiome is developed and mature but can still vary in an individual in response to lifestyle and diet change (Putignani et  al. 2014; Rodríguez et  al. 2015). Environment and medication usage also influence the microbiome, especially in older people. The microbiome has been shown to be similar among family members (Yatsunenko et al. 2012). Culture and geography also play a role in the variability of the gut microbiome. Adults from the United States have a less diverse microbiome compared to Malawian and Amerindian adults. A study conducted by Goodrich et al. (2014) examined the differences in the gut microbiome composition between monozygotic and dizygotic twins to assess the role genetics play in the shaping of the gut microbiome. It was shown that monozygotic twins had higher correlated microbiota. Understanding how genetics can influence the microbiome can lead to new breakthroughs in therapies. For example, Christensenellaceae has been found to be the most heritable taxon and has been associated with a lower BMI. Christensenellaceae has been shown to decrease in mice on a high-fat diet (Zhou et  al. 2017). Interestingly, it has been shown that Christensenella minuta treatment reduced weight gain in mice when transplanted with a sample of the gut microbiome from an obese human donor (Goodrich et al. 2014). Another important factor affecting the diversity of the gut microbiome is age (Lozupone et al. 2012). The genus composition varies between age groups, and the diversity of phyla changes with age (Odamaki et al. 2016). After the age of 70, the relative abundance of Bacteroidetes starts to rise and the presence of Actinobacteria lowers. It has been shown that the gut microbiome of elderly people can be extremely variable among individuals (Claesson et al. 2011). Atypical phylum proportions are also seen in elderly people. This could suggest that elderly people can benefit more

192

C. Galleher et al.

from therapeutics aiming at changing the gut microbiome but could be more susceptible to dysbiosis and potentially harmful pathogens. Extra caution should be exercised when elderly people take medications. Further research might elucidate methods to help elderly people maintain a healthy and stable gut microbiome which in turn may reduce their risk of disease. Environmental factors are known to play a major role in human health and disease. Research conducted by Rothschild et al. (2018) has shown that the environment has a substantially greater role in the shaping of the gut microbiome when compared to host genetics. Communities that undergo rapid urbanization have a large impact on the gut microbiome of the individuals living there (Tasnim et al. 2017). Environmental changes associated with urbanization are thought to interfere with the healthy development of the gut microbiota, including an increased risk of inflammatory diseases. However, researchers believe that the gut microbiome could be used as a novel target in therapy for environmental pollution-induced poisoning (Jin et al. 2017). Stress can also be an important factor affecting the health of the gut microbiome. Irritable bowel syndrome (IBS) is a stress-related disease that affects the colon. Studies have shown stress increases the risk of disease as well as the risk for relapse (Mawdsley and Rampton2005). Common symptoms of IBS are increased gas production, constipation, and diarrhea. Along with stress, anxiety and depression have also been associated with changes in the gut microbiome (Foster et al. 2017). The network through which stress influences the gut microbiome is complex with many factors involved. The neurological changes that occur during a time of stress influence the immune system and the gut epithelia. These changes to the immune system and gut epithelia influence the gut microbiome through cytokine production (Foster et al. 2017). Additionally, the brain directly produces hormones that can affect the homeostasis within the gut. These relationships are complex, but understanding the pathways can lead to more knowledge of how and why the gut microbiome changes. This understanding can lead to new therapeutic strategies that aim at altering the gut microbiome in a positive manner and also how stress might be related to other diseases that also are associated with gut microbiome changes. Additionally, research has shown that not only does the brain affect the gut microbiome but also the gut microbiome influences the brain and its pathways. A better understanding of these feedback mechanisms might reveal novel targets for the treatment of psychological disorders (Kelly et al. 2015). Exercise has a positive effect on the diversity of the gut microbiome (Monda et al. 2017). Specifically, research shows that beneficial microbial species increase in quantity. It has even been shown that exercise can influence the gut microbiome to the same extent as diet can (Kang et al. 2014). In studies conducted in rats, it was shown that exercise can induce alterations to the gut microbiome of obese mice at the genus level (Petriz et al. 2014). In these mice, species associated with a healthy gut microbiome were enhanced. Researchers also suggest that knowledge of how the mechanisms of exercise induced changes in the gut microbiome could be useful to research on psychological disorder through the gut-brain axis (Monda et al. 2017).

Gut Microbiome and Its Role in Enteric Infections with Microbial Pathogens

193

Diet is known to have a direct effect on health due to its nutrition and toxins, but it has also been shown to modify the gut microbiome (Singh et al. 2017). A high-fat diet alters the composition of the gut microbiome due to its effect on bacterial species known to be beneficial for our health. Akkermansia muciniphila and Lactobacillus are seen to decrease in response to a high-fat diet (Singh et al. 2017). Long-term diet is not the only factor that influences the gut microbiota, but daily variations in diet can also cause the gut microbiome to change (Conlon and Bird 2015). However, these changes are not thought to change the microbiome long term at the phylum level. It has become increasingly common for health practitioners to focus on the use of pro- and prebiotics or a combination of the two (known as synbiotics), as a way to promote a healthy lifestyle. As more knowledge is gained about how certain foods can affect the gut microbiome, many supplements have been designed for “easy at home” alterations of the gut microbiome. However, many interactions remain unproven, and there are most certainly more interactions and mechanisms to be discovered. Nevertheless, the dynamics of the gut microbiome play a major role in health and disease risk, and further research will elucidate in even more depth how the variability of the gut microbiome can be used in disease treatment and prevention.

4  C  ontribution of the Gut Microbiome in Host Defense and Immunity “The states of health or disease are the expressions of the success or failure experienced by the organism in its efforts to respond adaptively to environmental challenges” (Rene Dubos 1965). The gut microbiome is reflected in one’s health. People, for the most part, control the external factors that concern the health of the gut microbiome. The vast majority of the time, individuals are responsible for what goes inside their bodies. The food consumed either benefits or disrupts the gut microbes. It is also possible that, at times, the quality of environmental conditions of the individual’s geographic location may positively or negatively stimulate the gut microbes. The exceptions to what a person can control are genetic disorders and bacterial or viral diseases that directly affect the gut, regardless of the gut’s condition. As a result of all these factors, the consequences or benefits reflect as a healthy or unhealthy individual. As stated by Dubos, the state of health or disease is the body’s response to the adverse conditions that it encounters. Beneficial gut microbes are a precursor of good health, and the level of health shows how well the microbes are performing. Furthermore, the gut microbiome plays a crucial role in the host’s defense and immunity. As stated by Belkaid and Hand (2014), our gut microbiome “plays a fundamental role in the induction, training, and function of the host immune system.” Unfortunately, there is no control over the quantity of response from the body when it faces adverse situations that disrupt mostly beneficial bacteria residing in the gut. However, the host can surely influence and encourage better responses to

194

C. Galleher et al.

these harmful situations from the body, through proper nutrition and healthier lifestyles. Moreover, the body is mainly composed of a wide diversity of microbes. Without them, the body would not produce vitamins, absorb essential nutrients from the diet, and digest food. Most importantly, fighting disease is nearly impossible without them. The immune system is a complex network of innate and adaptive components that respond to challenges in the host’s environment. It maintains homeostasis, rebuilds damaged tissues, and mitigates microbial and environmental interactions. Immunity, especially the adaptive response, develops alongside the gut microbiome. The relationship of the gut microbiome and the host immune system is key to the host’s well-being. If this relationship is in balance, the organisms in the gut and the host can live in symbiotic harmony. However, this symbiosis is easily disrupted. Disruption of the gut microbiome leads to dysbiosis and disease, chronic and acute (Belkaid and Hand 2014). It is important to understand that the development of the immune system starts at birth. When a baby is born, it acquires many of the beneficial bacteria from the mother’s birth canal. These bacteria will later colonize the baby’s gut and contribute to the development of their immunity. Soon after birth, additional beneficial bacteria are acquired through colostrum, if the baby breastfeeds. Colostrum is usually packed with a variety of nutrients, immunoglobulins, and probiotics that also contribute to the baby’s immunity. These are crucial factors which define the effectiveness of the immune system for the rest of the baby’s life. Furthermore, as humans grow, there are additional factors that contribute to shaping the immune system, which build upon the base immunity acquired as infants. These additional factors train the immune system to become stronger as it is exposed to different antigens. As the body becomes exposed to different antigens, various types of mechanisms are activated as protective responses. The lining of the intestines, also known as epithelial cells, secretes IL-8, MCP-1, Rantes, TNFa, and IL-6 and works as microbial sensors responding to the presence of pathogens. When pathogens are present, epithelial cells release signals to attract other immune cells, such as neutrophils, eosinophils, monocytes or phagocytic macrophages, and T cells. Therefore, the epithelial cells improve the response of the host’s immunity. Koh and Kim (2017) state that “In the intestinal lumen, the microbiota is consistently monitored by the mucosal immune system. Although the intestinal epithelial cells (IECs) are not traditionally classified as cells of innate immune response, they express an extensive repertoire of pattern-recognition receptors, such as Toll-like receptors.” Toll-like receptors are proteins that make up the innate immune system. The innate immune system is a detection mechanism of pathogen invasion (Takeda and Akira 2005). The cell signaling caused by the microbiota in the intestinal epithelial cells maintains the balance between tolerating commensal microbes and eliminating pathogens (Koh and Kim 2017). Moreover, the layer of mucus produced by the intestinal epithelial cells creates a physical and chemical barrier between the mucosa and microbiota. This mucus layer secretes antimicrobial peptides and regenerates the islet-derived protein family. Additionally, the intestinal epithelial cells secrete cytokines, chemokines, and

Gut Microbiome and Its Role in Enteric Infections with Microbial Pathogens

195

hormones that help maintain a balance between the bacteria and the body’s immune system. A dysbiosis in the intestinal epithelial cells results in an increased chance of intestinal inflammation in the host (Koh and Kim 2017). In summary, intestinal epithelial cells produce cytokines and chemokines to stimulate immune cells in response to gut microbes and metabolites. Antigen-specific responses are stimulated. These responses can contribute to the tolerance of foods or act as a defense mechanism against pathogenic bacteria (Okumura and Takeda 2017). Many of the commensal bacteria are known to produce substances with antimicrobial properties to stop the growth of or eliminate pathogenic bacteria. Additional inhibition also results from the competition for nutrients between commensal and pathogenic bacteria. The commensal bacteria can then shape the gut environment of the host through specific metabolites and further inhibit competition. In this way, the microbiota is a heavy contributor to the host’s immunity. Pathogens can enter the body through the intestinal mucosa, so a proper immune response from the IECs is necessary as an initial step to fight off potential diseases. ECIs are an effective barrier for combating enteric diseases through many different specialized mechanisms, such as the immune response, metabolites of commensal bacteria, mediations, and gut homeostasis.

5  Competitive Exclusion of Transit Microbes A major disruption of the gut microbiome is caused by other microbes. The microbiome is constantly exposed to environmental challenges, one of the biggest challenges being other organisms. Animals are constantly exposed to microscopic organisms from the environment, in food, water, and even by swallowing saliva. The resident microflora has to compete with these new organisms for space, nutrients, and other vital survival factors. Contrary to the common conception that ecological competition is destabilizing, competition in the gut may actually have stabilizing effects. One of the ways competition stabilizes the gut microbiome is by balancing the effects of cooperation that can lead to decreased diversity. When species are cooperative, they increase in number and colonize the gut, thus excluding other species and further increasing in number. This increase of selective species and decrease of others lead to a decrease in overall diversity, which destabilizes the gut microbiome because competition increases negative feedback loops, which have a beneficial effect. Similarly, competition increases stability by dampening positive feedback loops (Coyte et al. 2015). Feedback loops are the effects of the microbes on their own abundance. In a negative feedback loop, a change results in the opposite effect occurring. For example, microbes produce metabolites that change host DNA expression to control gut retention time to avoid diarrhea and constipation, and disruption would cause signaling pathways to correct it. Similarly, in thermoregulation, the body produces sweat in response to increased heat and shivers in response to increased cold. These negative feedback loops maintain a stable environment within the host. In contrast,

196

C. Galleher et al.

positive feedback loops result in an ecosystem change, thus destabilizing the environment (Lozupone et al. 2012). The stabilizing effects of competition demonstrate the importance of diversity in the gut. Competition also plays a central role in immune response, by excluding pathogenic bacteria. The gut microbiome excludes organisms through competition of receptors, nutrients, metabolites, pH, gut morphology, and the host’s immune system. Each topic is briefly discussed below.

6  Receptor-Mediated Competitive Exclusion There are many different proteins involved in the colonization and adherence of microbes in the gut. Examples are lipopolysaccharides (LPS), the cytoplasmic membrane, the outer membrane, flagella, pili, and the periplasm. Elements of host-­ cell surfaces, adhesive glycoproteins, and integral host membrane receptors all play a major role in the adherence of bacteria. These factors can be used not only by desired bacteria but also by pathogens and other bacteria that provoke negative effects on our health. Pathogens can use these structures to invade the gut epithelia and to outgrow the native microbiota. However, when these structures are already occupied by commensal bacteria, this can form a protection mechanism against pathogenic growth and invasion. Glycoproteins play a major role in bacterial colonization of the gut. The mucus layer, which covers the gut epithelia, is formed by mucin glycoproteins (Juge2012). These mucins form binding sites for bacteria, both pathogenic and commensal bacteria. Competition of commensal is an important factor in keeping a balanced microbiome and a healthy gut. Different lectins are thought to be involved in bacterial adhesion to mucins. Many bacteria produce surface lectins (Sharon 1987). Different mucins and lectins have been identified, but not everything is clear on how these different types influence competition (Juge2012). However, if these molecular structures and interactions could be better understood, the knowledge may be used to make probiotics more effective and to target bacteria more specifically to eliminate them from the gut. For example, probiotics could be designed to have lectins with higher affinity to mucins, or specific antibodies or antagonists could be used to block pathogens from binding to the mucus layers of the gut. Additionally, certain lectins seem to have other functions influencing competitive exclusion aside from adhesion. Certain C-type lectins have been shown to play a role in innate antimicrobial defense (Cash et al. 2006). Mice studies have shown that symbiotic bacteria promote the epithelial cells of the intestines to secrete these antimicrobial proteins that bind peptidoglycan carbohydrates on the bacterial targets. This secretion seems to mainly occur in the small intestine. In humans, a known C-type lectin is human hepatocarcinoma-intestine-pancreas (HIP). It is identical to human pancreatitis-associated protein (PAP) and, therefore, known as HIP/ PAP protein (Christa et al. 1996). HIP/PAP is known to be involved in pathologic mucosal inflammation (Ogawa et al. 2003). Protein expression of HIP/PAP has seen

Gut Microbiome and Its Role in Enteric Infections with Microbial Pathogens

197

to be upregulated in epithelial cells of the colon in inflammatory bowel disease (IBD) patients. This could be a reaction of the body on the dysbiosis seen in IBD (Matsuoka and Kanai 2015). If the regulation of HIP/PAP secretion is better understood, this could be used to enhance the effects of probiotics. Also, this could be used as a more natural and less harsh way to correct the onset of minor dysbiosis. Additionally, if more of these naturally secreted antimicrobials can be identified, they could be used as therapy strategies for fighting and preventing infections. With a better understanding of the different types of receptors and ligands, probiotics could be designed to be more effective. Also, the molecular pathways these receptors are involved in could give further insight into the effects that bacterial colonization has on gut health and how receptor binding indirectly influences the competition of bacteria. The receptor-mediated competitive exclusion is not only a matter of competition for space in the gut but also a complex network of underlying molecular mechanisms which are still being explored.

