Microbiota

9 Key excerpts on "Microbiota"

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  Probiotic Foods in Health and Disease

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

    (Publisher)

  THE HUMAN Microbiota Microbes that colonize the human body during birth or shortly thereafter and remain throughout life are referred to as normal flora. The microbial communities of humans are complex mixture of microorganisms. The communities vary between hosts as a result of restricted migration of Host-microbe Interactions in the Gut: A Microbiologist’s Perspective R. Chaudhry, V.D. Bamola and P. Panigrahi * Department of Microbiology All India Institute of Medical Sciences New Delhi, India E-mail: drramach@ gmail.com * Department of Pediatrics, University of Maryland School of Medicine Baltimore 21201, Maryland, USA E-mail: [email protected] 6 50 Probiotic Foods in Health and Disease microorganisms between hosts and strong ecological interactions within hosts (8). The human Microbiota has not been fully described, but it is clear that microorganisms are present in site-specific communities in the human host. The microbial communities co-evolve with their human hosts. Each community contains microorganisms from certain families and genera that are found in the same habitat in most of the individuals. Microbiota of an individual at the species and strain level can be as unique as a fingerprint (9, 23, 48). Microbiota of humans is segmented into many local communities, each comprising an individual host with their symbi-onts. This ecological pattern, characterized by strong interactions within distinct local communities and limited interactions or migration between them, is described as a metacommunity (8). The composition of the vertebrate gut Microbiota is influenced by diet, host morphology and phylogeny and in this respect the human gut bacterial community is typical of an omnivorous primate. However, the vertebrate gut Microbiota is different from free-living communities that are not associated with animal body habitats (24).

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  Small Animal Microbiomes and Nutrition

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

    (Publisher)

  1 Section I Understanding a Microbiome 3 Small Animal Microbiomes and Nutrition, First Edition. Robin Saar and Sarah Dodd. © 2024 John Wiley & Sons, Inc. Published 2024 by John Wiley & Sons, Inc. Companion website: www.wiley.com/go/saar/1e 1 Common Definitions 1.1 Microbiome There are multiple functional definitions of the term “microbiome.” According to the Human Microbiome Consortium, the microbiome is considered as the community of all microbes recovered from a particular habitat or ecosystem [1]. These microscopic communities, including bacteria, fungi, and viruses, can be found in all living things, including plants, and are found in every different imaginable habitat, from life- forms to soils and bodies of water [2, 3]. Microbiomes can be found on outer surfaces, particularly as biofilms, and within several body systems of animals including the respiratory tract, reproductive organs, integu- mentary, oral cavity, urinary tract, neurological pathways via the brain- gut axis, and the gastrointestinal (GI) tract. Over 30 trillion microbes may reside within the GI system alone [4, 5]. This list is not exhaustive, as this area of knowledge is relatively novel, and innovations allow us to discover microbiomes in organs and systems once thought to be sterile. The total cumulative microbiomes in a human host may weigh as much as 1–3% body mass [4]. While some common trends are being observed in current research, microbiomes are unique for each individual with their diversity and density affected by several intrinsic (genetics, age, sex) and extrinsic (environment, physiological state, antibiotic therapy, health and nutri- tion) factors [6]. These incredibly diverse communities shape the health of the host and influence its physiology, through multiple complex 1 Common Definitions 4 pathways, including influencing remote organ and immune responses.

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  Bacterial Pathogenesis

  A Molecular Approach

  • Brenda A. Wilson, Malcolm Winkler, Brian T. Ho, Brenda A. Wilson, Malcolm Winkler(Authors)
  • 2019(Publication Date)
  • ASM Press

    (Publisher)

  5 IN THIS CHAPTER Importance of the Normal Resident Microbial Populations (Microbiota) of the Human Body Characterization of the Body’s Microbiota Taking a Microbial Census by Using Microbial rRNA Gene Sequence Analysis Characterizing Microbiomes by Using Metagenomic Analysis Beyond the Metagenome Overview of the Human Microbiota Skin Microbiota Oropharyngeal Microbiota Microbiota of the Small Intestine and Colon Microbiota of the Vaginal Tract The Other Microbiota: The Forgotten Eukaryotes Selected Readings Questions Solving Problems in Bacterial Pathogenesis CHAPTER 5 The Microbiota of the Human Body MICROBIOMES AND BEYOND

