Gut microbiome

12 Key excerpts on "Gut microbiome"

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  eBook - ePub

  Our Animal Connection

  What Sapiens Can Learn from Other Species

  • Michael Hehenberger, Zhi Xia, Michael Hehenberger, Zhi Xia(Authors)
  • 2019(Publication Date)
  • Jenny Stanford Publishing

    (Publisher)

  However, because of the lack of direct evidence, the relationship between intestinal microbes and human health could not yet be well explained. In 2001, another Nobel Laureate—the bacteriologist and geneticist Joshua Lederberg 68 —coined the term “human microbiome,” thereby emphasizing the importance of nutrition for human health. His definition of the microbiome (or “microbiota”) includes all members of the microbial community (bacteria, eukaryotic cells, viruses, etc.) that are housed in the human gut, the skin, the mouth, the nose, etc., as shown in Fig. 5.1. Our Animal Connection: What Sapiens Can Learn from Other Species Michael Hehenberger and Zhi Xia Copyright © 2020 Jenny Stanford Publishing Pte. Ltd. ISBN 978-981-4800-48-8 (Hardcover), 978-0-429-05332-0 (eBook) www.jennystanford.com Figure 5.1 The microbial community occupies 5 major sites in the human body (source: Wikipedia). Collectively, microbiome members are surpassing the number of cells making up the human body, and there are 100–150 times more genes in the microbiome, as compared to the number of genes in the human genome. There is mounting evidence that our microbial guests are playing an important role for our wellness, confirming that Metchnikov was up to something important when he more than 100 years ago suspected that the immune system is interacting with the microbiome. Without surface microbes, our bodies will not function properly. For example, intestinal probiotics can help digest food, suppress obesity, and fight invading microorganisms. Some microorganisms that colonize humans do coexist without harming humans; others have a mutualistic relationship with their human hosts. Certain microorganisms perform tasks that are known to be useful to the human host but the role of most of them is not well understood. Those that are expected to be present, and that under normal circumstances do not cause disease, are referred to as normal flora or normal microbiota

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  Probiotic Foods in Health and Disease

  • G. B. Nair, Yoshifumi Takeda(Authors)
  • 2011(Publication Date)
  • CRC Press

    (Publisher)

  Such studies serve as a prerequisite for the assessment of the potential dietary manipulation of beneficial microorganisms. This kind of dietary management has already been initiated in the form of probiotics, prebiotics as well as synbiotic mixtures of both (37). Host-microbe Interactions in the Gut: A Microbiologist’s Perspective 52 Probiotic Foods in Health and Disease ROLE OF GUT MICROFLORA IN HUMAN PHYSIOLOGY Gut flora is a very complex ecosystem which involves a delicate balance of harmful and beneficial bacteria. The gut flora is important and plays a vital role in different functions of our body, such as absorption of nutrients, modulation of the immune system and ability to fight against disease-causing organisms. The gut bacteria are involved in fermentation of undi-gested foodstuff in the large intestine. During the process of fermentation several nutrients are produced including vitamin K and biotin. A balanced gut flora plays a significant role in warding off pathogenic bacteria, toxins, allergens, chemicals and pollutants from penetrating the host body. This function is also called gut barrier effect. Disruption in the balance of this fragile microbial ecosystem of GI tract at any point of time may lead to a lot of gut related problems such as bloating, intestinal pains, nutritional deficiencies and constipation. Imbalances in gut microflora have also been linked to obesity, cancer, asthma and autoimmune diseases etc. Researchers are also analyzing the effects of the gut micro biome on carcinogens and sex hormone metabolism based on evidence that the gastrointestinal microbiota has an impact on estrogen balance and is important in estrogen metabolism. This might also enhance the knowledge of other sex hormone related diseases such as ovarian cancer, osteoporosis and endometriosis.