7  Nutrient-Mediated Competitive Exclusion Nutritional resources are a necessary part of microbial competition. Gastrointestinal pathogens compete with the endogenous microbiota for a colonization niche. A major nutrient source is carbon, and the impact of carbon nutrition on the colonization of the gut by the microbiota is significant. Competition for nutrient acquisition between enteric pathogens and the microbiota causes a protective mechanism against infection and is an important aspect of colonization resistance. Evolution of new nutrient acquisition mechanisms and metabolic diversification contributes to a pathogen’s survival and persistence and is an important determinant of the course of bacterial infections. Enteric pathogenic bacteria face a series of barriers to colonizing the GI tract. The human gut is a very complex ecosystem that has a high number of commensal bacteria that compete with pathogens for nutrients and space. There is a protective viscous mucus layer that covers intestinal epithelium to prevent easy bacterial access to the epithelium. The competition between both pathogenic and commensal bacteria arises from the fact that both are able to consume carbohydrates from the mucus as a carbon and energy source (Pacheco and Sperandio2015). Pathogens from enteric diseases contain several traits to maximize their rapid increase in numbers in the lumen, including motility, chemotaxis, and iron-­ scavenging and nutrient-sensing systems (Pacheco and Sperandio2015). A specific example that involves competitiveness of beneficial commensal bacteria against pathogens of enteric diseases involves customized diets or probiotic interventions aimed at improving pathogen exclusion based on nutrient competition. One study demonstrated that administration of a probiotic E. coli strain reduced murine colonization by S. typhimurium and also further concluded (Raffatellu M.) that probiotic bacteria reduce S. typhimurium intestinal colonization by competing for iron (Deriu et al. 2013). Not only do commensal and pathogenic E. coli share their preferences for particular carbon sources they utilize during intestinal colonization, but they

198

C. Galleher et al.

also present differences due to their spatial segregation inside the human gut. Commensal or good E. coli strains are found in the lumen and attached to the mucus layer, while pathogenic E. coli strains are able to cross the mucus layer, thus exposing them to nutrients available at the epithelium interface (Pacheco and Sperandio2015). Bacterial infections are influenced by the characteristics of good and pathogenic bacteria. Competition with members of the gut microbiota for the same nutrients is necessary for pathogen clearance. The utilization of limiting nutrients is the basis for the coexistence of members of the gut microbiota. It has also a major impact on bacterial infection, as pathogens are trying to find alternative nutrient sources to avoid competition with commensals (Pacheco and Sperandio2015). A study done on nutrient competition showed that virulence gene expression was triggered early but reduced during late stages of infection, moving a Citrobacter rodentium, a specific mouse pathogen, from the epithelium to the gut lumen, where the pathogen was exposed to commensal bacteria and had to compete for similar carbon sources for luminal growth. Results concluded that virulence and metabolism both act during bacterial infection, and both nutrient utilization and production of virulence traits are required to establish successful colonization by pathogenic bacteria. Nutrient competition was seen between C. rodentium and commensal E. coli and B. theta, thus presenting that E. coli can outcompete C. rodentium due to its ability to grow on monosaccharides, while B. theta cannot outcompete C. rodentium because it can grow on polysaccharides (Kamada et al. 2013). Overall, competition for similar nutrient sources is an important determinant of the outcome of bacterial infections of the mammalian intestine and suggests that shifting the commensal microbiota toward nutrient competition with pathogens may be an alternative to fight bacterial infections. Furthermore, from understanding nutrient competition, research suggests that if an enteric infection in which antibiotic treatment is not advisable, it is possible to use probiotic strains to reinforce colonization resistance as an alternative to treatment of enteric infections.

8  M  etabolite Production and PH Changes in Competitive Exclusion Competitive exclusion is defined as the interaction of, possibly, several different factors that can affect the gut microbiome population and results in constant changes in gut microbiota populations. These changes in population can range from millions to very miniscule. The factors that are responsible for changing the gut microbial communal population can include host diet, host environment, host genetic makeup, and lifestyle. Host diet can change the gut microbe population via possible changes in diet that deviate from the norm for that specific individual, while environmental and lifestyle changes can affect the gut microbiota via factors like radiation for example. Finally, the genetic makeup of an individual can affect the gut microbiota

Gut Microbiome and Its Role in Enteric Infections with Microbial Pathogens

199

tremendously via factors like immunity and many more. Many of these factors take into account the influences that a host can impose on their own body but are able to influence the gut population greatly. Ingestion of unhealthy foods is the most prevalent and common reason why competitive exclusion or even dysbiosis of the gut microbial community may occur (Salonen and de Vos2014). Around the world, we are able to detect changes in gut microbiota and the diseases they cause when in disbalance by tracking the foods people from different parts of the world consume (De Filippo et al. 2010). Competitive exclusion is not always a bad thing; in fact, it is the major driver that keeps opportunistic pathogens at bay and from over dominating healthy gut microbiota. It helps humans and animals maintain gut health and proper digestion and even results in providing the host with nutrients via microbial death, for example, by providing proteins that are very important for proper cattle growth. By eating healthy and promoting clean environmental practices, we can improve the gut health of humans and production animals. This benefit comes from the promotion of growth of beneficial bacteria like Lactobacillus and beneficial E. coli in cattle and in our own gut microbiome (De Filippo et al.2010). As the population of beneficial gut increases, they are able to “outcompete” other possibly harmful pathogenic species of bacteria in the gastrointestinal tracts of humans and animals. Many opportunistic pathogenic bacteria that normally live in the gut are unable to colonize under unfavorable circumstances such as pH. The true glandular stomach contains a pH that tends to stay stable at around 2 on the pH scale (Lee et al. 2000). This is considered to be the normal range for humans and has shown to be optimal for the beneficial bacteria within our flora as well as hindering the growth of pathogenic bacterial species mentioned before. Therefore, by adjusting human diets to promote appropriate gut pH, as well as a host of other beneficial factors, we can help in promoting the competitive exclusion of pathogenic species within the gut, ultimately leading to better human health. Although we can help our healthy microbiota in their fight to protect us by eating healthy foods or foods that have a component of fermentation added to them, it is also important to recognize the abilities of microbes to adapt and apply their own tools in competitive exclusion, mainly the different metabolites that they are able to secrete into their environment. Such metabolites may include lactic acid and antimicrobial factors. As mentioned briefly before, gut microbial species are also able to apply their own changes to their environment, the gastrointestinal tract, to improve conditions for their own population’s growth and survival (De Filippo et  al.2010). These changes are typically in response to and associated to host changes like diet and the aforementioned factors. These “tools” take the form of molecules, called metabolites, produced by said microbes and are important for individual or communal survival. These metabolites are often responsible for maintaining the microbe population as these metabolites can help a species more efficiently and effectively survive in the gastrointestinal system of humans and animals. This competitive edge evolved by gut microbes gives species an advantage toward survival as well as a tool for the use of outcompeting other microbes that may be fighting for the same real estate or nutritional components available within their environment. A healthy

200

C. Galleher et al.

i­ndividual should have a balance of the major populations of microbes that exist within the normal gastrointestinal tract, for example, bacteria that belong to the Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria families. A popular, beneficial, and yet underrated bacteria to the general public Lactobacillus is great for human health (Koenig et al. 2011). Lactobacillus is able to provide great strain on the pathogenic population of the gut microbiota and is essential in the attempt to dwindle the numbers and outcompete pathogenic populations within the gut like that of Campylobacter (Lee et  al. 2000). They are able to do this by producing metabolites that adjust the environment around them, giving them an edge in survival. Lactobacillus is able to produce the metabolite, lactic acid, which is able to hinder the growth of other opportunistic pathogenic bacteria like Pseudomonas aeruginosa and Campylobacter jejuni. With their decrease, an overall healthier gut microbiota community can flourish.

9  Shaping Gut Morphology for Competitive Exclusion Bacillus circulans and Paenibacillus polymyxa are able to produce bacteriocins which can cause different effects in regard to aiding in pathogenic resistance. These effects can result in a change in gut morphology (Cole et al. 2006). Bacteriocins are antimicrobial peptides produced by some bacteria that can affect the growth and survival of other, closely related or similar bacteria from a different strain. In more recent research, bacteriocins are being studied as a possible replacement or additional tool to assist in antibiotics. Meaning it is possible to one day use bacteriocins as an alternative to some antibiotics that can cause more long-term problems in terms of antibiotic resistance. Campylobacter, for example, has been studied to be the major cause of foodborne diseases in the US food production industry. Campylobacter is a bacterium that lives in the gastrointestinal tract of food animals like poultry and cattle. It can even be found in unpasteurized milk that comes from infected cattle. Campylobacter is able to invade the human gut if ingested and can contaminate and spread to other meats that have simply touched one another. Campylobacter is shown to be much more prevalent in the commercial farming industry than in natural environments (Cole et al. 2006). This may be a testament to how the density of animal production affects the spread of bacterial colonization in a group of animals. The prevalence of Campylobacter in chickens at the market was calculated to be at 47% and is responsible for giving affected humans diarrhea, bloating, and fevers after the consumption of infected meats (Padungtod and Kaneene2005). Before the application of bacteriocins to poultry infected with Campylobacter, colony-forming units were found to be at a density of 1.1 × 10^7, while after treatment with bacteriocins as a sort-of narrow-spectrum antibiotic, the colony-forming unit of Campylobacter had dropped to 1 × 10^2, a significant drop in density (Cole et al. 2006). This suggests that bacteriocins possess factors that are optimal for the management of Campylobacter within the gut microbiota.

Gut Microbiome and Its Role in Enteric Infections with Microbial Pathogens

201

As mentioned before, competitive exclusion is defined as being the introduction of beneficial bacteria (nonpathogenic) with the purpose of reducing or eliminating enteric pathogens in a microbial community. In this case, the Bacillus circulans and P. polymyxa were added into the gut microbiota of poultry in order to allow for the production of bacteriocins that would theoretically curve the population of Campylobacter and reduce instances of diarrhea in patients who have consumed the infected meat (Padungtod and Kaneene2005). Also, as bacteriocins are metabolites that are commonly known for their usefulness in controlling specific enteric microbes, they have been applied to foods for the purpose of preservation during storage and transportation. This may provide a better way to package and store meats without adding more harmful preservatives. The method of which it is hypothesized that bacteriocins are able to affect the growth of Campylobacter was via the alteration of the gut morphology, specifically in the intestinal lining of the gastrointestinal tract. In order to measure this, the effect of the treatments was determined by measurements of the microvilli in the intestines that were taken via standard methods of height, length, and density. This was accompanied by data via measuring the height of the villi, depth of intestinal crypts, and density of said crypts within a premeasured segment of the intestine. It was shown that after the treatment of poultry with bacteriocins, the measurements of all these factors, villi height and crypt depth, as well as the number and density of goblet cells, had decreased. Goblet cells are known to be the major players of mucosal development in the intestine. It is thought that the reason why this decrease in villi length, depth of crypts, and goblet cells reduced the presence of Campylobacter was due to the theory that Campylobacter requires a thick mucosal layer to be able to imbed themselves into the intestinal lining as well as survive attacking factors from other microbiota, overall increasing their prevalence (Cole et al. 2006). Thus, by reducing the layer thickness of their preferred environment, a decrease in their overall population was a result. Although this experiment was successful in decreasing the prevalence of Campylobacter within the gut microbiota of poultry, the methods still have to be researched as the decrease in microvilli height and crypt depth may have unwanted consequences in terms of absorption rate within the gut (Xu et al.2003). This can potentially decrease growth efficiency and possibly cut into farm cost versus benefit margins. Meaning that due to the loss of surface area from the very effects of bacteriocins that make it an option for reducing instances of disease as well as being a replacement for narrow-spectrum antibiotics could also be a negative effect when it comes to the overall production.

10  A  ctivating the Immune System as a Mechanism for Competitive Exclusion A normal, healthy gut microbiome can generate conditions that disfavor colonization of enteric pathogens. Colonization resistance (CR) is the prevention of enteric pathogen growth, and if disrupted, the pathogens can gain the opportunity to grow to high levels. Breakdown of CR can lead to increased susceptibility of infections.

202

C. Galleher et al.

Pathogen expansion can cause negative effects by triggering inflammatory host responses and pathogen-mediated disease. The inflammatory immune responses in the gut, such as those caused by pathogenic bacteria, can alter the gut luminal milieu and cause dysbiosis (Stecher2015). Probiotics are also important in stimulating immunity, regulating immune signaling pathways, producing antipathogenic factors, and inducing the host to make antipathogenic factors. Probiotics can also produce secretion factors that stimulate or suppress cytokines and cell-mediated immunity. These factors could interfere with key immune signaling pathways such as the MAP kinase cascades. Probiotic strains such as Lactobacillus rhamnosus GG (LGG) may activate NF-kB and the signal transducer while also activating transcription (STAT) signaling pathways in human macrophages (Britton and Versalovic2008). On the other hand, probiotic Lactobacillus strains can suppress signaling or MAP kinase-/c-Jun-mediated signaling. Stimulation of key signaling pathways and enhancement of pro-­inflammatory cytokine production may be important to begin the immune response for defense against gastrointestinal infections. The suppression of immune signaling may be an important mechanism to promote homeostasis and tolerance to microbial communities with many potential antigens, and these immunosuppressive functions may promote healing or resolution of infections. For example, rotavirus infection results in acute gastroenteritis with accompanying dehydration and vomiting mainly in young children. This infection of human rotavirus first infects intestinal epithelial cells of the distal small intestine, resulting in enterotoxin-mediated damage to intestinal barrier function (Britton and Versalovic2008). Recent studies indicate that probiotics may reduce the duration and ameliorate disease due to rotavirus infection (G. Preidis). Probiotics promoted intestinal immunoglobulin production and appeared to reduce the severity of intestinal lesions due to rotavirus infection in a mouse model. These findings and related investigations suggest that probiotics may diminish the severity and duration of gastrointestinal infections by mechanisms independent of direct pathogen antagonism. Probiotics may also promote healing and homeostasis by modulating cytokine production and facilitating intestinal barrier function. According to research studies observing gut hormones on immune activation, gut inflammation activates cells in the immune system. Two major products of enteric endocrine cascades are serotonin known as (5-hydroxytryptamine: 5-HT) and chromogranins (Cgs). These molecules help in immune activation and generation of inflammation (Khan and Ghia 2010). 5-HT activates the immune cells to produce proinflammatory mediators by manipulating the 5-HT system in order to modulate gut inflammation. Besides probiotics, the interaction between immune and endocrine systems is very likely to play an important role in immune activation in relation to gut pathology in various GI disorders and enteric diseases, including irritable bowel disease (Khan and Ghia 2010). GI endocrine cell (EC) also plays an important role since there is close proximity between EC cells and immune cells in the gut mucosa. Further research also suggests that cytokines from immune cells can activate EC cell secretion, which means that interaction between gut endocrine and immune

Gut Microbiome and Its Role in Enteric Infections with Microbial Pathogens

203

systems may be responsible for aspects of pathophysiology in GI inflammation (Khan and Ghia 2010). Overall, activating the immune system through stimulating immunity with probiotics can prevent enteric infections from worsening. Furthermore, the role of gut hormones in the pathogenesis of both GI and inflammatory and enteric infections can potentially lead to improved therapeutic strategies in inflammatory infections.

11  Biotherapeutic or Preventative Applications of Microbes The power of microbes can be harnessed in industrial methods through the varying forms of biotherapeutics. Biopharmaceuticals can include recombinant proteins like interferons and growth hormones that can be purified from genetically modified organisms that are designed to produce a certain product. This area of biotechnology relies heavily on the utilization of genetic cloning and plasmid vectors to insert the respective target human gene into the host genome. Once the gene is successfully transferred to the host genome, the microbe can begin producing the preferred biopharmaceutical drug for therapeutic use in humans. Escherichia coli is a common host microorganism used to express recombinant proteins for therapeutic use as E. coli is known for its quick rate of growth, efficient recombinant protein synthesis, and cost-effectiveness (Baeshen et al. 2015). Human proteins, like the peptide hormone insulin, can be produced in E. coli through heterologous expression, where the insulin can then be purified through chromatography and later packaged for human therapeutic use. In fact, E. coli was the first expression host approved for biopharmaceutical manufacturing of human insulin in 1982 (Quianzon and Cheikh2012). Insulin is incredibly important for those suffering from diabetes mellitus where the body’s production of insulin is limited. Microbial production of insulin eliminated the need for harvesting insulin from animals like swine and allowed a greater supply of insulin as well. However, there are some limitations to using E. coli as an expression host for different heterologous proteins, as errors in protein translation can occur due to the rare codons within human heterologous genes. Common problems such as amino acid substitutions, premature termination, or stalling of the ribosome can occur due to codon bias such as rare codons like AGA, AGG, CGG, and more within E. coli (Kane 1995). Other limiting factors for E. coli use in biotherapeutics are problems with protein solubility and folding, as the translated heterologous proteins often aggregate into inclusion bodies that require molecular chaperons to aid in proper protein solubilizing and folding (Carrió and Villaverde2003). Besides E. coli, other microbes play important roles in the production of biotherapeutics. Through the history of drug discovery, many drug metabolites have been found to be intermediates produced through microbial metabolism. Fungi have long been known to produce compounds of medicinal use, beginning with the discovery of the beta-lactam antibiotic penicillin in 1928 (Lobanovska and Pilla2017).