  T

  he ancient Greek philosopher Protagoras of Abdera (ca. 490–420 BCE) famously declared that “Of all things, the measure is Man,” but to the microbes that live in or on us we are more like the proverbial “free lunch.” Yet the microbes colonizing our bodies from shortly after our birth to our death do “pay rent” in various ways. They protect us from disease-causing microbes and contribute to our nutrition and healthy immune status. Our bodies are adapted not only to tolerate these resident microbes, but also to encourage their presence. Indeed,

  getting in touch with our microbial side is an important part of understanding what it is to be human.

  Importance of the Normal Resident Microbial Populations (Microbiota) of the Human Body

  A healthy human body harbors more than 10 times as many microbial cells as human cells. These microbes, which include bacteria, fungi, and archaea, are collectively known as the Microbiota.

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  Eden's Endemics

  Narratives of Biodiversity on Earth and Beyond

  • Elizabeth Callaway(Author)
  • 2020(Publication Date)
  • University of Virginia Press

    (Publisher)

  9 That means that the microbiome reveals biodiversity to be fractal, exponentially multiplying the challenges of biodiversity representation. Every single nonmicroscopic organism on the evolutionary supertrees of chapter 2, for example, is now known to contain thousands of other species of microbes within it.

  Moreover, these microbial partners are now recognized as integral to the functioning of larger multicellular organisms, like ourselves. The microbe affects not only health outcomes associated with diet like digestive conditions, heart disease, diabetes, and obesity but also the likelihood of developing arthritis in the joints and brain diseases like Alzheimer’s.10 One’s gut bacteria even affect aspects of interior life, influencing mood, depression, and anxiety.11 Microbes populate both our literal and figurative inner landscape, not only residing in our guts but also affecting our emotions and personality, which constitute who we are on the “inside.”12

  Microbes have shaped animal bodies from the beginning. Bacteria and archaea were the dominant forms of life when multicellular organisms first evolved, and they still are the dominant form of life today, teeming in every possible cubic inch of this planet. As Stephen Jay Gould has famously put it: “We live now in the ‘Age of Bacteria.’ Our planet has always been in the ‘Age of Bacteria,’ ever since the first fossils—bacteria, of course—were entombed in rocks more than 3 billion years ago. On any possible, reasonable or fair criterion, bacteria are—and always have been—the dominant forms of life on Earth.”13 Eukaryotic, or multicellular, life did not just transcend this microbial background to strike out on its own, independent path of development but evolved while deeply embedded in long-established microbial communities.14

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  Handbook of Prebiotics

  • Glenn R. Gibson, Marcel Roberfroid, Glenn R. Gibson, Marcel Roberfroid(Authors)
  • 2008(Publication Date)
  • CRC Press

    (Publisher)

  This is in contract to feces in which only 7% of the total bacterial ribosomal RNA from these species is found. 9 Figure 2.2 shows the relative presence of different domains within the intestinal Microbiota. Roles of the Microflora The presence of the gut Microbiota has influenced human evolution in that the human host cannot perform certain vital intestinal functions without them. Germ-free animal models have provided useful insights into the extensive roles of the microflora and the extent of interaction between the host and the gut microflora. The gut Microbiota can be thought of as a microbial organ within a human organ as the processes performed by this diverse population are extensive; it can communicate with itself (bacteria:bacteria) and with the host (bacteria:human). It is also a site of energy consumption, transformation, and distribution. 16 Handbook of Prebiotics Coprothermobacter Dictyoglomus Synergistes SC4 OP10 Guaymas 1 Thermodesulfobacteria Aquifacae Desulfobacteria 0.05 to the Archaea Proteobacteria CFB TM6 Deferribacter Gemmatimonadetes KSB1 Chlorobi Nitrospira Verrucomicrobi VadinBE9 7 Chlamiydiae WS2 Planctomycetales WS3 BRC1 Acidobacteria OS-K OP8 SBR1093 NKB19 Deinococcus-Thermus OP5 Fusobacteria Actinobacteria Spirochaeates Fibrobacteres Cyanobacteria Green Non Sulfur OP9 OD1 ABY1 OP 11 OP 1 EM3 Thermotogae SR1 WS6 TM7 SC3 BD1-5 WS5 Termite Group 1 Firmicutes OP3 NC10 Marine Group A A a FIGURE 2.2 Bacterial domains (super kingdoms) in human intestinal microflora. Phylogenetic tree is con-structed from 8903 different 16S rRNA gene sequences. The wedges represent super kingdoms. Those in red are numerically predominant in the human gut, whereas those in green are also human isolates but not numerically predominant. Wedge length represents the distance in evolu-tionary terms from a common ancestor. (Reprinted from Backhed, F., Ley, R. E., Sonnenburg, J. L., Peterson, D. A., Gordon, J. I., Science 2005, 307(5717), 1915–1920.