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  Health Benefits of Fermented Foods and Beverages

  • Jyoti Prakash Tamang(Author)
  • 2015(Publication Date)
  • CRC Press

    (Publisher)

  4.10 Conclusion The human gut is a natural habitat for a large and dynamic bacterial community. The microbiome (genes and genomes of all the bacteria inhabiting the gut) of each person is distinct and variable but each individual possesses a shared core microbiome which is required for proper maintaining of cross species homeostasis between the gut bacteria and the host. The recent interest in the struc-ture and function of the Gut microbiome, its dynamic evolution throughout an individual’s life in a host specific manner and how it is modified by diets, has resulted in a series of exciting findings. The advent of culture-independent techniques to study the microbiome has enabled scientists to decipher the dynamics of the complex bidirectional interactions between diet and the microbiome in relation to human health and diseases. Although details of the complex interactions between diet, the microbiome and host health is an emerging area of science, existing knowledge is being 220 ◾ Health Benefits of Fermented Foods and Beverages used in leveraging the microbiome to develop dietary interventions to counterbalance dysbiosis and to increase overall well-being. However, it is essential to assess the efficacy of the pro/prebiotics to molecular detail and the long-term safety of probiotics, as the impact of prolonged perturbation of the microbiome is largely unknown. Collectively, the research findings reviewed here suggest that more integrative studies will provide all-encompassing knowledge of the complex, multi-level interactions between diet, the microbiome, and host health, which can be utilized to design microbiome-based biomarkers for those at risk of various infectious and metabolic diseases and formulate diet-driven microbiota alteration strategies to improve human health. References Aagaard, K., J. Ma, K. M. Antony, R. Ganu, and J. Versalovic. 2014. The placenta harbors a unique microbi-ome.

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  Microbes and the Mind

  The Impact of the Microbiome on Mental Health

  • Caitlin S. M. Cowan, Brian E. Leonard, C.S.M. Cowan, B.E. Leonard, Caitlin S.M., Cowan, Brian E., Leonard, Brian E. Leonard, Brian E., Leonard, Caitlin, Cowan, Brian E., Leonard(Authors)
  • 2021(Publication Date)
  • S. Karger

    (Publisher)

  Abstract The dynamic population of microbes that reside in the gastrointestinal tract plays a pivotal role in orchestrating several aspects of host physiology and health, including but not limited to nutrient extraction and metabolism, as well as the regulation of intestinal epithelial barrier integ-rity. Gut microbes interact with the host in a bi-direction-al manner as the microbiota can support the develop-ment and education of the innate and adaptive immune systems, thereby conferring protection against patho-gens and harmful stimuli while training the host to main-tain a homeostatic tolerance towards commensal symbi-otics. Recent advances in the field have highlighted the importance of the host-microbiota relationship in neuro-development and behaviour, with relevant implications for the onset and progression of brain disorders of inflam-matory origin. Microbial modulation of brain function is Cowan CSM, Leonard BE (eds): Microbes and the Mind. The Impact of the Microbiome on Mental Health. Mod Trends Psychiatry. Basel, Karger, 2021, vol 32, pp 40–57 (DOI: 10.1159/000510416) Gut Microbiota as a Mediator of Host Neuro-Immune Interactions: Implications in Neuroinflammatory Disorders Valentina Caputi a, b Jelena Popov c Maria Cecilia Giron d Siobhain O'Mahony a, b a Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; b APC Microbiome Ireland, University College Cork, Cork, Ireland; c College of Medicine and Health, University College Cork, Cork, Ireland; d Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padua, Italy achieved throughout complex neuro-immune-endo-crine pathways of the microbiome-gut-brain axis. Chang-es in the composition of the gut microbiota or perturba-tion in microbial-derived metabolites and neuroactive compounds are sensed by the afferent branches of the sympathetic and vagal innervation and transmitted to the central nervous system, which in turn produces be-havioural responses.