204

C. Galleher et al.

However, fungi are also known to produce mycotoxins that can cause diseases relatively benign such as athlete’s foot or produce carcinogenic aflatoxins that could ultimately cause cancer. Other fungal organisms can synthesize chemotherapeutic compounds like paclitaxel, cholesterol-lowering statins like lovastatin, and immunosuppressants such as cyclosporine that are needed by humans living with autoimmune disorders or organ transplants. Filamentous fungi have also seen widespread application in the production of extracellular enzymes like β-d-galactosidase, also known as lactase, the enzyme capable of catabolizing the disaccharide lactose into its monomers galactose and glucose. This biotherapeutic use of fungi is incredibly important to humans that are lactose intolerant, as through supplements of the lactase enzyme produced from fungi; these humans can now enjoy dairy products without worrying about how the body will react to their meal. Recently, there has been groundbreaking research into the efficacy of using psilocybin-producing fungi for the treatment and preventative care for psychiatric disorders like major depression and anxiety (Griffiths et  al. 2016). As noted, fungal microbes can produce both beneficial and detrimental metabolites in relation to human health. Bacteriophages have shown promising results in preventing colonization and subsequent infection from pathogenic bacteria. Bacteriophage therapy is the utilization of viruses as antibacterial agents, a technique becoming increasingly important as the amount of antibiotic-resistant bacteria increases. Bacteriophage therapy was first implemented in treating bacterial dysentery in 1919. Bacteriophages are dependent upon their bacterial hosts in order to finish the lytic cycle, in which the bacteriophage reprograms the metabolism of the host to produce progeny virions. The bacteriophages then lyse the bacterial cell wall and are released into the surrounding environment to find new bacterial hosts to infect. Microbes can also be utilized as a live biotherapeutic product (LBP) in which the microbes are administered in various routes for an intended preventive effect in humans or animals. LBPs commonly contain microorganisms from the genera Lactobacillus or Bifidobacterium, which are applicable for treating, preventing, or curing human diseases. However, an LBP cannot be a vaccine. Within the United States, LBPs are regulated by the Food and Drug Administration’s Center for Biologics Evaluation and Research (CBER). In order to be allowed for sale on the biopharmaceutical market, clinical trials must be completed and reviewed to evaluate the safety and efficacy of the product. LBPs can perform a wide range of preventative functions, such as limiting the growth of other microbes. Researchers recently studied the efficacy of implementing asymptomatic bacteriuria for the treatment of recurrent uncomplicated bacterial urinary tract infections within dogs (Segev et al. 2018). Results indicated that this E. coli-based LBP was able to clinically cure a portion of the dogs afflicted with the chronic UTIs, which shows the clinical application of LBPs to veterinary medicine. A table of recent LBPs in development is presented below (Olle 2013) (Table 1).

Gut Microbiome and Its Role in Enteric Infections with Microbial Pathogens

205

Table 1   Live biotherapeutic products and their associated agents Company Actogenix Enterologics Osel

Oxthera Vedanta Biosciences Viropharma Vithera Pharmaceuticals

LBP agent Engineered Lactococcuslactis Escherichia coli M17 Lactobacillus crispatus Clostridium butyricum Engineered Lactobacillus jensenii Oxalobactor formigenes Consortium of Clostridium strains Nontoxigenic Clostridium difficile Engineered Lactococcuslactis

Indications Oral mucositis

Stage of development Phase 1

Pouchitis Urinary tract infections, bacterial vaginosis CDI, antibiotic-associated diarrhea HIV prevention Hyperoxaluria IBD

Preclinical Phase 2 Phase 2 Preclinical

Preclinical Preclinical

CDI

Phase 1

IDB

Preclinical

12  Conclusions The gut microbiome is a community of organisms that interact with each other and their host to maintain a symbiotic relationship. Bacteria, viruses, fungi, and other microscopic organisms are constantly cooperating and competing for resources in the gut of humans and other animals. These interactions can be symbiotic and beneficial to the host or even detrimental to the human host. The microbiome contributes to all aspects of human health, not solely gut health, suggesting the importance of research in this field. Future research is needed to more thoroughly understand the health and wellness implications these microbes can have on various aspects of human life. A cataclysmic event that wipes out all microbes on Earth would have far-reaching effects on humans. Human applications of bactericides, fungicides, and virucides appear to have positive effects, but there could be detrimental side effects down the road. With antibiotic resistance on the rise, the importance of long-term research is evident. Long-term research may elucidate better ways to mitigate antibiotic resistance and treat diseases that require antibiotics.

References Bäckhed, F., Roswall, J., Peng, Y., Feng, Q., Jia, H., Kovatcheva-Datchary, P., et  al. (2015). Dynamics and stabilization of the human gut microbiome during the first year of life. Cell Host & Microbe, 17, 690–703. Baeshen, M. N., Al-Hejin, A. M., Bora, R. S., Ahmed, M. M. M., Ramadan, H. A. I., Saini, K. S., Baeshen, N. A., & Redwan, E. M. (2015). Production of biopharmaceuticals in E. coli: Current scenario and future perspectives. Journal of Microbiology and Biotechnology, 25, 953–962.

206

C. Galleher et al.

Barka, E. A., Vatsa, P., Sanchez, L., Gaveau-Vaillant, N., Jacquard, C., Klenk, H. P., et al. (2016). Taxonomy, physiology, and natural products of Actinobacteria. Microbiology and Molecular Biology Reviews, 80, 1–43. Belkaid, Y., & Hand, T. W. (2014). Role of the microbiota in immunity and inflammation. Cell, 157, 121–141. Britton, R. A., & Versalovic, J. (2008). Probiotics and gastrointestinal infections. Interdisciplinary Perspectives on Infectious Diseases, 2008. Carrió, M. M., & Villaverde, A. (2003). Role of molecular chaperones in inclusion body formation. FEBS Letters, 537, 215–221. Cash, H. L., Whitham, C. V., Behrendt, C. L., & Hooper, L. V. (2006). Symbiotic bacteria direct expression of an intestinal bactericidal lectin. Science, 313, 1126–1130. Christa, L., Carnot, F., Simon, M.  T., Levavasseur, F., Stinnakre, M.  G., Lasserre, C., et  al. (1996). HIP/PAP is an adhesive protein expressed in hepatocarcinoma, normal Paneth, and pancreatic cells. American Journal of Physiology-Gastrointestinal and Liver Physiology, 271, G993–G1002. Claesson, M. J., Cusack, S., O'Sullivan, O., Greene-Diniz, R., de Weerd, H., Flannery, E., et al. (2011). Composition, variability, and temporal stability of the intestinal microbiota of the elderly. Proceedings of the National Academy of Sciences, 108, 4586–4591. Cole, K., Farnell, M. B., Donoghue, A. M., Stern, N. J., Svetoch, E. A., Eruslanov, B. N., et al. (2006). Bacteriocins reduce Campylobacter colonization and alter gut morphology in Turkey poults. Poultry Science, 85, 1570–1575. Conlon, M., & Bird, A. (2015). The impact of diet and lifestyle on gut microbiota and human health. Nutrients, 7, 17–44. Cornejo-Pareja, I., Muñoz-Garach, A., Clemente-Postigo, M., & Tinahones, F.  J. (2018). Importance of gut microbiota in obesity. European Journal of Clinical Nutrition, 1. Coyte, K. Z., Schluter, J., & Foster, K. R. (2015). The ecology of the microbiome: Networks, competition, and stability. Science, 350, 663–666. De Filippo, C., Cavalieri, D., Di Paola, M., Ramazzotti, M., Poullet, J. B., Massart, S., et al. (2010). Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proceedings of the National Academy of Sciences, 107, 14691–14696. Deriu, E., Liu, J.  Z., Pezeshki, M., Edwards, R.  A., Ochoa, R.  J., Contreras, H., et  al. (2013). Probiotic bacteria reduce salmonella typhimurium intestinal colonization by competing for iron. Cell Host & Microbe, 14, 26–37. Dubos, J. R. (1965). Man Adapting. New Haven: Yale Uniervsity Press. Flores, G. E., Caporaso, J. G., Henley, J. B., Rideout, J. R., Domogala, D., Chase, J., et al. (2014). Temporal variability is a personalized feature of the human microbiome. Genome Biology, 15, 531. Foster, J. A., Rinaman, L., & Cryan, J. F. (2017). Stress & the gut-brain axis: Regulation by the microbiome. Neurobiology of Stress, 7, 124–136. Goodrich, J. K., Waters, J. L., Poole, A. C., Sutter, J. L., Koren, O., Blekhman, R., et al. (2014). Human genetics shape the gut microbiome. Cell, 159, 789–799. Griffiths, R. R., Johnson, M. W., Carducci, M. A., Umbricht, A., Richards, W. A., Richards, B. D., Cosimano, M. P., & Klinedinst, M. A. (2016). Psilocybin produces substantial and sustained decreases in depression and anxiety in patients with life-threatening cancer: A randomized double-blind trial. Journal of Psychopharmacology, 30, 1181–1197. Jin, Y., Wu, S., Zeng, Z., & Fu, Z. (2017). Effects of environmental pollutants on gut microbiota. Environmental Pollution, 222, 1–9. Johnson, E. L., Heaver, S. L., Walters, W. A., & Ley, R. E. (2017). Microbiome and metabolic disease: Revisiting the bacterial phylum Bacteroidetes. Journal of Molecular Medicine, 95, 1–8. Juge, N. (2012). Microbial adhesins to gastrointestinal mucus. Trends in Microbiology, 20, 30–39. Jung, C., Hugot, J. P., & Barreau, F. (2010). Peyer's patches: The immune sensors of the intestine. International Journal of Inflammation, 2010.

Gut Microbiome and Its Role in Enteric Infections with Microbial Pathogens

207

Kamada, N., Chen, G. Y., Inohara, N., & Núñez, G. (2013). Control of pathogens and pathobionts by the gut microbiota. Nature Immunology, 14, 685. Kane, J. F. (1995). Effects of rare codon clusters on high-level expression of heterologous proteins in Escherichia coli. Current Opinion in Biotechnology, 6, 494–500. Kang, S. S., Jeraldo, P. R., Kurti, A., Miller, M. E. B., Cook, M. D., Whitlock, K., et al. (2014). Diet and exercise orthogonally alter the gut microbiome and reveal independent associations with anxiety and cognition. Molecular Neurodegeneration, 9, 36. Kelly, J. R., Kennedy, P. J., Cryan, J. F., Dinan, T. G., Clarke, G., & Hyland, N. P. (2015). Breaking down the barriers: The gut microbiome, intestinal permeability and stress-related psychiatric disorders. Frontiers in Cellular Neuroscience, 9, 392. Khan, W. I., & Ghia, J. E. (2010). Gut hormones: Emerging role in immune activation and inflammation. Clinical and Experimental Immunology, 161(1), 19–27. Koenig, J.  E., Spor, A., Scalfone, N., Fricker, A.  D., Stombaugh, J., Knight, R., et  al. (2011). Succession of microbial consortia in the developing infant gut microbiome. Proceedings of the National Academy of Sciences, 108, 4578–4585. Koh, J. H., & Kim, W. U. (2017). Dysregulation of gut microbiota and chronic inflammatory disease: From epithelial defense to host immunity. Experimental & Molecular Medicine, 49, e337. Lee, Y. K., Lim, C. Y., Teng, W. L., Ouwehand, A. C., Tuomola, E. M., & Salminen, S. (2000). Quantitative approach in the study of adhesion of lactic acid bacteria to intestinal cells and their competition with enterobacteria. Applied and Environmental Microbiology, 66, 3692–3697. Li, Z., Quan, G., Jiang, X., Yang, Y., Ding, X., Zhang, D., et  al. (2018). Effects of metabolites derived from gut microbiota and hosts on pathogens. Frontiers in Cellular and Infection Microbiology, 8. Lobanovska, M., & Pilla, G. (2017). Penicillin’s discovery and antibiotic resistance: Lessons for the future? The Yale Journal of Biology and Medicine, 90, 135–145. Lozupone, C. A., Stombaugh, J. I., Gordon, J. I., Jansson, J. K., & Knight, R. (2012). Diversity, stability and resilience of the human gut microbiota. Nature, 489, 220. Matsuoka, K., & Kanai, T. (2015). The gut microbiota and inflammatory bowel disease. Seminars in Immunopathology, 37, 47–55. Mawdsley, J. E., & Rampton, D. S. (2005). Psychological stress in IBD: New insights into pathogenic and therapeutic implications. Gut, 54, 1481–1491. Monda, V., Villano, I., Messina, A., Valenzano, A., Esposito, T., Moscatelli, F., et  al. (2017). Exercise modifies the gut microbiota with positive health effects. Oxidative Medicine and Cellular Longevity, 2017. Nagpal, R., Mainali, R., Ahmadi, S., Wang, S., Singh, R., Kavanagh, K., et al. (2018). Gut microbiome and aging: Physiological and mechanistic insights. Nutrition and Healthy Aging, 4, 267–285. Odamaki, T., Kato, K., Sugahara, H., Hashikura, N., Takahashi, S., Xiao, J. Z., et al. (2016). Age-­ related changes in gut microbiota composition from newborn to centenarian: A cross-sectional study. BMC Microbiology, 16, 90. Ogawa, H., Fukushima, K., Naito, H., Funayama, Y., Unno, M., Takahashi, K. I., et al. (2003). Increased expression of HIP/PAP and regenerating gene III in human inflammatory bowel disease and a murine bacterial reconstitution model. Inflammatory Bowel Diseases, 9, 162–170. Okumura, R., & Takeda, K. (2017). Roles of intestinal epithelial cells in the maintenance of gut homeostasis. Experimental & Molecular Medicine, 49, e338. Olle, B. (2013). Medicines from microbiota. Nature Biotechnology, 309–315. Pacheco, A. R., & Sperandio, V. (2015). Enteric pathogens exploit the microbiota-generated nutritional environment of the gut. Microbiology Spectrum, 3. Padungtod, P., & Kaneene, J. B. (2005). Campylobacter in food animals and humans in northern Thailand. Journal of Food Protection, 68, 2519–2526. Petriz, B. A., Castro, A. P., Almeida, J. A., Gomes, C. P., Fernandes, G. R., Kruger, R. H., et al. (2014). Exercise induction of gut microbiota modifications in obese, non-obese and hypertensive rats. BMC Genomics, 15, 511.

208

C. Galleher et al.

Putignani, L., Del Chierico, F., Petrucca, A., Vernocchi, P., & Dallapiccola, B. (2014). The human gut microbiota: A dynamic interplay with the host from birth to senescence settled during childhood. Pediatric Research, 76, 2. Quianzon, C. C., & Cheikh, I. (2012). History of insulin. Journal of Community Hospital Internal Medicine Perspectives, 2. Raetz, C.  R., & Whitfield, C. (2002). Lipopolysaccharide endotoxins. Annual Review of Biochemistry, 71, 635–700. Rodríguez, J. M., Murphy, K., Stanton, C., Ross, R. P., Kober, O. I., Juge, N., et al. (2015). The composition of the gut microbiota throughout life, with an emphasis on early life. Microbial Ecology in Health and Disease, 26, 26050. Rolhion, N., &Chassaing, B. (2016).When pathogenic bacteria meet the intestinal microbiota. Philosophical Transactions of the Royal Society B: Biological Sciences, 371. 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, 210. Salonen, A., & de Vos, W. (2014). Impact of diet on human intestinal microbiota and health. Annual Review of Food Science and Technology, 5, 239–262. Segev, G., Sykes, J. E., Klumpp, D. J., Schaeffer, A. J., Antaki, E. M., Byrne, B. A., Yaggie, R. E., & Westropp, J. L. (2018). Evaluation of the live biotherapeutic product, asymptomatic bacteriuria Escherichia coli 2-12, in healthy dogs and dogs with clinical recurrent UTI. Journal of Veterinary Internal Medicine, 32, 267–273. Sharon, N. (1987). Bacterial lectins, cell-cell recognition and infectious disease. FEBS Letters, 217, 145–157. Shin, N. R., Whon, T. W., & Bae, J. W. (2015). Proteobacteria: Microbial signature of dysbiosis in gut microbiota. Trends in Biotechnology, 33, 496–503. Shreiner, A. B., Kao, J. Y., & Young, V. B. (2015). The gut microbiome in health and in disease. Current Opinion in Gastroenterology, 31, 69. Singh, P., Teal, T. K., Marsh, T. L., Tiedje, J. M., Mosci, R., Jernigan, K., Zell, A., Newton, D. W., Salimnia, H., Lephart, P., Sundin, D., Khalife, W., Britton, R. A., Rudrik, J. T., et al. (2015). Intestinal microbial communities associated with acute enteric infections and disease recovery. Microbiome, 3, 45. Singh, R. K., Chang, H. W., Yan, D., Lee, K. M., Ucmak, D., Wong, K., et al. (2017). Influence of diet on the gut microbiome and implications for human health. Journal of Translational Medicine, 15, 73. Stecher, B. (2015). The roles of inflammation, nutrient availability and the commensal microbiota in enteric pathogen infection. Metabolism and Bacterial Pathogenesis, 297–320. Takeda, K., & Akira, S. (2005). Toll-like receptors in innate immunity. International Immunology, 17, 1–14. Tasnim, N., Abulizi, N., Pither, J., Hart, M. M., & Gibson, D. L. (2017). Linking the gut microbial ecosystem with the environment: Does gut health depend on where we live? Frontiers in Microbiology, 8, 1935. Vinolo, M. A., Rodrigues, H. G., Nachbar, R. T., & Curi, R. (2011). Regulation of inflammation by short chain fatty acids. Nutrients, 3, 858–876. Xu, Z. R., et al. (2003). Effects of dietary fructooligosaccharide on digestive enzyme activities, intestinal microflora and morphology of male broilers. Poultry Science, 82(6), 1030–1036. Yatsunenko, T., Rey, F. E., Manary, M. J., Trehan, I., Dominguez-Bello, M. G., Contreras, M., et al. (2012). Human gut microbiome viewed across age and geography. Nature, 486, 222. Zhou, D., Pan, Q., Shen, F., Cao, H. X., Ding, W. J., Chen, Y. W., & Fan, J. G. (2017). Total fecal microbiota transplantation alleviates high-fat diet-induced steatohepatitis in mice via beneficial regulation of gut microbiota. Scientific Reports, 7, 1529.