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  Visualizing Human Biology

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

    (Publisher)

  Bacteroidetes A bacterial phylum characterized by an unusual cell wall, Gram-negative staining, no endospore formation, and mutualistic lifestyles. Spor, A., Koren, O., Ley, R. Unravelling the effects of the environment and host genotype on the gut microbiome. Nat Rev Microbiol. 2011; 9[4]:281. 238 CHAPTER 11 The Human Microbiome study, more than 1,000 people provided specimens of gut bacteria. When these were analyzed for proportions of Firmicutes and Bacte- roidetes, it was found that people in colder climates had higher per- centages of Firmicutes in their gut microbiome (Figure 11.13). This coincides with the ecological “Bergman’s rule” that states that body size increases with latitude. It has been proposed that this increase is a survival trait, designed to provide insulation against a colder climate. Here is another bit of data adding to the research indicating that met- abolic activity is tied to the composition of the human microbiome. Concept Check 1. What bacteria are found most often in the skin microbiome? 2. Which body system’s developmental process is affected by the gut microbi- ome during childhood? 3. What does the balance between Firmicutes and Bacteroidetes in the gut microbiome relate to? 11.3 The Microbiome in Diagnoses and Treatments LEARNING OBJECTIVES 1. Explore the usefulness of the microbiome in medical diagnoses. 2. Explain the benefits of probiotics. 3. Recognize the potential for uses of microbiome information beyond medical applications. We now understand that keeping our microbiome in balance is important to maintaining homeostasis and general good health. See I Wonder… How Can I Keep My Microbiome Healthy? for more information. As research into the microbiome continues, the list of diseases that are related to imbalances in bacterial popula- tions expands. Diseases as simple to treat as tooth decay (dental caries) and as difficult to handle as depression and inflammatory bowel disease have ties to the microbiome.

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  Unifying Microbial Mechanisms

  Shared Strategies of Pathogenesis

  • Michael F. Cole(Author)
  • 2019(Publication Date)
  • Garland Science

    (Publisher)

  DNA and Cell Biology, 28(8): 405–411.

  Backhed F et al. 2015. Dynamics and stabilization of the human gut microbiome during the first year of life. Cell Host & Microbe, 17: 690–703.

  Banerjee S et al. 2018. Keystone taxa as drivers of microbiome structure and functioning. Nature Reviews Microbiology, 16: 567–576.

  Bassis CM et al. 2015. Analysis of the upper respiratory tract Microbiotas as the source of the lung and gastric Microbiotas in Healthy Individuals. MBio, 6(2): e00037–15.

  Biagi E et al. 2010. Through ageing, and beyond: Gut Microbiota and inflammatory status in seniors and centenarians. PloS One, 5(5): e10667.

  Bik EM et al. 2006. Molecular analysis of the bacterial Microbiota in the human stomach. PNAS, 103(3): 732–737.

  Byrd Al et al. 2018. The human skin microbiome. Nature Reviews Microbiology, 16: 143–155.

  Cao B et al. 2014. Placental microbiome and its role in preterm birth. NeoReviews, 15(12): e537.

  Charlson ES et al. 2011. Topographical continuity of bacterial populations in the healthy human respiratory tract. American Journal of Respiratory and Critical Care Medicine, 184: 957–963.

  Cogen AL et al. 2008. Skin Microbiota: A source of disease or defence? British Journal of Dermatology, 158(3): 442–455.

  Dong Q et al. 2011. Diversity of bacteria at healthy human conjunctiva. Investigative Ophthalmology & Visual Science, 52(8): 5408–5413.