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  Human Microbiota and Microbiome, The

  • Julian Marchesi, Julian R Marchesi(Authors)
  • 2014(Publication Date)
  • CAB International

    (Publisher)

  6 Function of the Human Gut Microbiota

  Takahiro Matsuki* and Ryuichiro TanakaYakult Central Institute for Microbiological Research, Tokyo, Japan

  6.1 Introduction

  In the mammalian gut, considerable numbers and species of microorganisms make up a bacterial community referred to as the gut microbiota. The number of microbes present in the gut exceeds the number of human cells and represents a weight of 2 kg, which is more than the weight of the human brain. Recent 16S rRNA sequence-based analyses have revealed that there are several hundred species present in a given individual that are relatively stable over time, although they vary widely between different individuals. The Bacteroidetes and Firmicutes are the two dominant bacterial divisions represented in the human gut microbiota, followed by the Actinobacteria , Proteobacteria , Verrucomicrobia and others (Eckburg et al ., 2005).

  Recent studies have demonstrated that the relationship between the gut microbiota and humans is not merely commensal; rather, it is a symbiotic relationship. Germ-free (GF) animals have been instrumental in elucidating the contribution of the gut microbiota to host health. Comparisons between GF and conventional (CV) animals have suggested that the bacterial community plays a role in fermenting unused energy substrates, synthesizing and converting bioactive compounds, alteration of intestinal morphology and motility, inducing maturation of the immune system, preventing pathogenic infection and influencing host behaviour, among other effects. Thus, the importance of the intestinal microbiota in human health is increasingly acknowledged and there has been a surge in the number of research papers on these subjects in recent years. In this chapter, the functions of the gut microbiota will be reviewed in six categories, as summarized in Fig. 6.1

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  Metabolism of Nutrients by Gut Microbiota

  • Joseph F Pierre(Author)
  • 2022(Publication Date)
  • Royal Society of Chemistry

    (Publisher)

  CHAPTER 1 Introduction and Background to Microbiome Research

  Joseph F. Pierre*

  Department of Nutritional Sciences, College of Agriculture and Life Science, University of Wisconsin–Madison, Wisconsin, USA, * E-mail: [email protected]

  Metabolism of Nutrients by Gut Microbiota is a timely collection of works focussing on the functional roles of intestinal microorganisms and their diverse metabolites that interface with the host under various dietary inputs and circumstances relevant to human health. Chapters focus on host–microbial interactions under different major macronutrient dietary intakes, the state of prebiotics, probiotics, and synbiotics, interactions between microbes and drug metabolism, how initial microbial colonizers following birth shape lifelong chronic disease risk and metabolism, and the role of microbes in bariatric surgically induced weight loss. We have placed specific emphasis on the functional roles microbes play within the host, as we move beyond descriptive explorations of the microbiome and delve into more focused determination of the mechanisms underpinning microbial contribution to health and disease. This collection of work will be of interest to the lay audience, science enthusiast, industry partners, and career academics alike.

  1.1 Introduction to the Gut Microbiota

  Microbial communities colonize the gut and virtually all other body compartments, including the skin, mammary ducts, respiratory tract, and, as recent evidence supports, even the circulation. These dynamic communities are fundamentally involved in homeostasis and disease progression under environmentally and genetically shaped susceptible conditions. Through their assistance with digestion and fermentation, stimulation of nutrient absorption and endocrine regulation, production of vitamins, priming and agonism of immune education and response, and production of many small molecules, a growing number of relevant host–microbial interactions have been uncovered rapidly by microbiome researchers in recent years.

  1

  Despite the enormous effect microbiome research has already had on our understanding of health and many diseases, this field is still young and continues to evolve in both the amount of empirical data collected annually and through the continuous improvements in the methodological approaches and techniques used to explore the microbiome.

  Scientists had historically long attempted to investigate microorganisms, but for hundreds of years the investigation into microbial life forms was limited by what could be observed under the microscope or by indiscriminately cultivating organisms in artificial broths and solid substrates. While historical descriptions over several centuries more or less accurately described major microbial kingdoms – bacteria, fungi, and protists – the work of Louis Pasteur most notably first tied the importance of microbes to human health with his experimentation and theory of germs. Pasteur posited that certain microbes could cause specific diseases when introduced, setting into motion an unravelling of the superstition surrounding the origins of disease and improved understanding of microbial life. This new framework of empirical testing of microbes led Robert Koch to demonstrate that a single bacterium – bacilli – could cause anthrax in animals.