Antibiotic Therapy and Its Effect on Gut Microbiome in Obesity and Weight Loss Paola I. Bonilla-Carrero, Hannah Mader, Nathan Meier, Isis Olivas, Bridget Boyle, and P. Bonilla-Carrero

1  Introduction An increase in the numbers of gastrointestinal diseases has become a serious problem in the United States. Millions of people are diagnosed with Crohn’s disease, inflammatory bowel syndrome (IBS), ulcerative colitis, along with other gastrointestinal issues (Kappelman et al. 2012; Locke III et al. 2004). All of these disorders have been associated with a disbalance of microbes present in the gastrointestinal tract. Gut dysbiosis causes other adverse effects and can be involved in several health problems, including obesity. Obesity in children and adults has increased substantially in the past decades. The excessive use of antibiotics and the Western pattern diet are commonly attributed to the increase of obesity in the United States. The discovery of synthetic antibiotics was a breakthrough in medicine. It drastically increased life expectancy by fighting infections and epidemics that were thought to be lethal to humans. Different categories of antibiotics are used to treat specific illness or help control many diseases in patients. Due to their efficacy in treating infection, populations across the world relied on them for many medical complications. Antibiotics are being prescribed to patients at an escalating rate every year, the CDC indicating that in 2016, 270.2 million antibiotics were sold in the United States alone (CDC 2017; Durkin et al. 2018). Nevertheless, there are consequences to this prolonged use of antibiotics, which include antibiotic resistance and imbalance of the gut microbiota. Most humans in developed countries are becoming increasingly reliant on antibiotics to treat infections. While this may be successful in some cases of bacterial infections, the short- and long-term overuse and misuse of antibiotics can lead to chronic consequences (Pichichero 1999; McGowan Jr 1983). This review aims to explain the concept of antibiotic therapy and its impact on the gut microbiome, as well as antibiotic resistance. Gut dysbiosis, obesity, and other P. I. Bonilla-Carrero (*) · H. Mader · N. Meier · I. Olivas · B. Boyle · P. Bonilla-Carrero Department of Animal and Avian Sciences, University of Maryland, College Park, MD, USA e-mail: [email protected] © Springer Nature Switzerland AG 2020 D. Biswas, S.O. Rahaman (eds.), Gut Microbiome and Its Impact on Health and Diseases, https://doi.org/10.1007/978-3-030-47384-6_10

209

210

P. I. Bonilla-Carrero et al.

gastrointestinal diseases will be defined while also illustrating alternate methods for treating infections without the use of synthetic antibiotics.

2  The Gut Microbiome The gut microbiome is one of the most vital organs in the human body. Different microorganisms make up the gut microbiota including bacteria, virus, yeast, fungi and are involved in systematic functions of the body, including the production of hormones, peptides, and modulating immune response (Martin et al. 2019; Conlon and Bird 2015; Koskinen et al. 2017; Belkaid and Hand 2014). Many of the gastrointestinal problems known to date are now being attributed to an imbalance in the gut microbiome. There is increasing evidence supporting the issues regarding antibiotic use as a cause for disrupting the integrity of the gut microbiota imbalance (Jakobsson et  al. 2010; Francino 2016; Theriot et  al. 2014). This negative effect corresponds with changes in gene expression, protein activity, metabolism, and susceptibility to disease (Francino 2016; Bonder et  al. 2016; Xiong et  al. 2015; Ni Lochlainn et al. 2018). In order to understand how antibiotics affect the microorganisms in the gastrointestinal tract, their mechanisms and properties must be discussed.

2.1  Microbial Distribution and Gut Ecology As previously mentioned, the gut microbiome plays an essential role in the training and maturing the immune system to protect against pathogens. Aside from this, it is also responsible for synthesizing vitamins and nutrients, maintaining adequate energy homeostasis, and influencing host behavior. Gut dysbiosis is defined as a persistent imbalance in the gut’s microbial integrity and can lead to inabilities of the gut microbiome to fulfill many of its vital functions (Belizário and Faintuch 2018). Antibiotics have been shown to disrupt the ecology of the gut, altering the function of the immune function and its capacity for metabolizing food (Langdon et al. 2016). Different antibiotics alter the ecology of the gut microbiome in various ways depending on their mode of action. Maintaining a balance of commensal microbial species within the gut ensures that nutrients and space are adequately utilized to prevent infection or inflammation. Antibiotics not only kill harmful bacteria, but they also kill mutualistic microbes, which benefit the host through physiological functions (Gad EL-Hak et al. 2018). Removal of any species of microbes may give opportunistic pathogens the physiological and spatial chance to thrive. These pathogens are bacteria that reside in the host at low levels and do not cause a significant harm. However, when given the opportunity, these microbes can replicate and become pathogenic to the host. Prescribed antibiotics commonly treat infections; nevertheless, specific pathogens are not targeted by antibiotics. Instead, they generally target cells that are either Gram-negative or Gram-positive. There have been

Antibiotic Therapy and Its Effect on Gut Microbiome in Obesity and Weight Loss

211

multiple studies displaying that antibiotics can cause long-term effects on the composition of the gut microbiota (Langdon et al. 2016; Francino 2016). One such study observed the impact that a seven-day treatment of clindamycin on the microbiota. There was a sharp decline in the diversity of the Bacteroides, which persisted through the sampling period of 2 years (Jernberg et al. 2007). Yet another study by Panda (2014) examined the composition of the gut microbiome after treatment with the broad-spectrum antibiotics, fluoroquinolones, and beta-lactams. Samples were collected from participants a week before and a week after treatment, and results showed that there was a decrease of 25% in microbial diversity and a reduction in the core phylogenetic microbiota from 29 taxa to 12 taxa. When antibiotics are administered, the bacteria they eliminate can present an opening in both nutrients and space on the intestinal wall for other bacteria to colonize. In some cases, this can result in pathogenic microbes growing in significant numbers. A common example of this is Candida overgrowth after antimicrobial treatment. Candida is the species of fungus responsible for yeast infections that can take advantage of the destruction of bacteria that results from a course poly-antibiotic treatment (Jenkinson and Douglas 2002). Taking antibiotics unnecessarily puts the patient at risk of developing other infections such as those caused by Candida.

2.2  Interactions Between Antimicrobials and Gut Microbiome Antimicrobials are any compounds that kill or inhibit the growth of microbes. When we are referring to antimicrobials, these can vary between natural or synthetic substances (Kourkouta et al. 2017). The natural world provides compounds with a valuable antimicrobial activity which have been used before synthetic antibiotics were discovered (Hayashi et  al. 2013). Some examples of these are garlic, cinnamon, onion, apple cider vinegar, turmeric, among others. The natural antimicrobials may be unavoidable. Citric acid comes from common fruits like oranges and lemons, and lactoferrin is present in milk. Synthetic antibiotics are produced through chemical synthesis involving sulfa drugs, or they can also be synthesized by modifying the chemistry of natural compounds (Kümmerer 2009). Synthetic antibiotics are more commonly prescribed by doctors to combat infections. All antimicrobials have a degree of impact on the composition of the gut microbiome. Antimicrobial agents are found both within an individual’s natural body and can be found in the food that individual eats. Most microbes present in the gut grow best at a neutral pH at or around 7.0 (Krulwich et al. 2011). This range is why the acidity of the stomach is one of the first lines of defense against pathogenic bacteria in the diet. Citric acid from citrus fruits, acetic acid from vinegar, and other organic acids reduce the pH of the stomach. Most of the bacteria that inhabit the stomach are either acidophiles or microbes such as Helicobacter pylori, which may have mechanisms that protect the mucosal layer from the outside pH (Blaser 1997; Mishra

212

P. I. Bonilla-Carrero et al.

2013). However, low pH from acids can prevent microbes from passing through the stomach to the colon where they can begin to colonize. Plants, fruits, and vegetables can also be sources of antimicrobials. Herbs and spices have been used for many years to add flavoring, as well as essential oils from cloves, oregano, rosemary, thyme, sage, and vanillin, which their phenolic group exerts activity against Gram-positive bacteria. The impact that naturally occurring antimicrobials exert does not go unnoticed. Their natural chemistry is used as phytomedicine, like aloe and opium. However, they can also be a base for developing synthetic drugs (Iwu et al. 1999).

2.3  Synthetic Antibiotics and Its Applications The use of antibiotics had a tremendous impact on medicine and public health through the elimination of undesired and pathogenic microorganisms. In less than a century, these drugs have changed the way populations across the world treat infections, grow livestock, as well as the changes that it has brought to the composition of the gut microbiome. Antibiotics target different cellular components and systems. They can be classified as bactericidal drugs or bacteriostatic drugs. Common antibiotics are bactericidal and can affect the synthesis of DNA, RNA, protein, or cell wall (Kohanski et al. 2010a). Bactericidal antibiotics mechanism is to reduce the number of viable cells. The production of hydroxyl radicals is triggered by bactericidal antibiotics (Kohanski et al. 2007). The increased level of OH− radicals attacks DNA, lipids, and proteins (Foti et al. 2012). The model presented by Kohanski et al. (2007) brings forth bactericidal antibiotic interactions with cells and goes as follows. The drugs stimulate oxidation of NADH via the electron transport chain, which depends on the TCA cycle. Since the antibiotic is hyperactivating the electron transport chain, it stimulates superoxide formation. The result of superoxide formation is the damaging of iron-sulfur clusters, making ferrous iron available for the Fenton reaction. This leads to hydroxyl radical formation, which in turn damages DNA, proteins, and lipids, leading to cell death (Kohanski et al. 2007). The cell death is irreversible, and this is the main difference between the two types of antibiotics. Kohanski et  al. (2010b) conferred that administering sublethal levels of antibiotics resulted in poly-­ antibiotic resistance. This mechanism is mainly mediated by bactericidal drugs (Kohanski et  al. 2010b). When bacteria are exposed to bacteriostatic antibiotics, they remain stagnant without dying (Pankey and Sabath 2004). Bacteriostatic drug’s effect on bacteria can be reversed with the removal of the antibiotic (Kümmerer 2009). Common antibiotics are usually bactericidal, but modern antibiotic therapy has implemented the combination of both bactericidal and bacteriostatic to increase.

Antibiotic Therapy and Its Effect on Gut Microbiome in Obesity and Weight Loss

213

2.4  Major Class of Antibiotics The chemical structure of each antibiotic is what distinguishes them from each other. It also determines its properties: whether physical, chemical, microbiological, pharmacological, or clinical. There are different classifications for antibiotics (Table 1) with distinct mechanism of actions. The mode of action of the different class of antibiotics varies. Still, they tend to target the following parts of microbes: the cell membranes, the cell-wall synthesis, protein synthesis, and the replication of nucleic acid (Hancock 2005). These processes will be explained further on the next section. Nevertheless, just as antibiotics can fight against pathogenic bacteria, these same bacteria have developed resistance against them, which are also discussed on Table  1. There are changes that the microbiota suffers when it undergoes broad-­ spectrum antibiotic courses like macrolide. If this treatment is administered when the organism is young, it can have an obesogenic effect (Block et al. 2018).

2.5  Mechanism of Actions of Commonly Used Antibiotics As mentioned earlier, there are different mechanisms by which antibiotics target and kill bacteria. These can be within a host, inhibiting DNA synthesis, RNA synthesis, cell wall synthesis, and protein synthesis. The first form of killing antibiotics is inhibiting DNA synthesis, during cell replication as seen in Quinolones (Table 1). DNA must unwind and transcribe itself through various mechanisms and enzymes. The way these antibiotics work is by diffusing into the outer membrane of the bacteria and reaching their target. The antibiotic molecule binds itself to DNA gyrase, inhibiting its activity, preventing DNA from replicating and, thereby inhibiting bacterial multiplication (Munita and Arias 2016). The second mechanism by which antibiotics kill bacteria is by inhibiting RNA synthesis as seen in rifamycins (Table  1). This form of antibiotic inhibits RNA synthesis by inhibiting bacterial DNA-dependent RNA polymerase. This antibiotic penetrates the outer membrane of the bacteria and diffuses inside the bacterium, reaching their target. In this case, the enzyme DNA-dependent RNA polymerase and the antibiotics attach itself to this particular enzyme, preventing it from binding itself to the DNA strand, therefore not being able to replicate itself (Munita and Arias 2016). The last form of mechanism antibiotics use to kill bacteria is by inhibiting protein synthesis (e.g., tetracycline, phenicols, and oxazolidinones). The way through which antibiotics inhibit protein synthesis is by penetrating the outer membrane of the bacteria. Once inside the bacteria, the antibiotics find tRNA synthetases, an enzyme required to activate amino acids for peptide synthesis, to bind to it, thereby preventing the bacteria from undergoing protein synthesis (Munita and Arias 2016). By using one form of these methods, antibiotics are able to kill the bacteria itself or prevent the bacteria from multiplying.

214

P. I. Bonilla-Carrero et al.

Table 1  List of common synthetic antibiotics, their classification, and mechanism of actions, and their resistance pattern Antibiotic classification β-Lactams

Mechanism of action Impairment of peptidoglycan biosynthesis (Williamson et al. 1986) Bacteria’s cells die by autolytic enzymes (Heesemann 1993)

Amino-­ glycosides

Inhibit protein synthesis (Kanoh and Rubin 2010a) as they adhere to the A-Site on the 16S ribosomal RNA of the 30S ribosome (Kotra et al. 2000)

Macrolides

Prevents synthesis of protein in bacteria by inhibiting ribosome function (Kanoh and Rubin 2010b)

Glycopeptides

Inhibit the formation of the cell wall (Allen and Nicas 2003)

Tetracycline

Enters the bacterial cell and blocks protein biosynthesis when negatively interacting with the ribosome (Chopra et al. 1992).

Streptogramins

Inhibits protein synthesis by targeting the 50S ribosomal subunit of bacteria (Hancock 2005)

Resistance Modification of the permeability barrier of the cell Inhibition of its enzymatic target Production of enzymes that inactivate the antibiotic Fail to release autolytic enzymes (Heesemann 1993) Decreased permeability of the bacterial cell wall Environmental triggers which alter its gene and/ or protein expression Fusion of exogenous genetic material or mutation of an existing gene (Garneau-Tsodikova and Labby 2015) It can be target-based when there is a shift in the 23S ribosomal RNA residue Mutation in ribosomal proteins (Fyfe et al. 2016) Biosynthesis of an altered peptidoglycan precursors that the glycopeptides fails to bind with (Allen and Nicas 2003). Limiting tetracycline access to the ribosome Alter the effective binding of tetracycline to the ribosome Producing enzymes that inactivate tetracycline (Speer et al. 1992) Target modification, synthesis of enzymes that modify proteins, drug efflux (Leclercq and Courvalin 1998).