  Eckburg PB et al. 2005. Diversity of the human intestinal microbial flora. Science, 308(5728): 1635–1638.

  El Kaoutari A et al. 2013. The abundance and variety of carbohydrate-active enzymes in the human gut Microbiota. Nature Reviews Microbiology, 11(7): 497–504.

  Feil EJ, Spratt BG. 2001. Recombination and the population structures of bacterial pathogens. Annual Review of Microbiology, 55: 561–590.

  Fettweis JM et al. 2012. A new era of the vaginal microbiome: Advances using next-generation sequencing. Chemistry and Biodiversity, 9(5): 965–976.

  Findley K et al. 2013. Topographic diversity of fungal and bacterial communities in human skin. Nature

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  Microbiology

  • Dave Wessner, Christine Dupont, Trevor Charles, Josh Neufeld(Authors)
  • 2020(Publication Date)
  • Wiley

    (Publisher)

  Modern molecular tech- niques are just beginning to provide some clues. Differences in the microbial communities of healthy individuals versus patients with a range of disease conditions such as ulcerative colitis, inflammatory bowel disease, Crohn’s disease, and colon cancer have been noted. Microbial diversity is frequently diminished in patients with these conditions. However, it remains to be estab- lished if these differences are the result or the cause of pertur- bations in microbial populations. The Mini‐Paper presents Fecal Microbiota may not, however, be completely represen- tative of the colon. Feces probably contain organisms car- ried from the small intestine and are likely predominated by lumen species, with species in mucus less represented. Although these studies may not be ideal and are subject to some interpretation, they give some insight into the diversity and variation of the human microbial inhabitants of the gut. Analyses of rRNA genes show that the human gut micro- biota is dominated by bacteria. Only three or four species of archaea, all methanogens, have been found along with a small number of eukaryotic species, mostly yeast. Little disagree- ment is reported among studies on the major groups and their proportions, but the specific genera and their numbers vary widely among individuals. The most abundant bacteria found in the colon and feces of young healthy adults are anaerobes belonging to the phylum Firmicutes, class Clostridia, followed by the phylum Bacteroidetes , predominated by members FIGURE 15.16 Biofilm of the intestinal mucus Most colonizing symbiotic microorganisms are not attached to the epithelial cells lining the lumen of the intestine. Instead, they form a biofilm on the outer edge of the mucus layer that extends into the lumen of the intestine. The ability to colonize and/or invade the intestinal epithelium is largely a feature of specialized intestinal pathogens.

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  Microbe

  • Michele S. Swanson, Elizabeth A. Joyce, Rachel E. A. Horak(Authors)
  • 2022(Publication Date)
  • ASM Press

    (Publisher)

  538 | PART III MICROBIAL ECOLOGY Introduction K nowing how complex and diverse microbial communities are in the environment (chapter 19) and the impact that their collective activ- ities have on our planet (chapter 20), it may come as no surprise to learn that microbes are highly interactive, not only with each other, but also with other types of organisms. Their interactions are as diverse as the microbes themselves and involve any living component of their ecosystem such as other microbes, plants, and animals. In fact, these interactions are so widespread in nature that biologist Lynn Margulis, credited with developing endosymbiotic theory, said, “Life did not take over the globe by combat, but by networking.” The field of microbial ecology is currently abuzz with new host- microbe and microbe-microbe interactions being discovered at an astonishing pace, likely because of the development of new tools in sequencing, micros- copy, and multi-omics. Throughout the book we have discussed how microbes communicate and how they interact to live as surface-attached communities or biofilms. But microbial interactions are far more diverse than what we have described thus far. No partner is off-limits; microbes interact with other microbes of the same or different species, plants, and animals. Sometimes microbes cooperate; other times they antagonize or even kill their partner. In fact, a single microbe may cooperate one minute, just to turn against its partner the next. Why? Because microbes are constantly sensing and responding to chemical, physical, and biological cues from their environment, all of which fluctuate rapidly. Their ability to tune their responses to other cells, microbial or nonmicrobial, is key to their survival. Whether through cooperation or conflict, microbial interactions shaped the path of life’s evolution, and in doing so, microbes transformed the Earth into the life-supporting planet it is today.

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