  2

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  Big Data Analysis and Artificial Intelligence for Medical Sciences

  • Bruno Carpentieri, Paola Lecca(Authors)
  • 2024(Publication Date)
  • Wiley

    (Publisher)

  149 7 The Potential of Microbiome Big Data in Precision Medicine: Predicting Outcomes Through Machine Learning Silvia Turroni and Simone Rampelli Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, 40126, Bologna, Italy 7.1 The Gut microbiome: A Major Player in Human Physiology and Pathophysiology The Gut microbiome, i.e. the 10-trillion microbial community that inhabits our gut, is undoubtedly a leading player in human physiology. Countless studies have in fact shown that this microbial counterpart is essential for the extraction of energy from the diet (i.e. from fibers), the synthesis of vitamins (mainly of group B), the barrier effect against potential enteropathogens, the development, and regulation of the immune system (involving both innate and adaptive arms), as well as the modulation of the central nervous system (the so-called “gut-brain axis”), just to name a few (Candela et al. 2015; de Vos et al. 2022). These actions are due to the large and diversified pool of small bioactive molecules produced or contributed by the microbiome, which enter the bloodstream and reach extraintestinal organs (Turroni et al., 2018). Among these, it is certainly worth mentioning the short-chain fatty acids (SCFAs), i.e. the end-products of the fermentation of polysac- charides, which act as signaling molecules and exert decisive roles in the maintenance of metabolic and immunological homeostasis (Koh et al. 2016). Indeed, SCFAs have generally been attributed to anti-inflammatory and immunomodulatory activities and overall beneficial metabolic effects, e.g. by affecting satiety, intestinal gluconeogenesis, adipose tissue, and liver function.

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  Gut Microbiota

  Brain Axis

  • Alper Evrensel, Bar?? Önen Ünsalver, Barış Önen Ünsalver, Alper Evrensel, Barış Önen Ünsalver(Authors)
  • 2018(Publication Date)
  • IntechOpen

    (Publisher)

  Significant efforts have been made in characterizing compositions and functions of microbiota along with this advancement in sequencing technologies and have reported complex and diverse groups of microbiota residing in various regions of hosts including skin, oral cavity, nasal cavity, urogenital tract, and gut [5, 6 ]. Such type of variations can occur not only among different regions but can also within different locations of the same area (e.g., lumen vs. mucosa of the gut), as shown in Figure 1 [7]. Among various microbes residing inside and outside of both humans and animals, bacteria living in the gut have been widely studied and have been found to have an effect on health and diseases through complex interactions with their hosts. Various factors such as diets, antibiotics, a method of delivery and infant feeding, illness, stress, aging, lifestyles, and host genetics can affect gut microbiota [ 8, 9]. The proper balance Figure 1. PCoA plot showing significant difference in bacterial community structure among different regions and locations of gastrointestinal tract of 3-week old chickens. MRS-recovered cells from cecal lumen (M-CL), cecal mucosa (M-CM) and ileal mucosa (M-IM), and total bacterial cells from cecal lumen (T-CL) (ANOSIM results; R = 0.67, p = 0.001). This figure is adapted from reference [ 7 ], figure 6(A). Gut Microbiota - Brain Axis 4 of microbiota is needed to maintain microbial homeostasis inside gut, which potentially affect the health of individuals. Change in composition of gut microbiota by any factors as described earlier is called dysbiosis, which can cause several diseases and disorders includ-ing allergies, inflammatory bowel disease (IBD), diabetes, cancer, and autism as reviewed earlier [8].