Examples Penicillin, cephalosporins, penems, monobactams

Streptomycin, gentamicin, spectinomycin

Erythromycin, azithromycin

Teicoplanin, vancomycin

Minocycline, tigecycline

Synercid

(continued)

Antibiotic Therapy and Its Effect on Gut Microbiome in Obesity and Weight Loss

215

Table 1 (continued) Antibiotic classification Mechanism of action Oxazolidinones Inhibits protein synthesis by blocking early stages on the small (30S) ribosomal subunit (Champney and Miller 2002). Phenicols Inhibits synthesis of bacterial protein by binding to the ribosome (Dinos et al. 2016) Quinolones

Sulfonamides

Rifamycins

Lipopeptides

Resistance Modification of oxazolidinone target (Bozdogan and Appelbaum 2004)

Examples Linezolid

Chloramphenicol Target mutations in the rRNA Alteration in ribosomal proteins (Dinos et al. 2016) Ciprofloxacin Modifying the target Obstructs DNA synthesis, by targeting on DNA gyrase enzymes Shifts in drug entry and and topoisomerase IV efflux Compromises the linking Plasmids produce number of DNA by two Quinolone-resistant (Fabrega et al. 2008) protein, which shields the target enzymes from quinolones (Jacoby 2005) Chromosomal mutation, Sulfamethoxazole Competitive antagonist of which causes lower para-aminobenzoic acid causes an inhibitory effect. affinity of enzymes to sulfonamides. Alternative This prevents folic acid metabolic pathways synthesis and thereafter, DNA synthesis (Tačić et al. (Tačić et al. 2017) 2017) Creates an enzyme complex Structural mutations on a Rifampicin subunit of RNA that inhibits the bacterial polymerase (Wehril RNA polymerase (Wehril 1983) 1983) Binding to the bacterial cell Resistance is rare, and it Daptomycin has been difficult to membrane and Calcium-­ dependent insertion into the generate in vitro or in clinical studies cytoplasmic membrane (Steenbergen 2005) (Thorne and Alder 2002)

2.6  Antibiotic Therapy and Methods of Resistance The increasing use of antibiotics consequently leads to the spread of antibiotic resistance across human pathogens, which lessens the opportunity for controlling such pathogens (Langdon et al. 2016). The introduction of antibiotics revolutionized the field of medicine and public health, increasing life expectancy, and saving lives by preventing more severe infections (Davies and Davies 2010; Adedeji 2016). Data from the research by Van Boeckel et al. (2014) reveal how in a matter of a decade, from 2000 to 2010, the emergence and consumption of antibiotics rose by 35%. This accelerated usage, as well as utilizing antibiotics “last resort antibiotic” has

216

P. I. Bonilla-Carrero et al.

been detrimental to public health (Van Boeckel et al. 2014). All in all, the use of these drugs has been rapidly abused by physicians, livestock producers, and pharmacologist, thereby causing the emergence of resistant strains (Davies and Davies 2010). The emergence of new resistant strains occurs at a higher rate than the discovery and introduction of new antimicrobial treatments to fight these infections (Langdon et al. 2016). The most common mechanism used by bacteria, which causes resistance, is through changing of target sites of antibiotics (Kohanski 2010a). In this particular method, the bacteria act on membranes and substrates use chemical mechanisms to change the target, and this prevents the antibiotics from binding to its site, allowing the bacteria to resist death (Blair et al. 2014). Another mechanism used by bacteria to become resistant to antibiotics using efflux pumps, commonly seen in Escherichia coli, Campylobacter jejuni, Salmonella enterica, and Pseudomonas aeruginosa. Bacteria produce pumps that sit on the cell wall. When antibiotics penetrate the cell wall,  they are able to pump out the antibiotics before it has time reach its target site with the help of this efflux pumps (Blair et al. 2014). Bacteria can also become resistant to antibiotics by destroying the antibiotic all together. With this form of resistance, bacteria are able to create enzymes that inactivate antibiotics; an example of this form of resistance is beta-lactamase, and this particular enzyme destroys the active component of penicillin (Blair et al. 2014). A developed mechanism by bacteria is modifying their cell wall, especially its permeability, often used by Gram-negative bacteria to target hydrophilic molecules like tetracyclines (Munita and Arias 2016). In order for an antibiotic to be able to kill bacteria, it needs to penetrate the outer membrane; when a bacterium changes the composition of its outer membrane, it becomes harder for the antibiotic to penetrate through the membrane. Due to the ongoing development and spread of antibiotic-resistant microbes, it is increasingly vital to restrict how antibiotics are used. In doing so, many things must be considered, such as type of drug, frequency of use, age of use, administration route, and dosage. If these factors are not controlled, it could have negative consequences on controlling pathogenic dissemination. A major contributing factor to the spread of antibiotic resistance is their overuse. Although antibiotics require a physician’s prescription, the tendency of treatment of nonbacterial infections has shifted toward a firm reliance on these drugs. Every time an individual uses an antibiotic when there is no bacterial infection present, it kills the sensitive bacteria that have not developed resistance, and it leaves the resistant bacteria behind. This pattern creates a problem when antibiotics are repeatedly used because it allows resistant bacteria to continually accumulate and become abundant. Aside from overuse, antibiotic misuse is another contributing factor to the spread of antibiotic resistance. These drugs are only effective against bacterial infections; however, many people resort to using antibiotics against common viral infections such as a common cold or bronchitis (Pecheré 2001). Overall, it is essential to utilize antibiotics effectively and correctly. As the incidence of antibiotic resistance drastically increases, the development of novel antibiotics moves at a slower pace, with only one of the five new drugs being able to reach

Antibiotic Therapy and Its Effect on Gut Microbiome in Obesity and Weight Loss

217

the Food and Drug Administration for approval and with difficulties in undergoing clinical trials (PEW 2019). This creates a huge problem and has proven to be life threatening. In 2015, it was reported that antibiotic-resistant pathogens caused over 50,000 deaths a year across the United States and Europe (Langdon et al. 2016). Antibiotics should only be used in situations where the patient benefits and when there are no equally effective alternatives. Other antimicrobial options can be utilized in many cases to fight bacterial infections. Therefore, the reliance developed on antibiotics needs to be reconsidered, as well as other alternatives to reduce this global health concern of spreading resistance.

2.7  Effect of Broad-Spectrum and Narrow-Spectrum Antibiotics Antibiotic therapy is the use of antibiotics to treat acute illnesses for a determined period (Monteagudo-chu and Shaeshaa 2017). Before starting antibiotic treatment, some factors should be taken into consideration. Such are patient health, age, length of antibiotic use, and antibiotic resistance. The patient’s health is a prime factor when starting antibiotic therapy. Individuals with renal and hepatic complications should avoid the use of antibiotics unless it is urgent (Yeung et al. 2004). If the liver and kidneys are not functional, the elimination of drugs from the body does not happen, causing an imbalance in the gut microbiota (Leekha et  al. 2011). Genetics influences the type of antibiotic therapy going under, due to possible sensitivities or adverse effects (Leekha et al. 2011). Age is another crucial factor, especially if the patient is too young or too elderly for the treatment. The differences in body size, immunity, and kidney function differ when younger than 2  years and older than 53 years. Those in between are more than likely to have the same body size, immunity, and kidney function unless otherwise (Leekha et al. 2011). Broad-spectrum antibiotics, e.g., aminoglycosides, are used to treat a broad range of bacterial groups, while narrow-spectrum, e.g., penicillin, are antibiotics used to treat a specific bacterial group (Leekha et al. 2011). Broad-spectrum antibiotics are usually used when a patient is in critical condition, and there is not time to determine the cause of the bacterial infection. On the other hand, narrow-spectrum antibiotics are used when the patient is more stable, and a section of the infection can be sampled (Leekha et al. 2011).

2.8  Antibiotics’ Role in Obesity Obesity has become a growing epidemic affecting countries worldwide. Obesity can cause many different illnesses including, type 2 diabetes, high blood pressure, heart disease, strokes, particular types of cancer, sleep apnea, osteoarthritis, fatty

218

P. I. Bonilla-Carrero et al.

liver disease, kidney disease, along with other health conditions. Although predisposition to being overweight has hereditary patterns, the increasing global numbers have brought the conclusion that Western-style diet, sedentary lifestyles, and poor health choices have made obesity an epidemic (Turta et al. 2016). Shifts in the gut microbiome composition have also been correlated with obesity (functional interactions between the gut microbiota and host metabolism). There is a distinct difference between the predominant microbial species between body types. A study on mice concluded that there is a shift between having less Bacteroidetes and more Firmicutes in obese mice compared to the lean mice (Ley et al. 2005). The increase in Firmicutes leads to an increased amount of energy harvesting abilities of the gut microbiota and ultimately the onset of obesity (Turnbaugh et al. 2006). As mentioned previously, antibiotics significantly impact the succession and diversity of the microbiome. Antibiotics create alterations within the gut microflora, and they can potentially create permanent dysbiosis (Lange et  al. 2016). Obese adults portray different gastrointestinal physiology, reduced bacterial diversity, and changes in the metabolic pathways associated with these microorganisms (Turnbaugh et al. 2009). The role of new age antibiotics in the onset of childhood obesity has been studied as obesity rates, and pediatric antibiotic use continues to climb. Many of these studies have reported that exposure to antibiotics at a young age increases the risk of a child becoming overweight (Shao et al. 2018). Infants who were treated with antibiotics before their first year of life had increased adiposity and the likelihood of adult obesity (Azad et al. 2014). The overuse and misuse of antibiotics in children influences the metabolism and body weight homeostasis within the user (Andrade et al. 2017). This shift can be due to the permanent disruption of gut microbes; for instance, there is a prevalent increase in the number of H. pylori in obese individuals (Arslan et al. 2009). Gut microbes are responsible for producing metabolites and signaling the brain to produce certain hormones that regulate hunger. Leptin, a protein hormone, regulates hunger by controlling the energy balance and signals the brain to cease eating. Studies have shown that the prevalence of H. pylori is linked with leptin expression (Azuma et al. 2001). By disrupting H. pylori with the use of antibiotics, the signaling between the gut and the brain is disrupted. Another study on the impact of microorganisms on childhood obesity revealed that a higher body mass index in children between the age of 1 and 3 years was associated with Bacteroidetes fragilis (Vael et al. 2011). Therefore, the onset of obesity holds a relationship with the inadequate release of hormones which regulate hunger, and this process is mediated by the gut microbiota.

Antibiotic Therapy and Its Effect on Gut Microbiome in Obesity and Weight Loss

219

2.9  Risk for Other Diseases Dysbiosis can result from imbalance of the commensal and pathogenic microorganisms which are present in the gastrointestinal tract, or with a loss of diversity of these gut microbes (Petersen and Round 2014). Although dysbiosis is common in obese individuals, different diseases correspond with this imbalance. The human gut microbiome is highly variable, and the factors that can cause dysbiosis and diseases associated with the gastrointestinal tract are equally so. Inflammatory bowel diseases (IBD) are a group of diseases including Crohn’s disease and ulcerative colitis that cause inflammation in the mucosal epithelium. Research done to understand how the gut microbiome is affected by IBD demonstrated that patients suffering from Crohn’s disease had lower number of Firmicutes (Manichanh et  al. 2006). As a response, the presence of Gram-negative bacteria increases and could contribute to the inflammation observed in this condition. Ulcerative colitis limits its effect to the large intestines and the rectum (Henson and Phalak 2017). It is considered that the inflammation caused by these bowel diseases contributes to dysbiosis of the gut, where chronic inflammation induces increased oxygen levels resulting in an imbalance between obligate anaerobes and facultative anaerobes (Rigottier-Gois 2013). This observation is referred to as “the oxygen hypothesis” (Rigottier-Gois 2013). Complications associated with altering the gastrointestinal microflora can be displayed as interferences with digestion, food intolerances, disrupted glucose metabolism, increased stress and anxiety, and depression (Gad EL-Hak et  al. 2018). Therefore, the outcome of a triggered immune response is inflammation and alteration in the epithelial barrier of the gut.

2.10  O  ther Factors Synergistically Involved with Antibiotics in Obesity Diet The microbes present in the human gut require different nutrients to grow. The food consumed can influence which bacteria thrive and which dwindle based on the nutritional components of meals. Dietary fibers are complex carbohydrates that human’s gastrointestinal system cannot digest on its own. Microorganisms present in the gut break down fiber into short-chain fatty acids, providing the body with the necessary energy sources (Bäckhed et al. 2004). Additionally, dietary fiber has proven to be a valuable dietary source for obese individuals to improve their insulin secretion and prevent diabetes. (Bodinham et  al. 2012). By-products of fiber digestion favorably impact the gut microbiota by providing metabolites, which aid in dilutions of toxins and movement of the digestive tract (Conlon and Bird 2015).

220

P. I. Bonilla-Carrero et al.

The composition of the gut microbiome affects how they process the caloric intake of the food consumed. This phenomenon often causes human’s predisposition to obesity (Bäckhed et al. 2005). Protein is a primary nitrogen source for the microbes of the large intestines. They are broken down into peptides and amino acids, which are helpful for bacterial metabolism. Additionally, as the carbohydrates in the digestive progress through the colon to be metabolized, protein fermentation becomes more necessary (Conlon and Bird 2015). However, the end products produced by protein fermentation can be poisonous to some of the gut microbes and even host cells if present in large enough numbers (Conlon and Bird 2015). Several undesirable metabolic end products like ammonia, hydrogen sulfide, amines, and phenols have been thought to be possible carcinogens (Windey et  al. 2012). Putrefaction is a result of protein degradation, and it is associated with ulcerative colitis and other bowel problems (Windey et al. 2012). Protein fermentation alone is not enough for the host to have healthy digestion. It is essential to have a balance of both carbohydrates and proteins to provide enough energy for the eukaryotic cells of the gut. Iron is a mineral necessary for the growth and proliferation of almost all microbial species (Cherayil 2011). However, readily available iron is both scarce and heavily competed for due to its low solubility and the high demand for the mineral. Lactoferrin is an iron-chelating protein, preventing microbes from using it (Rosa et  al. 2017). Lactoferrin, therefore, exerts a large impact on the gut microbiome (Valenti and Antonini 2005). By reducing the amount of iron available for microbial cells, the microbes with the most limited ability to compete for iron may dwindle in number. However, some bacterial pathogens have developed mechanisms to counter lactoferrin. They do this either by synthesizing high-affinity chelators for themselves that can compete with lactoferrin or by developing the ability to attach to lactoferrin (Valenti and Antonini 2005). However, lactoferrin does not have a tendency of negatively impacting beneficial microbes. Neutrophils carry lactoferrin, and it is deposited in sites of bacterial infection where it performs its iron-­scavenging abilities (Masson et al. 1969; Parrow et al. 2013). Lactoferrin also has other anti-­ pathogenic functions such as inhibition of bacterial adhesion, inhibition of viral entry into host cells, and anti-inflammatory activity (Marnila and Korhonen 2009). It would be unfavorable to the host if production of antimicrobials like lactoferrin takes place, which tend to damage or destroy beneficial microbes. Also, supplementing iron can restore its deprivation caused by lactoferrin’s competition for the mineral (Valenti and Antonini 2005).

Antibiotic Therapy and Its Effect on Gut Microbiome in Obesity and Weight Loss

221

3  Recommendations for Proper Antimicrobial Therapy Without Gut Microbiome Dysbiosis As mentioned before, the consequences of improper antibiotic therapy can yield a wide array of negative results, whether it involves incorrectly prescribing antibiotics to illnesses that do not require them, not finishing their doses, or using inadequate antibiotic for the bacterial infection. For this reason, there have been different strategies including target therapy, enhancement of the gut microflora, probiotics, phage therapy, and fecal microbiota transplantation to foster positive outcomes for combating infections while reducing the detrimental effects of antibiotic use (Gagliardi et  al. 2018). These alternatives serve as a promising mechanism to potentially reduce adverse effects such as obesity.

3.1  Targeted Therapy Targeted therapy is a nonspecific, typically broad-spectrum antibiotic therapy prescribed by physicians. One of these targeted therapy practices is quorum sensing, which is the ability of a bacteria to coordinate its behavior based on population density of the flora, an action that plays a heavy role in the virulence of many different pathogens (Langdon et al. 2016). Since normal, healthy microflora have no reason to use quorum sensing, as the majority of natural flora are non-virulent to us when in the right place, this targeted therapy would allow for the reduction of the pathogens in the gut while still maintaining the commensal microflora and ensuring the best possible gut health (Langdon et al. 2016). Pathogenic bacteria that find them in the human gastrointestinal system often produce toxins in order to increase pathogenicity and virulence. Another possible target for narrow spectrum therapies includes toxin production. These toxins are highly specific to each bacterium, and targeted therapies that would inhibit the production of these toxins would potentially help decrease the virulence of a pathogen’s virulence (Langdon et al. 2016). This could be an effective target due to the high number of bacteria that actually use toxin production as a virulence factor against the normal microflora in the gastrointestinal tract. At the same time, this may not be the best method as an antibiotic therapy because of the gut flora’s natural selective pressure toward antitoxin-resistant mutant flora (Langdon et  al. 2016). Based on this, more research into the specifics of each toxin-producing bacteria would need to be done in order to create an effective antibiotic therapy. Other potential targets for antibiotic therapies are less universal among bacteria and could only be applied in specific cases. For example, it is known that the formation of pilus on E. coli, one of the more common disease-causing bacteria, is extremely important for the ability of the pathogen to adhere to host tissue (Langdon et  al. 2016). Targeting this pilus formation would cause E. coli to not be able to adhere in the host, which would therefore not allow this pathogen to cause disease

222

P. I. Bonilla-Carrero et al.

while still maintaining the diversity of nearby natural host microflora. Similar targeting strategies that focus on the virulence factors of a pathogen are possible for another bacterium as well, though not impervious to developing drug resistance (Langdon et al. 2016).