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  Visualizing Human Biology

  • Kathleen A. Ireland(Author)
  • 2018(Publication Date)
  • Wiley

    (Publisher)

  Additionally, these bacteria are anaerobic and undergo fermen- tation constantly while in our gut. This excess digestion provides us with up to 10% of our daily energy needs. Perhaps the most far-reaching activity the Gut microbiome pro- vides is in regulating our immune system. As our Gut microbiome develops, so too does our immune system. These two are very closely connected. The immune system and the potentially pathogenic bac- teria of the GI tract are separated only by the lining of the intestine, with our immune system on the inside of our body and the gut bacte- ria on the outside. It is important that we are able to identify our own cells from the host of infecting cells that can attack us at any point. Recall from Chapter 9 that the first line of defense that we have is con- tained in our antigen-presenting cells (APCs). As we develop our FIGURE 11.10 Nutritional quality and quantity can dramatically influence the makeup of your micro- bial community as can unhealthy conditions, including obesity. Age Breast-fed Formula-fed Healthy Obese KEY Class Firmicutes, including Lactobacillus sp., Bacillus, sp. Clostridium sp., Streptomyces sp., Staphlococcus sp., Eubacterium sp. Class Bacteroidetes, including Bacteriodes sp. Class Actinobacteria, including Proprionibacterium sp. Class Proteobacteria, including Enterobacteria sp, Escherichia sp., Haemophilus sp. Other, including Streptococcus sp. Healthy Malnourished 65-80 years >100 years Geriatric Adult Toddler Infant Alistair Berg / Getty Images Courtesy Linda Young Courtesy Linda Young Courtesy Linda Young Think Critically 1. Does it make sense to keep a record of your per- sonal microbiome over the course of your life- time? Would this information provide any useful avenues for illness prevention? 2. Many diseases have a genetic component, and can be traced through families. Obesity may have both a genetic component and a microbiome component.

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  Gut Health For Dummies

  • Kristina Campbell(Author)
  • 2024(Publication Date)
  • For Dummies

    (Publisher)

  CHAPTER 3 Getting to Know Your Gut’s Ecosystem of Microbes 51 Tracking microbes as you age As you grow from childhood into adolescence and from adulthood into older adulthood, your gut microbes naturally change with each life stage. Throughout childhood the ecosystem is dynamic, becoming more and more diverse. It reaches a relatively stable state in adulthood. Later in life, once-rare microbes increase in number, making the Gut microbiome more eclectic. Proinflammatory microbes also increase in older age and correlate with the extent of frailty. Chapter 19 covers specific ways to take care of your Gut microbiome in older age. Considering the genetic connection Your human genes also account for a portion of your Gut microbiome composition. That is, some microbes are heritable (passed from one generation to the next) — so people with certain genes (for example, ones that confer a lean physique) tend to have some of the same gut microbes throughout their adult lives. When scientists have studied large groups of people and tried to find patterns between their human genes and their gut bacteria, they’ve found that specific gut microbes tend to occur with genes that determine your digestion of lactose in dairy products and others with genes that encode blood type. The fascinating part about these observed gene-microbe co-occurrences is that they seem to extend back through evolutionary time. Apparently over a span of 15 million years, some bacterial lineages diversified at the same time as the humans and primates that harbored them. Scientists still see evidence of this co-evolution today, with specific strains of Helicobacter pylori, for example, occur- ring in genetically similar human populations worldwide. This evidence suggests gut microbes and humans have undergone parallel evolution and that certain lineages of bacteria have been paired with the same human genes from generation to generation over time.

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  Small Animal Microbiomes and Nutrition

  • Robin Saar, Sarah Dodd(Authors)
  • 2023(Publication Date)
  • Wiley-Blackwell

    (Publisher)

  Some metabo- lites, such as SCFA, can cross the blood–brain barrier to influence a change on neurological systems [38]. Additionally, alternative systems such as the hepatic, renal, and subsequently urinary systems are affected by metabolites. For example, excessive uremic toxin production in the GI tract has been implicated in the development of renal diseases [39]. 2.6 Chapter Summary ● The gastrointestinal microbiome is a diverse community of microbes that interact with the host animal in a plethora of ways ● Microbes in the gut metabolize or otherwise alter some ingested nutrients and can synthesize nutrients de novo for host animal absorption 2 Functions of the Gastrointestinal Microbiome 40 ● Short-chain fatty acids are synthesized by microbes in the colon and are of key importance for colonocyte health ● Gut microbes stimulate physical and immunological changes in the gut wall to maintain a barrier permeable to essential substances like nutrients but impermeable to pathogens ● The gastrointestinal microbiome is not static, it is constantly shifting and adapting. References 1 Marchesi, J. (2017). What is a microbiome? https://microbiologysociety. org/blog/what-is-a-microbiome.html (accessed 11 May 2022). 2 Olofsson, L. and Bäckhed, F. (2022). The metabolic role and therapeutic potential of the microbiome. Endocrine-Reviews 43: 907–926. 3 Costa, M. and Weese, J. (2018). Understanding the intestinal microbiome in health and disease. Veterinary-Clinics-of-North-America:-Equine 34: 1–12. 4 Lee, D., Goh, T., Kang, M. et al. (2022). Perspectives and advances in probiotics and the Gut microbiome in companion animals. Journal-of- Animal-Science-and-Technology 64 (2): 197–217. 5 Pilla, R. and Suchodolski, J. (2021). The Gut microbiome of dogs and cats, and the influence of diet. Veterinary-Clinics-of-North-America:- Small-Animal-Practice 51: 605–621. 6 Swanson, K., Grieshop, C., Flickinger, E. et al. (2002).

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  Probiotics, Prebiotics and Synbiotics

  Technological Advancements Towards Safety and Industrial Applications

  • Parmjit Singh Panesar, Anil Kumar Anal, Parmjit Singh Panesar, Anil Kumar Anal(Authors)
  • 2022(Publication Date)
  • Wiley

    (Publisher)

  and Gordon, J. I. (2013). The long-term stability of the human gut microbiota. Science , 341(6141). Fava, F., Gitau, R., Griffin, B., Gibson, G., Tuohy, K. and Lovegrove, J. (2013). The type and quantity of dietary fat and carbohydrate alter faecal microbiome and short-chain fatty acid excretion in a metabolic syndrome ‘at-risk’population. International Journal of Obesity , 37(2): 216–223. Fei, N. and Zhao, L. (2013). An opportunistic pathogen isolated from the gut of an obese human causes obesity in germfree mice. ISME Journal , 7(4): 880–884. Festi, D., Schiumerini, R., Eusebi, L.H., Marasco, G., Taddia, M. and Colecchia, A. (2014). Gut microbiota and metabolic syndrome. World Journal of Gastroenterology , 20(43): 16079–16094. Flint, H.J., Scott, K.P., Duncan, S.H., Louis, P. and Forano, E. (2012). Microbial degradation of complex carbohydrates in the gut. Gut Microbes , 3(4): 289–306. Foster, J.A. and Neufeld, K.A.M. (2013). Gut–brain axis: how the microbiome influences anxiety and depression. Trends in Neuroscience , 36(5): 305–312. 17 Gut microbiome as Source for Prevention of Metabolic-Related Diseases 432 Fraher, M.H., O’toole, P.W., Quigley, E.M. (2012). Techniques used to characterize the gut microbiota: a guide for the clinician. Nature Reviews Gastroenterology and Hepatology , 9(6): 312. Francavilla, R., Calasso, M., Calace, L., Siragusa, S., Ndagijimana, M., Vernocchi, P., Brunetti, L., Mancino, G., Tedeschi, G. and Guerzoni, E. (2012). Effect of lactose on gut microbiota and metabolome of infants with cow’s milk allergy. Pediatric Allergy and Immunology , 23(5): 420–427. Geurts, L., Neyrinck, A.M., Delzenne, N.M., Knauf, C. and Cani, P.D. (2014). Gut microbiota controls adipose tissue expansion, gut barrier and glucose metabolism: Novel insights into molecular targets and interventions using prebiotics. Beneficial Microbes , 5(1): 3–17. Ghanim, H., Abuaysheh, S., Sia, C.L., Korzeniewski, K., Chaudhuri, A., Fernandez-Real, J.

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