3.2  Preventing Dysbiosis by Improving the Gut Microflora One of the more effective ways to avoid gut microflora dysbiosis is enhancing the gut flora to prevent illness. To achieve this, probiotics, phage therapies, or even fecal microbe transplants can be implemented. By potentially improving the diversity of the gastrointestinal microflora, an individual might be able to prevent the onset of a disease. Researchers have acquired an increased interest in the use of probiotics to improve gut health. When administered, probiotics are thought to be an effective treatment for several gastrointestinal diseases, as well as restore and protect balance of the gut microbiota (Langdon et al. 2016). If given as an alternative to antibiotic treatment therapies, probiotics have the potential to play a significant role in treating and possibly healing gastrointestinal conditions like Crohn’s disease and irritable bowel disease. Additionally, preliminary research has shown success with probiotics as genetically bioengineered strains (Langdon et  al. 2016). Despite the overwhelming benefits of this kind of alternative therapy, there are still some potential dangers. Genetically engineering probiotics for human consumption can sound worrisome for the general public. Overcoming consumer wariness will likely be the biggest issue for the use of this kind of treatment. Regardless, the use of probiotics as a treatment to prevent gut microflora dysbiosis when using broad-spectrum antibiotic therapies could be highly effective. Bacteriophages or viruses that lyse bacteria are other potential alternatives to traditional antibiotic therapies. These are sometimes found naturally in a balanced gastrointestinal microflora. Phage therapy has become of increasing interest as an alternative to antibiotics. They also have the ability to be more precisely targeted toward a specific pathogen or a class of pathogens, which helps avoid damaging natural microbes (Langdon et al. 2016). This type of therapy can be focused for a particular infection, and treatment may be more straightforward and effective while still preventing future instances of dysbiosis. One of the more significant issues with broad-spectrum antibiotic therapies is how easily bacteria tend to develop resistance to them. With phage therapy, this issue does not go away all together, since bacteria still have the ability to develop resistance to this treatment. But despite that, phage-­ resistant pathogens have yet shown to be less damaging and virulent than average (Langdon et al. 2016). While overuse and misuse of this kind of therapy would still be a concern as a long-term solution to antibiotic treatments, phage therapy is always a potentially sustainable alternative. Similar to probiotics, genetically engineering these bacteriophages to improve modulation of the gut microbiome have proven to be successful (Langdon et al. 2016). While genetically altering organisms

Antibiotic Therapy and Its Effect on Gut Microbiome in Obesity and Weight Loss

223

and introducing it to a human’s natural flora can be concerning and potentially dangerous, there are a lot of directions in which research for treatments and prevention strategies can go to improve health by using phage therapy. As an alternative to traditional antibiotic medicines, bacteriophage therapy is a reliable substitute. The use of fecal microbe transplants, or using the microflora found in feces to the human gut, is a method of treatment that is only used in extreme situations. For example, treating Clostridium difficile infections can be done with antibiotics, but with a very high change of resistance to these antibiotics as well as spore formation capability. Replacement of the lost natural flora of the gastrointestinal system with the microbes found in feces is an attempt to push out the C. difficile bacterium, which does not survive well in healthy gut microflora (Langdon et al. 2016). Therapy is efficient for this specific infection due to the nature of the pathogen and disease. Nevertheless, it is difficult to apply to other infections and could be dangerous if the transplant is not conducted right.

3.3  Caution of Antibiotic Treatment Exposure to antibiotic therapy during the first years of life has been linked to dysbiosis in the gut of children, causing obesity, autoimmune diseases, and allergies later in adulthood (Vangay et al. 2015). Using these kinds of treatments on young children has damaging and lasting adverse health effects because of the disruption that the antibiotics cause in the gut microflora. An effort to avoid this adverse health outcome could be to apply age restrictions and guidelines for clinicians to follow when deciding what to prescribe a young patient. This way, physicians would only give a course of antibiotics to young children who imperatively need it and reduce the adverse outcomes of incorrect antibiotic use.

4  Conclusion Overuse and misuse of antibiotic therapies, without a doubt, are harmful to an individual’s gut microbiology and often lead to dysbiosis of the gastrointestinal flora. It has long been suspected dysbiosis can play a factor in the manifestation of obesity, autoimmune diseases, and other severe chronic diseases. Despite that, the use of antibiotic therapies can be beneficial to curing diseases and stopping infections. It is essential to seek out and find the best antibiotic treatment possible with the least harmful effects. Many negative factors are attributed to the use of antibiotics, especially in how it compromises the gastrointestinal microbiota. Gut dysbiosis is one of the risks associated, and this imbalance is responsible for numerous diseases. Obesity is also one of the consequences of gut dysbiosis, and it is an increasing problem in the United States and worldwide. Administering antibiotics to young children before their gut

224

P. I. Bonilla-Carrero et al.

microbiome is fully developed is one of the leading causes of obesity in children and also as they reach adulthood. Furthermore, antibiotic resistance is a dangerous consequence of the overuse and misuse of these drugs. Methods have been slowly integrating the medical field to control the use of antibiotics. Probiotics, phage therapy, as well as fecal transplants, are underway to substitute antibiotic treatment. It is crucial to limit the usage of synthetic antibiotics, balance our diet with the correct ratio of fiber and protein, and implementing natural antimicrobials as part of our diet. It is imperative to find ways to restrict this antibiotic abuse and misuse before we reach a dangerous post-­ antibiotic era. The consequences will not only increase obesity in individuals, gastrointestinal diseases, and general well-being but also could be lethal to many humans with high antibiotic resistance.

References Adedeji, W. A. (2016). The treasure called antibiotics. Annals of Ibadan Postgraduate Medicine, 14(2), 56. Allen, N.  E., & Nicas, T.  I. (2003). Mechanism of action of oritavancin and related glycopeptide antibiotics. FEMS Microbiology Reviews, 26(5), 511–532. https://doi. org/10.1111/j.1574-6976.2003.tb00628.x. Andrade, M. J., Jayaprakash, C., Bhat, S., Evangelatos, N., Brand, A., & Satyamoorthy, K. (2017). Antibiotics-induced obesity: A mitochondrial perspective. Public Health Genomics, 20(5), 257–273. https://doi.org/10.1159/000485095. Arslan, E., Atılgan, H., & Yavaşoğlu, İ. (2009). The prevalence of Helicobacter pylori in obese subjects. European Journal of Internal Medicine, 20(7), 695–697. Azad, M. B., Bridgman, S. L., Becker, A. B., & Kozyrskyj, A. L. (2014). Infant antibiotic exposure and the development of childhood overweight and central adiposity. International Journal of Obesity, 38(10), 1290. Azuma, T., Suto, H., Ito, Y., Ohtani, M., Dojo, M., Kuriyama, M., & Kato, T. (2001). Gastric leptin and Helicobacter pyloriinfection. Gut, 49(3), 324–329. Bäckhed, F., Ding, H., Wang, T., Hooper, L.  V., Koh, G.  Y., Nagy, A., et  al. (2004). The gut microbiota as an environmental factor that regulates fat storage. Proceedings of the National Academy of Sciences, 101(44), 15718–15723. https://doi.org/10.1073/pnas.0407076101. Bäckhed, F., Ley, R. E., Sonnenburg, J. L., Peterson, D. A., & Gordon, J. I. (2005). Host bacterial mutualism in the human intestine. Science, 307(5717), 1915–1920. https://doi.org/10.1126/ science.1104816. Belizário, J. E., & Faintuch, J. (2018). Microbiome and gut dysbiosis. Experientia Supplementum Metabolic Interaction in Infection, 459–476. https://doi.org/10.1007/978-3-319-74932-7_13. Belkaid, Y., & Hand, T. W. (2014). Role of the microbiota in immunity and inflammation. Cell, 157(1), 121–141. Blair, J. M., Richmond, G. E., & Piddock, L. J. (2014). Multidrug efflux pumps in Gram-negative bacteria and their role in antibiotic resistance. Future Microbiology, 9(10), 1165–1117. https:// doi.org/10.2217/fmb.14.66. Blaser, M. J. (1997). Ecology of Helicobacter pylori in the human stomach. The Journal of Clinical Investigation, 100(4), 759–762. Block, J.  P., Bailey, L.  C., Gillman, M.  W., Lunsford, D., Daley, M.  F., Eneli, I., et  al. (2018). Early antibiotic exposure and weight outcomes in young children. Pediatrics, 142(6). Retrieved from: http://pediatrics.aappublications.org/content/142/6/e20180290.long#ref-3.

Antibiotic Therapy and Its Effect on Gut Microbiome in Obesity and Weight Loss

225

Bodinham, C. L., Smith, L., Wright, J., Frost, G. S., & Robertson, M. D. (2012). Dietary fibre improves first-phase insulin secretion in overweight individuals. PLoS One, 7(7), e40834. https://doi.org/10.1371/journal.pone.0040834. Bonder, M. J., Kurilshikov, A., Tigchelaar, E. F., Mujagic, Z., Imhann, F., Vila, A. V., et al. (2016). The effect of host genetics on the gut microbiome. Nature Genetics, 48(11), 1407–1412. Bozdogan, B., & Appelbaum, P. C. (2004). Oxazolidinones: activity, mode of action, and mechanism of resistance. International Journal of Antimicrobial Agents, 23(2), 113–119. https://doi. org/10.1016/j.ijantimicag.2003.11.003. Champney, W.  S., & Miller, M. (2002). Linezolid is a specific inhibitor of 50S ribosomal subunit formation in Staphylococcus aureus cells. Current Microbiology, 44, 350–356. https://doi. org/10.1007/s00284-001-0023-7. Cherayil, B. J. (2011). The role of iron in the immune response to bacterial infection. Immunologic Research, 50(1), 1–9. https://doi.org/10.1007/s12026-010-8199-1. Chopra, I., Hawkey, P. M., & Hinton, M. (1992). Tetracyclines, molecular and clinical aspects. Journal of Antimicrobial Chemotherapy, 29(3), 245–277. https://doi.org/10.1093/jac/29.3.245. Conlon, M. A., & Bird, A. R. (2015). The impact of diet and lifestyle on gut microbiota and human health. Nutrients, 7, 17–44. Centers for Disease Control and Prevention and Centers for Disease Control and Prevention (2017). Outpatient antibiotic prescriptions—United States, 2014. Dentistry, 24, p. 203. Davies, J., & Davies, D. (2010). Origins and evolution of antibiotic resistance. American Society for Microbiology Journals, 74(3), 417–433. https://doi.org/10.1128/MMBR.00016-10. Dinos, G. P., Athanassopoulos, C. M., Missiri, D. A., Giannopoulou, P. C., Vlachogiannis, I. A., Papadopoulos, G. E., & Papaioannou, D. (2016). Chloramphenicol derivatives as antibacterial and anticancer agents: Historic problems and current solutions. Antibiotics, 5(2), 20. https:// doi.org/10.3390/antibiotics5020020. Durkin, M. J., Jafarzadeh, S. R., Hsueh, K., Sallah, Y. H., Munshi, K. D., Henderson, R. R., & Fraser, V. J. (2018). Outpatient antibiotic prescription trends in the United States: A national cohort study. Infection Control & Hospital Epidemiology, 39(5), 584–589. Fabrega, A., Madurga, S., Giralt, E., & Vila, J. (2008). Mechanism of action of and resistance to quinolones. Microbial Technology, 2(1), 40–61. https://doi. org/10.1111/j.1751-7915.2008.00063.x. Foti, J. J., Devadoss, B., Winkler, J. A., Collins, J. J., & Walker, G. C. (2012). Oxidation of the guanine nucleotide pool underlies cell death by bactericidal antibiotics. Science, 336(6079), 315–319. https://doi.org/10.1126/science.1219192. Francino, M. P. (2016). Antibiotics and the human gut microbiome: Dysbioses and accumulation of resistances. Frontiers Microbiology. https://doi.org/10.3389/fmicb.2015.01543. Fyfe, C., Grossman, T. H., Kerstein, K., & Sutcliffe, J. (2016). Resistance to macrolide antibiotics in public health pathogens. Cold Spring Harbor Perspective in Medicine, 6(10). https://doi. org/10.1101/cshperspect.a025395. Gad El-Hak, H. N., Moustafa, A. A., & Mansour, S. R. (2018). The gut microbiome - implications for human disease. Advanced Research in Gastroenterology and Hepatology, 10(3). https://doi. org/10.5772/61423. Gagliardi, A., Totino, V., Cacciotti, F., Iebba, V., Neroni, B., Bonfiglio, G., et al. (2018). Rebuilding the gut microbiota ecosystem. International Journal of Environmental Research and Public Health, 15(8), 1679. Garneau-Tsodikova, S., & Labby, K. (2015). Mechanisms of resistance to aminoglycoside antibiotics: Overview and perspectives. Medchemcomm, 7(1), 11–27. https://doi.org/10.1039/ C5MD00344J. Hancock, R. E. (2005). Mechanisms of action of newer antibiotics for Gram-positive pathogens. The Lancet Infectious Diseases, 5(4), 209–218. https://doi.org/10.1016/S1473-3099(05)70051-7. Hayashi, M., Bizerra, F., & Da Silva, P. (2013). Antimicrobial compounds from natural sources. Frontiers in Microbiology, 4, 195. https://doi.org/10.3389/fmicb.2013.00195.

226

P. I. Bonilla-Carrero et al.

Heesemann, J. (1993). Mechanisms of resistance to beta-lactam antibiotics. Infection, 21(1), 4–9. https://doi.org/10.1007/BF01710336. Henson, M.  A., & Phalak, P. (2017). Microbiota dysbiosis in inflammatory bowel diseases: in silico investigation of the oxygen hypothesis. BMC Systems Biology, 11(1), 145. https://doi. org/10.1186/s12918-017-0522-1. Iwu, M. M., Duncan, A. R., Okunji, C. O. (1999). New antimicrobials of plant origin. Perspectives on new crops and new uses. 457–462. https://hort.purdue.edu/newcrop/proceedings1999/pdf/ v4-457.pdf. Jacoby, G. A. (2005). Mechanisms of resistance to quinolones. Clinical Infectious Diseases, 41(2), S120–S126. https://doi.org/10.1086/428052. Jakobsson, H. E., Jernberg, C., Andersson, A. F., Sjölund-Karlsson, M., Jansson, J. K., & Engstrand, L. (2010). Short-term antibiotic treatment has differing long-term impacts on the human throat and gut microbiome. PLoS One, 5(3), e9836. Jenkinson, H. F., & Douglas, L. J. (2002). Interactions between Candida species and bacteria in mixed infections. https://www.ncbi.nlm.nih.gov/books/NBK2486/. Jernberg, C., Lofmark, S., Edlund, C., & Jansson, J. K. (2007). Long-term ecological impacts of antibiotic administration on the human intestinal microbiota. The ISME Journal, 1(1), 56–66. https://doi.org/10.1038/ismej.2007.3. Kanoh, S., & Rubin, B. (2010a). The mechanism of action of aminoglycosides. Clinical Microbial Reviews, 23(3), 590–615. https://doi.org/10.1128/CMR.00078-09. Kanoh, S., & Rubin, B. K. (2010b). Mechanisms of action and clinical application of macrolides as immunomodulatory medications. Clinical Microbiology Reviews, 23(3), 590–615. https:// doi.org/10.1128/CMR.00078-09. Kappelman, M. D., Moore, K. R., Allen, J. K., & Cook, S. F. (2012). Recent trends in the prevalence of Crohn’s disease and ulcerative colitis in a commercially insured US population. Digestive Diseases and Sciences, 58(2), 519–525. https://doi.org/10.1007/s10620-012-2371-5. Kohanski, M. A., Dawyer, D. J., Hayete, B., Lawrence, C. A., & Collins, J. J. (2007). A common mechanism of cellular death induced by bactericidal antibiotics. Cell, 130(5), 797–810. https:// doi.org/10.1016/j.cell.2007.06.049. Kohanski, M.  A., Dawyer, D.  J., & Collins, J.  J. (2010a). How antibiotics kill bacteria: from targets to networks. Nature Reviews Microbiology, 8(6), 423–435. https://doi.org/10.1038/ nrmicro2333. Kohanski, M. A., DePristo, M. A., & Collins, J. J. (2010b). Sublethal antibiotic treatment leads to multidrug resistance via radical-induced mutagenesis. Molecular Cell, 37(2), 311–320. https:// doi.org/10.1016/j.molcel.2010.01.003. Koskinen, K., Pausan, M.  R., Perras, A.  K., Beck, M., Bang, C., Mora, M., et  al. (2017). First insights into the diverse human archaeome: specific detection of archaea in the gastrointestinal tract, lung, and nose and on skin. MBio, 8(6), e00824–e00817. Kotra, L., Haddad, J., & Mobashery, S. (2000). Aminoglycosides: Perspectives on mechanisms of action and resistance and strategies to counter resistance. Antimicrobial Agents and Chemotherapy, 44(12), 3249–3256. Retrieved from: https://www.ncbi.nlm.nih.gov/pmc/ articles/PMC90188/. Kourkouta, L., Kotsiftopoulos, C.  H., Papageorgiou, M., Iliadis, C.  D., & Monios, A. (2017). The rational use of antibiotic medicine. Journal of Healthcare Communications. https://doi. org/10.4172/2472-1654.100076. Krulwich, T.  A., Sachs, G., & Padan, E. (2011). Molecular aspects of bacterial pH sensing and homeostasis. Nature Reviews. Microbiology, 9(5), 330–343. https://doi.org/10.1038/ nrmicro2549. Kümmerer, K. (2009). Antibiotics in the aquatic environment – A review – Part I. Chemosphere, 75(4), 417–434. https://doi.org/10.1016/j.chemosphere.2008.11.086. Langdon, A., Crook, N., & Dantas, G. (2016). The effects of antibiotics on the microbiome throughout development and alternative approaches for therapeutic modulation. Genome Medicine,

Antibiotic Therapy and Its Effect on Gut Microbiome in Obesity and Weight Loss

227

8(1), 39. Retrieved from: https://genomemedicine.biomedcentral.com/articles/10.1186/ s13073-016-0294-z. Lange, K., Buerger, M., Stallmach, A., & Bruns, T. (2016). Effects of antibiotics on gut microbiota. Digestive Diseases, 34(3), 260–268. Leclercq, R., & Courvalin, P. (1998). Streptogramins: An answer to antibiotic resistance in gram-positive bacteria. The Lancet, 352(9128), 591–592. https://doi.org/10.1016/ S0140-6736(05)79570-2. Leekha, S., Terrell, C.  L., & Edson, R.  S. (2011). General principles of antimicrobial therapy. Mayo Clinic Proceedings, 86(2), 156–167. https://doi.org/10.4065/mcp.2010.0639. Ley, R. E., Bäckhard, F., Lozupone, C. A., Knight, R. D., & Gordon, J. I. (2005). Obesity alters gut microbial ecology. PNAS, 102(31), 11070–11075. https://doi.org/10.1073/pnas.0504978102. Locke, G. R., III, Yawn, B. P., Wollan, P. C., Melton, L. J., III, Lydick, E., & Talley, N. J. (2004). Incidence of a clinical diagnosis of the irritable bowel syndrome in a United States population. Alimentary Pharmacology & Therapeutics, 19(9), 1025–1031. Manichanh, C., Rigottier-Gois, L., Bonnaud, E., Gloux, K., Pelletier, E., Frangeul, L., et  al. (2006). Reduced diversity of faecal microbiota in Crohn’s disease revealed by a metagenomic approach. Gut, 55(2), 205–211. https://gut.bmj.com/content/55/2/205.short. Marnila, P., & Korhonen, H. (2009). Lactoferrin for human health. Dairy-derived ingredients. Food and Nutraceutical Uses, 290–307. https://doi.org/10.1533/9781845697198.2.290. Martin, A.  M., Sun, E.  W., Rogers, G.  B., & Keating, D.  J. (2019). The influence of the gut microbiome on host metabolism through the regulation of gut hormone release. Frontiers in Physiology, 10, 428. Masson, P.  L., Heremans, J.  F., & Schonne, E. (1969). Lactoferrin, an iron-binding protein Ni neutrophilic leukocyte. Journal of Experimental Medicine, 130(3), 643–658. https://doi. org/10.1084/jem.130.3.643. McGowan, J. E., Jr. (1983). Antimicrobial resistance in hospital organisms and its relation to antibiotic use. Reviews of Infectious Diseases, 5(6), 1033–1048. Mishra, S. (2013). Is Helicobacter pylori good or bad? European Journal of Clinical Microbiology & Infectious Diseases, 32(3), 301–304. https://doi.org/10.1007/s10096-012-1773-9. Monteagudo-chu, M.  O., & Shaeshaa, N. (2017). Duration of antibiotic therapy: General principles. https://www.pharmacytimes.com/publications/health-system-edition/2017/july2017/ duration-of-antibiotic-therapy-general-principles Munita, J. M., & Arias, C. A. (2016). Mechanisms of antibiotic resistance. Microbiology Spectrum, 4(2). https://doi.org/10.1128/microbiolspec.VMBF-0016-2015. Ni Lochlainn, M., Bowyer, R.  C., & Steves, C.  J. (2018). Dietary protein and muscle in aging people: the potential role of the gut microbiome. Nutrients, 10(7), 929. Panda, S., El khader, I., Casellas, F., López Vivancos, J., García Cors, M., Santiago, A., et  al. (2014). Short-term effect of antibiotics on human gut microbiota. PLoS One, 9, e95476. Pankey, G.  A., & Sabath, L.  D. (2004). Clinical relevance of bacteriostatic versus bactericidal mechanisms of action in the treatment of gram-positive bacterial infections. Clinical Infectious Diseases, 38(6), 870–864. https://doi.org/10.1086/381972. Parrow, N. L., Fleming, R. E., & Minnick, M. F. (2013). Sequestration and scavenging of iron in infection. Infection and Immunity, 81(10), 3503–3514. https://doi.org/10.1128/IAI.00602-13. Pecheré, J. C. (2001). Patients’ interviews and misuse of antibiotics. Clinical Infectious Diseases, 33(3), 5170–5173. Petersen, C., & Round, J. L. (2014). Defining dysbiosis and its influence on host immunity and disease. Cellular Microbiology, 16(7), 1024–1033. https://doi.org/10.1111/cmi.12308. Pew. (2019). Tracking the global pipeline of antibiotics in development. The Pew Charitable Trust. Pichichero, M. E. (1999). Understanding antibiotic overuse for respiratory tract infections in children. Pediatrics, 104(6), 1384–1388. Rigottier-Gois, L. (2013). Dysbiosis in inflammatory bowel diseases: the oxygen hypothesis. The ISME Journal, 7(7), 1256–1261. https://doi.org/10.1038/ismej.2013.80.

228

P. I. Bonilla-Carrero et al.

Rosa, L., Cutone, A., Lepanto, M. S., Paesano, R., & Valenti, P. (2017). Lactoferrin: A natural glycoprotein involved in iron and inflammatory homeostasis. International Journal of Molecular Sciences, 18(9), 1985. https://doi.org/10.3390/ijms18091985. Shao, X., Ding, X., Wang, B., Li, L., An, X., Yao, Q., Song, R., & Zhang, J. (2018). Antibiotic exposure in early life increases risk of childhood obesity: A systematic review and meta-­ analysis. In Yearbook of pediatric endocrinology. https://doi.org/10.1530/ey.15.15.4. Speer, B.  S., Shoemaker, N.  B., & Salyers, A.  A. (1992). Bacterial resistance to tetracycline: mechanisms, transfer, and clinical significance. Clinical Microbiology Reviews, 5(4), 387–399. Retrieved from: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC358256/?page=1. Steenbergen, J.  N., Alder, J., Thorne, G.  M., & Tally, F.  P. (2005). Daptomycin: a lipopeptide antibiotic for the treatment of serious Gram-positive infections. Journal of Antimicrobial Chemotherapy, 55(3), 283–288. https://doi.org/10.1093/jac/dkh546. Tačić, A., Nikolić, V., Nikolić, L., & Savić, I. (2017). Antimicrobial sulfonamides drugs. Advanced Technologies, 6(1), 58–71. Retrieved from http://www.tf.ni.ac.rs/casopis-arhiva/ sveska6vol1/c8.pdf. Theriot, C. M., Koenigsknecht, M. J., Carlson, P. E., Jr., Hatton, G. E., Nelson, A. M., Li, B., et al. (2014). Antibiotic-induced shifts in the mouse gut microbiome and metabolome increase susceptibility to Clostridium difficile infection. Nature Communications, 5, 3114. Thorne, G.  M., & Alder, J. (2002). Daptomycin: A novel lipopeptide antibiotic. Clinical Microbiology Newsletter, 24(5), 33–40. https://doi.org/10.1016/S0196-4399(02)80007-1. Turnbaugh, P. J., Ley, R., Mahowald, M. A., Magrini, V., Mardis, E. R., & Gordon, J. I. (2006). An obesity-associated gut microbiome with increased capacity for energy harvest. Nature, 444, 1027–1031. https://www.nature.com/articles/nature05414. Turnbaugh, P. J., Hamady, M., Yatsunenko, T., Cantarel, B. L., Duncan, A., Ley, R. E., et al. (2009). A core gut microbiome in obese and lean twins. Nature, 457(7228), 480. Turta, O., & Rautava, S. (2016). Antibiotics, obesity and the link to microbes - what are we doing to our children? BMC Medicine, 14, 57. https://doi.org/10.1186/s12916-016-0605-7. Vael, C., Verhulst, S. L., Nelen, V., Goossens, H., & Desager, K. N. (2011). Intestinal microflora and body mass index during the first three years of life: an observational study. Gut Pathogens, 3(1), 8. Valenti, P., & Antonini, G. (2005). Lactoferrin. Cellular and Molecular Life Sciences, 62(22), 2576. https://doi.org/10.1007/s00018-005-5372-0. Van Boeckel, T.  P., Gandra, S., Ashok, A., Caudron, Q., Grenfell, B.  T., Levin, S.  A., & Laxminarayan, R. (2014). Global antibiotic consumption 2000 to 2010: An analysis of national pharmaceutical sales data. The Lancet Infectious Diseases, 14(8), 742–750. https://doi. org/10.1016/S1473-3099(14)70780-7. Vangay, P., Ward, T., Gerber, J.  S., & Knights, D. (2015). Antibiotics, pediatric dysbiosis, and disease. Cell Host & Microbe, 17(5), 553–564. Wehril, W. (1983). Rifampin: mechanisms of action and resistance. Reviews of Infectious Diseases, 5(3), 407–411. Retrieved from: https://www.ncbi.nlm.nih.gov/pubmed/6356275. Williamson, R., Collatz, E., & Gutmann, L. (1986). Mechanisms of action of beta-lactam antibiotics and mechanisms of non-enzymatic resistance. Presse Médicale, 15(46). Retrieved from https://www.ncbi.nlm.nih.gov/pubmed/2949269. Windey, K., De Preter, V., & Verbeke, K. (2012). Relevance of protein fermentation to gut health. Molecular Nutrition & Food Research, 56(1), 184–196. https://doi.org/10.1002/ mnfr.201100542. Xiong, W., Abraham, P. E., Li, Z., Pan, C., & Hettich, R. L. (2015). Microbial metaproteomics for characterizing the range of metabolic functions and activities of human gut microbiota. Proteomics, 15(20), 3424–3438. Yeung, E., Yong, E., & Wong, F. (2004). Renal dysfunction in cirrhosis: Diagnosis, treatment, and prevention. Medscape General Medicine, 6(4), 9. https://www.ncbi.nlm.nih.gov/pmc/articles/ PMC1480573/.

Impact of Gut Microbiota on Host by Exploring Proteomics Thomas E. Angel and Uma K. Aryal

1  Introduction Microbes are present in all ecosystems and play important roles in biogeochemical cycle and human health. The human body functions in the presence of trillions of microbes that colonize different parts of the body. There are an estimated 37 trillion cells in an average human body, and the microbiome is estimated to be comprised of slightly more cells with an estimated count of 39 trillion (Sender et al. 2016). Colonization of human intestine by microbes is the result of coevolution of relationship between the human and the gut microbiota (Fig. 1). The microbes that are present in human intestine are referred as “gut microbiota” and the genes or proteins expressed by them are referred as “gut microbiome” (Turnbaugh et al. 2006, 2007). In general, such relationships are symbiotic, and the intestine provides a complex environment for a dynamic interaction between the microbial cells and the host cells (Moeller et al. 2016). This interaction modulates many aspects of human physiology from normal postnatal development to adult health (Moeller et  al. 2016; Gordo 2019). Human health can be affected positively or negatively by the composition of microbes living in the gut (Mohajeri et  al. 2018). Altered gut microbiomes are linked to obesity, diabetes, and heart disease, and may also have implications in disorders like autism, multiple sclerosis, and Parkinson’s disease (Karlsson et al. T. E. Angel (*) GlaxoSmithKline, Collegeville, PA, USA e-mail: [email protected] U. K. Aryal Purdue Proteomics Facility, Bindley Bioscience Center, Purdue University, West Lafayette, IN, USA Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, IN, USA e-mail: [email protected] © Springer Nature Switzerland AG 2020 D. Biswas, S.O. Rahaman (eds.), Gut Microbiome and Its Impact on Health and Diseases, https://doi.org/10.1007/978-3-030-47384-6_11

229

230

T. E. Angel and U. K. Aryal

Fig. 1  Human gut microbiome analysis is typically accomplished through sampling isolates (fecal materials of mucosal luminal interface outline in Table 1) from the gut. Resultant protein isolates are derived from a complex community of bacteria as well as human cells

2013; Sharon et al. 2016). Recent studies have also revealed a link between mental health (brain function) and gut microbiota (Wong et al. 2016). Advances in genome sequencing and complimentary post-genomic technologies such as transcriptomics, proteomics, metabolomics, and bioinformatics have enabled researchers to describe the gut microbiome with unprecedented precision and detail. There is growing interest to obtain new information how life style factors such as diet, antibiotic use, sleep, exercise, and family history (genetics) influence human health through mechanism involving gut microbes. This chapter covers various topics related to the gut microbiome and focuses on how proteomics and bioinformatic approaches are enabling advances in the field of microbiome research.

2  Factors Influencing Gut Microbial Communities The relationship between gut microbes and the human host is the hallmark of a long-term coevolution (Munson et al. 1991; Moeller et al. 2016; Garud et al. 2019). Factors such as host genetics (Goodrich et  al. 1991), evolutionary co-occurrence (Ochman et al. 2010; Moeller et al. 2014), short- and long-term diets (David et al. 2014), geography (Yatsunenko et  al. 2012), and medical intervention (Forslund et  al. 2013) influence microbial profiles. Microbiomes of family members and cohabiting partners are more similar than between unrelated individuals (Song et al. 2013), indicating that families play an important role in the formation of gut microbiota (Goodrich et al. 2014; Schloss et al. 2014). Many gut microbes are inherited. For example, the family of Christensenellaceae taxon and its partners are enriched in the individuals with low body mass index (BMI) (Goodrich et al. 2014). The phylogeny of gut microbes clustered closely with the ape species phylogeny, but the close link was not related to geographical proximity because apes within the same location showed phylogenetically distinct gut microbes (Ochman et al. 2010). This study suggests that diet has little or no i­ nfluence on the relationship between host phylogeny and the gut microbial composition.

Impact of Gut Microbiota on Host by Exploring Proteomics

231

Table 1  Summary of major proteomics studies of human gut microbiota in recent years Study Patient with CD Premature infant Children Microbiota gene catalogue Healthy monozygotic twin Preterm infant Identical twins Premature female infant Mucosal-luminal interface T1D Healthy adult Patient under antibiotics T1D Stool Healthy and CD patients Healthy adult

Analytical method Nano RPLC

Instruments Orbitrap Elite

Proteins 2969 >3500

MetaPro-IQ

LTQ Orbitrap Elite Orbitrap Fusion MetaPro-IQ

Nano 2D-LC

LTQ Orbitrap

Nano-2D-LC RPLC, SCX Nano 2D-LC-MS/MS Nano-2D-­ LC-MS/MS Nano RPLC

LTQ Orbitrap Velos LTQ Orbitrap

Nano 2D-LC, RPLC, SCX Nano RPLC

Nano RPLC 1D-PAGE, Nano-2D-LC Nano RPLC Nano 2D-LC-MS/MS Nano RPLC Nano RPLC

1D-PAGE, Nano RPLC 2D-DIGE/Nano Health and CD patients (both men and RPLC women) Infant 2D-PAGE Healthy adult

Lean and obese adolescent Healthy adult

19,011 predicted 600–1000 4031 1250

LTQ Orbitrap Velos Q Exactive Orbitrap Q Exactive Orbitrap LTX Orbitrap XL LTQ Orbitrap

3011

Q Exactive

2400

Q Exactive

9147

LTQ Orbitrap Elite LTQ linear ion trap LTQ Orbitrap Discovery

14,850

MALDI TOF-MS/MS LTQ Orbitrap

1D PAGE, Nano2D-LC-MS/ MS 1D-PAGE, Nano LTQ Orbitrap UPLC Nano RPLC LTQ Orbitrap

CD Crohn’s disease, T1D type 1 diabetes

20,558

>1000 >14,000 10,908 1790

2331 peptides 141 human & 89 bacterial spots >200 protein spots >5200

613 3911 (DE) & 4587 (DC)

References Lehmann et al. (2019) Xiong et al. (2015) Zhang et al. (2018b) Zhang et al. (2016) Verberkmoes et al. (2009) Young et al. (2015) Erickson et al. (2012) Brooks et al. (2015) Zhang et al. (2018a) Gavin et al. (2018) Kolmeder et al. (2012) Perez-Cobas et al. (2013a) Heintz-Buschart et al. (2016) Zhang et al. (2018b) Blakeley-Ruiz et al. (2019) Kolmeder et al. (2016) Juste et al. (2014)

Klaassens et al. (2007) Cantarel et al. (2011) Ferrer et al. (2013) Tanca et al. (2015)

232

T. E. Angel and U. K. Aryal

This is in contrast to the report by David and co-workers (2014), who reported that short-term consumption of different diets rapidly alters microbial community in the human gut. Consumption of entirely animal-based diet increased the abundance of bile-tolerant microorganisms and decreased the levels of Firmicutes that metabolize dietary plant polysaccharides in human (David et al. 2014). Age, geography, disease state, and medical intervention change the diversity and function of human gut microbiome. Bacterial species and gene content were different between the US residents and those from the Amazon as of Venezuela and rural Malawi (Yatsunenko et al. 2012). The difference included age-related changes in genes involved in vitamin biosynthesis and metabolism. Metagenome analysis of fecal samples of 252 people from Spain, Italy, France, Denmark, Japan, and the United States revealed the persistence of antibiotic resistance genes in human gut flora for a year, and the resistance genes were more abundant in fecal samples from Spain, Italy, and France than from Denmark, the United States, and Japan (Forslund et al. 2013). Composition of gut microbes was different between lean and obese individuals (Qin et al. 2010). The gut of obese and diabetic patients contained increasing number of Firmicutes (Ley et al. 2005, 2006). Obesity-resistant mice become obese and increase their energy harvest and caloric uptake following microbiota transplant (Turnbaugh et al. 2006, 2007). Gut microbiomes are found to play a role in stress-­ related behaviors such as anxiety and depression (Foster et al. 2017). Transfer of stress-prone Balb/C microbiota to germ-free (GF) Swiss Webster (SW) mice increased anxiety-related behavior, while transfer of SW microbiota to GF Balb/C mice reduced such behavior (Bercik et  al. 2011; Crumeyrolle-Arias et  al. 2014). Evidence suggests that gut bacteria are vital for social development and normal brain development (Clarke et al. 2013; Desbonnet et al. 2014) and brain function (Ogbonnaya et al. 2015). The human gut microbiome has become the subject of intense research interests in recent years. The numbers of available microbial genomes are increasing and genome sequence database of thousands of microbes are currently available. In the last decade, there has been tremendous progress in complementary mass-­ spectrometry-­ based proteomics techniques, which are revealing new research opportunities to investigate and explain the diversity of the gut microbiome in the context of human physiology and disease. The completion of the Human Microbiome Project in 2012 and the establishment of the microbial genome reference database (Human Microbiome Project 2012) opened a new era of microbiome research. Additionally, the most recent publication of 1520 reference genome sequences from cultivated human gut bacteria (Zou et al. 2019) is another milestone in this field.

3  Principles of Proteome Analysis The proteome consists of all of the proteins within an organism, tissue, organelle, biofluid, or biological isolate. Genome sequencing informs on the potential repertoire of proteins expressed by a cell while proteomics establishes which proteins

Impact of Gut Microbiota on Host by Exploring Proteomics

233

(and proteoforms) are present and at what abundances (relative or absolute). The proteome is spatially (Lundberg and Borner 2019), temporally (Price et al. 2010, 2012a, b; Aryal et  al. 2011, 2012; Holmes et  al. 2015; Naylor et  al. 2017), and chemically dynamic (Aryal et al. 2008; Aryal and Ross 2010; Angel et al. 2012a). Proteins are the essential molecular machines of the cell, structural and functional components of signaling pathways, and biological networks. Proteome studies provide a foundation for understanding the emergent properties inherent in biology at a systems wide scale. Advances in a wide variety of sample preparation methodologies (analyte isolation, enrichment, and complexity reduction through sample fractionation) coupled with improvements in mass spectrometry (MS) technologies (ion sources, optics, and mass analyzers (Nolting et  al. 2017; Zheng et  al. 2017)) are enabling highly multiplexed, high-throughput characterization and quantification of thousands of proteins and associated proteoforms in biological samples on time scales previously unattainable (Angel et al. 2012a; Percy et al. 2016; Keshishian et al. 2017; Bache et al. 2018; Meier et al. 2018; Pfammatter et al. 2018). Collectively advances in methods and technologies are providing a means for the direct observation, characterization, and measure of the biological components important to health, biomedical research, and drug discovery.

4  Bottom-Up Proteomics MS-based proteome analysis is broadly divided into top-down analysis of intact proteins/proteoforms (Smith, et al. 2013) or bottom-up analysis of proteolytic peptides present in a sample or sample fraction (Angel et al. 2010, 2012a, b, c; Schutzer et al. 2010, 2011, 2013; Aryal et al. 2011, 2013, 2014; Brown et al. 2012; Price et al. 2013; Smith et al. 2014). In this chapter, we focus only on bottom-up proteomics. Bottom-up proteomics is one of the most common and widely used MS-based methods for studying the proteome. In bottom-up shotgun proteomics studies, a mixture of proteins is isolated and enzymatically or chemically digested into peptides. To increase depth and breadth of proteome coverage, samples are processed to reduce complexity. Common approaches to reduce sample complexity are to fractionate at the protein level either enriching low abundance proteins or depleting highly abundant proteins prior to enzymatic digestion (Fig. 2). Often, multidimensional separation and fractionation are implemented for simplifying protein or peptide mixtures prior to analysis (e.g., at the mass spectrometer). For example, gel and gel-free separations of proteins can simplify complex matrices by grouping proteins based on molecular weight and isoelectric point (1D and 2D PAGE). Alternatively, affinity immuno-depletion can remove abundant, unwanted proteins from matrices. Fractionation at the peptide level (after enzymatic or chemical digestion) has become the most common approach to decrease sample complexity for proteomic experiments (Fig. 2). Two-dimensional liquid chromatography (2D LC) separation, with low-pH reversed phase as the second dimension, is a common strategy to fractionate a peptide mixture prior to MS/MS analysis. Strong cation exchange (SCX) chromatography has been implemented in the first dimension of 2D LC workflows

234

T. E. Angel and U. K. Aryal

Fig. 2  Proteomics sample preparation workflow. Extracted proteins can be fractionated based on physiological properties, such as molecular weight (e.g., SDS-PAGE) or by charge or hydrophobicity (SCX, HpH, HPLC) or combination of all to reduce sample complexity and to increase proteome coverage. Alternatively, specific subset of proteins can be enriched or depleted to enable target analysis using antibody or other affinity enrichment methods. Similarly, modified peptides (phosphorylated, demethylated, or acetylated) can be targeted through enrichment using affinity-­based resins or antibody-based IPs. SCX strong cation exchange, HpH high pH reverse phase

because the mechanism of separation is considerably different from that of reversed phase liquid chromatography, offering good separation orthogonality (Slebos et al. 2008). Strong cation exchange has drawbacks, such as extra time required to desalt samples before and after fractionation with poor sample recovery. High-pH reverse-­ phase chromatography with sample fraction concatenation has become a widely employed method for peptide fractionation prior to low-pH reversed phase LC-MS (Yang et al. 2012). For bottom up proteome analysis, after chromatographic separation peptides are typically ionized by electrospray ionization (ESI) and analyzed by MS (Fig. 3). MS analysis of ionized peptides, given the ability to perform unbiased and untargeted tandem MS (MS/MS) measurements providing peptide amino acid sequence i­nformation, yields qualitative and quantitative results of high specificity due to high mass measurement accuracy. Typical LC-MS/MS involves the acquisition of a preliminary mass spectrum (MS1) of the intact (precursor) peptide, dissociation of the isolated precursor ion of interest into smaller fragments, and subsequent mass analysis of the fragments (MS/MS). The process is

Impact of Gut Microbiota on Host by Exploring Proteomics

235

Fig. 3  LC-MS/MS workflow. Prefractionated or target purified peptide samples are introduced to the LC via HPLC system, and peptides eluting through the LC are electrospray ionized and detected by the MS and MS/MS analysis. After ionization, peptide precursor ions (MS1) are introduced into the mass spectrometer, which records their mass-to-charge (m/z) ratio with high accuracy. For identification, single precursors are selected based on observed intensity and subjected to fragmentation and tandem MS (MS/MS) event. The MS and MS/MS spectra are then matched to known peptide sequence database using search algorithms such as MaxQuant, Mascot, SEQUEST, or X!Tandem. The identified peptides and protein data are quantified (either relatively or absolutely) using quantitative tools such as MaxQuant. Identified proteins and abundance information is used to determine microbial communities and their changes across samples. The results are further analyzed using bioinformatic tools to interpret results, determine related pathways, modifications, and protein-protein interactions

repeated for the duration of the LC separation of the peptide mixture. Peptides are identified matching theoretical MS and MSMS patterns generated in silico from protein sequence databases with experimental MS spectra. In addition to the identification and cataloging the proteins and proteoforms present in a sample is the quantitative analysis of protein abundance.

5  Label-Free Protein Quantitation Relative or absolute protein abundance can be quantified by label or label-free methods (Angel et  al. 2012a). Label-free quantitation at the peptide level (MS) (also referred as precursor-ion signal intensity) or peptide fragment level (MS/MS) (also referred as spectral counts) are quite popular and less cumbersome methods.

236

T. E. Angel and U. K. Aryal

It provides precise and robust relative protein expression measurements when performed using replicate runs and reproducible LC retention time (Aryal et al. 2017; McBride et al. 2019). Label-free quantitation should be performed with minimal analysis variation (Schwanhausser et al. 2011; Altelaar et al. 2013). This method is applicable to any number of samples, any organisms, cells, or tissue types and does not require any sophisticated software for data analysis. However, care should be taken to minimize sample-to-sample variation during sample preparation, and data acquisition. It is also important to make sure that an equal amount of peptides is loaded to the LC column for each sample because each sample is processed independently.

6  Label-Based Protein Quantitation Metabolic stable isotope labeling in cell culture (SILAC) or animals (SILAM) is a common MS1 peptide centric approach for quantitation of relative protein abundances (Ong et al. 2002; Price et al. 2010). Errors in protein abundance measurement due to variation in sample handling in label-free quantitation can be minimized by using metabolic labeling strategy (Altelaar et al. 2013). Advances in mass spectrometry instrumentation, delivering resolving powers >240,000 at m/z = 400, have facilitated the development of the MS1-based peptide centric stable isotope labeling approach, notably enabling sample multiplexing for SILAC/ SILAM samples (Hebert et  al. 2013; Richards et  al. 2013; Rhoads et  al. 2014; Overmyer et al. 2018). While metabolic labeling works very well in cultured cells, a limitation of this strategy such as SILAC or 15N is that primary cells or mammalian tissues are difficult to culture and label to saturation. An alternative to metabolic labeling is chemical labeling of peptides with isobaric tagging reagents (e.g., TMT and iTRAQ), following protein digestion which allows MS/MS level quantification of relative protein abundance and the highest degree of sample multiplexing (Moulder et al. 2018). Quantification for chemical labeling is achieved at the MS/MS reporter ion level. An advantage of chemical labeling is multiplexing allowing analysis of multiple perturbations in parallel (Bantscheff et  al. 2007; Mertins et al. 2012). However, multiplexing increases sample complexity, which requires peptide-level fractionation of the pooled chemically labeled samples before LC-MS/MS. Another limitation is that TMT and iTRAQ-based chemical regents are relatively expensive. A cost-­effective chemical labeling approach is to use dimethyl labeling, which allows highly efficient and accurate quantification of all samples including primary cells and tissues (Boersema et al. 2009; Klimmeck et  al. 2012; Munoz et  al. 2012). Both SILAC (MS level) and isobaric tagging approaches (MS/MS level) have enabled quantification of relative protein abundance, as well as protein synthesis and degradation rates (Welle et  al. 2016; Savitski et al. 2018; Zecha et al. 2018).

Impact of Gut Microbiota on Host by Exploring Proteomics

237

7  C  urrent State of Proteomic Analysis of Human Gut Microbiota Proteomics analysis of human gut microbiome is relatively new. One of the greatest challenges is the lack of suitable genome sequence databases to interrogate LC-MS/ MS data. Despite this limitation, there have been several excellent studies on human gut metaproteome over the past decade (Hartman et al. 2009; Turnbaugh et al. 2009; Verberkmoes et al. 2009; Kolmeder and de Vos 2014; Muth et al. 2015; Xiong et al. 2015; Young et al. 2015; Lee et al. 2017; Zwittink et al. 2017; Zhang et al. 2018b; Lehmann et al. 2019). These reports have provided a lot of new information about how the structure and diversity of the human gut microbiota changes from preterm infant to monozygotic twins, healthy adults, and diabetes patients. Table 1 summarizes the recent proteomic studies of human gut microbiota. Early studies employed 1D gel to separate proteins by molecular weight. A major drawback of this technique was the difficulty of identifying individual proteins in each band by MS because shotgun proteomics techniques were not that advanced during that period. With the advent of two-dimensional (2D) gel electrophoresis, researchers adopted 2D separation (Klaassens et  al. 2007), where proteins are resolved by pH (isoelectric point) on the first dimension and by molecular weight on the second dimension (O’Farrell 1975). These protein spots were later analyzed by MALDI TOF MS for protein identification (Klaassens et  al. 2007). More recent investigations have taken full advantage of the gel-free and label-free shotgun proteomics, which is based on reverse-phase separation of proteins or peptides by liquid chromatography (LC) and their analysis by tandem MS for protein identification. In gel-based method, proteins are in-gel digested into peptides and subsequently analyzed by MS. Early on, one of the pioneering works was carried out by Klaassens and co-­ workers (2007), who investigated fecal samples of two infants. Although this study only identified Bifidobacterial transaldolase protein by de novo sequencing, it was a major step forward in the field. Later years witnessed continuing progress in analytical methods and metagenome sequences, providing new opportunity for comprehensive metaproteome analyses. Shotgun proteomics of preterm infant fecal during the first month of the child’s life resulted identification of over 4000 human and microbial proteins and provided new clues on how composition and functional diversity of gut microbiota change during the early stage of child development (Young et al. 2016). Metaproteome analysis of fecal samples from a healthy monozygotic twin pairs found different but stable proteome profiles between the twins (Verberkmoes et al. 2009). Temporal analysis of intestinal proteome of three female adults further identified a common core proteome largely representing metabolic pathways and again suggested a relatively stable metaproteomes in adults than in a developing child (infant) (Kolmeder and de Vos 2014). These and several recent studies (Xiong et  al. 2015; Lee et  al. 2017; Li et  al. 2018; Zhang et  al. 2018b; Lehmann et al. 2019; Liu et al. 2019) have further highlighted the importance of

238

T. E. Angel and U. K. Aryal

microbial communities in the early stage of child development. These studies revealed that microbes related to biomass growth, protein synthesis, and lipid metabolism were predominant at the early developmental stages and change to a more complex, functionally diverse but metabolically stable proteome at the later stage of the development. Intestinal microbiome composition varies spatially and temporally. Mucosa-­ associated microbiota differ from those residing inside the lumen (Eckburg et  al. 2005). In animal model, metaproteome analysis showed variation in profiles between mucus, gut content, and feces (Haange et al. 2012). Mucosa-associated microbiota were different in different location of the human intestine, implying functional diversity within specific intestinal niches (Li et al. 2011). Apart from temporal and spatial variations, antibiotics and physiological condition of an individual impact the composition of gut microbiota (Hernandez et al. 2013; Perez-­Cobas et al. 2013a, b). For example, β-lactam therapy drastically changed proteome profiles of gut-associated microbiota (Perez-Cobas et al. 2013a, b). Inflammatory bowel diseases (IBD) such as Crohn’s disease (CD) and ulcerative colitis (UC) severely impact microbiome profiles in the intestine (Erickson et al. 2012; Matsuoka and Kanai 2015). Changes in microbiomes were linked to disease and host immune response and inflammation (Li et  al. 2011; Presley et  al. 2012). Increasing evidences suggest a direct link between intestinal microbial composition with obesity and diabetes (Ferrer et  al. 2013; Kolmeder and de Vos 2014; Gerard 2016; Heintz-Buschart et al. 2016). More gut microbiota proteins related to cell motility, and vitamin B12 synthesis were present in obese adolescent subjects and more active B6 synthesis proteins were present in lean adolescent (Ferrer et al. 2013). Microbes belonging to phylum Bacteroidetes were more active in obese groups (Kolmeder and de Vos 2014). Disturbances of gut microbial communities due to liver cirrhosis (Wei et al. 2016), dysbiosis with cystic fibrosis (Debyser et al. 2016), and probiotic consumption have also been reported (Kolmeder et al. 2016; Kristensen et al. 2016). These evidence suggest that the technique of metaproteomic analysis is gradually growing; nevertheless, many studies reported so far are preliminary, and more studies are needed to better understand the gut microbial community structure and interaction with the host.

8  New Tools of Proteomics for Microbiome Study While protein identification and quantification are necessary, it is often not sufficient to enable a deep understanding of the relationships and complexities of most if not all biological systems. Proteome characterization of complex biological ­samples has resulted in identification of many putative biomarkers, and very few candidate biomarkers have translated to clinical utility (Paulovich et  al. 2008; Diamandis 2012; Anderson et  al. 2013), which suggests that there is a missing dimension to the results from proteome characterization and discovery studies. Historically stable isotope labeling and molecular flux measurements have led to critically important discoveries in biological sciences resulting in deep insight and

Impact of Gut Microbiota on Host by Exploring Proteomics

239

understanding into fundamental biological processes such as metabolism (Schoenheimer and Rittenberg 1936; Buchanan 2002). These past successes suggest that an understanding of protein dynamics or flux (protein synthesis and degradation) can enable deeper insight into the complex biology that is causal in disease or reflects disease modulation and as such represent the next generation of protein biomarkers (Hellerstein 2003; Turner and Hellerstein 2005; Holmes et  al. 2015; Decaris et al. 2017; Anderson 2018). Measurement of fractional synthesis rates in vivo requires perturbing a system by introducing an isotopic label (e.g., 2H, 13C, 15N) and measuring its rate of incorporation into the molecules of interest over time. Isotopic tracer exposure allows quantification of time-dependent changes and the determination of kinetic rate constants (k, half-life, and growth rate) of processes and for molecules of interest. Use of deuterium oxide as a universal stable isotope tracer is advantageous as it is nontoxic at low exposure levels (