Biological Sciences
Microbiome
The microbiome refers to the diverse community of microorganisms, including bacteria, viruses, fungi, and other microbes, that inhabit a particular environment, such as the human body, soil, or water. These microorganisms play a crucial role in maintaining the health and functioning of their host organism, and their composition can be influenced by various factors such as diet, environment, and genetics.
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11 Key excerpts on "Microbiome"
eBook - PDF- 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.
eBook - ePub- D. Dhanasekaran, Dhiraj Paul, N. Amaresan, A. Sankaranarayanan, Yogesh S. Shouche, D. Dhanasekaran, Dhiraj Paul, N. Amaresan, A. Sankaranarayanan, Yogesh S. Shouche(Authors)
- 2021(Publication Date)
- CRC Press(Publisher)
1 An Insight of Microbiome Science T. Savitha Tiruppur Kumaran College for Women A. Sankaranarayanan Uka Tarsadia University Ashraf Y. Z. Khalifa King Faisal UniversityUniversity of Beni-Suef Contents 1.1 Introduction 1.2 Ecological Theory in Understanding of the Microbiome 1.3 Different Types of Microbiome 1.3.1 Microbiome 1.3.2 Types of Microbiome 1.3.2.1 Soil Microbiome 1.3.2.2 Marine Microbiome 1.3.2.3 Animal Microbiome 1.3.2.4 Plant Microbiome 1.3.2.5 Human Microbiome 1.4 Classification of Microbiomes in Human Health 1.4.1 The Skin Microbiome 1.4.2 Oral Microbiome 1.4.3 The Respiratory Microbiome 1.4.4 Gut Microbiome 1.4.5 Genital Microbiome 1.5 Future Perspectives References1.1 Introduction
Microbiome is a popular and repeatedly used term due to its widespread activities in various scientific platforms and due to its influential roles. It is sprawling its wings in the diversified fields of biology, and the microbes have a symbiotic and pathogenic association with various biotic organisms, including all vertebrates and plants. It is a great promising tool and that’s the reason in the past decade more than 1.7 billion US $ spent toward human Microbiome research (Proctor, 2019). The Microbiome science nowadays attracts more researchers due to its importance in diversified fields. Further, the new discoveries and concepts have been emerging from this field changing the perception of the importance of this field among the researchers (Walter and Ley, 2011; O’Callaghan et al., 2016).Microbiome is defined as a “collective genes and genomes” of all the microorganisms dwelling in a particular environment (Marchesi and Ravel, 2015). Another short definition is, “Microbiome means genes associated with the microbiota” (Amato, et al., 2016). Diversified Microbiomes are present in the different parts of body, environment, and other habitats (Gilbert and Stephens, 2018). In addition, their presence depends on the surrounding conditions (Derrien et al., 2019; de Steenhuijsen Piters et al., 2015). There are many factors that are involved in cohabitation of Microbiome in biota.
eBook - ePubEpigenetics and Responsibility
Ethical Perspectives
- Emma Moormann, Anna Smajdor, Daniela Cutas(Authors)
- 2024(Publication Date)
- Bristol University Press(Publisher)
7Responsibility and the Microbiome
Kristien Hens and Eman AhmedIntroduction
The gut Microbiome is a diverse ecosystem encompassing trillions of micro-organisms, including bacteria, viruses, fungi, archaea and protozoa. It establishes a symbiotic relationship with the human host via Microbiome–host interactions that occur at various levels of complexity and that are essential for maintaining bodily homeostasis (Wu and Wang, 2019 ). The Microbiome’s ‘cross-talk’ with the host physiology is demonstrated via its contribution to a wide range of functions, including digestion, production of metabolites, and development of the immune system (Cryan and Dinan, 2012 ). The gut Microbiome as an ecosystem has thus emerged as a key factor in understanding human health and disease. Although the exact number is unknown, the number of microbial genes present in the human body may equal or exceed the number found in the human genome. Indeed, the genome of these microbes is sometimes called ‘our second genome’(Meisel and Grice, 2017 ).At this point, the reader may wonder what a chapter on the human Microbiome is doing in a volume on epigenetics. There are a number of reasons for its inclusion here. First, it has been demonstrated that there is an interplay between the gut Microbiome and epigenetics. Research suggests that gut Microbiome metabolites are crucial epigenetic regulators of the host genome. They can induce epigenetic changes in key human genes and ultimately lead to the development of disease (Yuille et al, 2018 ). For example, changes in the diet seem to influence Microbiome composition and affect the regulation of histone methylation and demethylation in the host genome (Krautkramer et al, 2016 ). A more specific but relatively recent area of research explores the ways in which epigenetic alterations brought about by the Microbiome influence the development of cognitive function and behaviour and the development of neuropsychiatric disorders. Even though the specific underlying mechanisms are not yet fully understood, promising strands of research suggest that changes in the Microbiome alter neuroactive signals via the vagus nerve, thus bringing about epigenetic changes in the brain (Kaur et al, 2021 ). It has also been suggested that neuroepigenetic modifications can occur due to production of short-chain fatty acids by the Microbiome. These modifications underlie the pathogenesis of many neuropsychiatric conditions via inhibition of histone deacetylases (Peedicayil and Santhosh, 2021
- Niklaus P. Lang, Tord Berglundh, William V. Giannobile, Mariano Sanz, Niklaus P. Lang, Tord Berglundh, William V. Giannobile, Mariano Sanz(Authors)
- 2021(Publication Date)
- Wiley-Blackwell(Publisher)
Dental biofilms develop on the hard surfaces of the mouth, such as teeth, dentures, and implants. These dental biofilms form part of the oral Microbiome, which in turn is part of the human Microbiome. Contemporary studies show that the human Microbiome plays an essential role in the health and well-being of their host. Humans have evolved to have an intimate and largely beneficial relationship with these microorganisms; however, this relationship is dynamic and fragile, and a number of intrinsic and extrinsic factors can damage this exquisite balance, and such events can lead to disease.The human Microbiome
The human body is estimated to be composed of approximately 1014 cells, of which only half are mammalian (Sender et al. 2016 ). The other 50% are the microorganisms that form the human Microbiome, which has been defined as the microbes and their collective genomes that are living in or on our body (Cho & Blaser 2012 ). The human Microbiome plays a fundamental role in the normal development of the body and confers significant benefits to the host. For example, the human Microbiome contributes to the differentiation and maturation of the host mucosa and its immune system, to the breakdown of dietary components and the generation of energy, and to the exclusion of exogenous microbes, many of which could be pathogenic (Cho & Blaser 2012 ; Kilian et al. 2016 ). In general, this relationship is mutually beneficial (i.e. symbiotic) in that the microorganisms gain a warm and nutritious environment in which to grow while delivering the benefits described above to the host. On occasions, the balance of the Microbiome at a site can be disrupted which can result in this synergistic relationship breaking down, and disease can be a consequence (a process termed dysbiosis).The composition of the Microbiome varies at distinct surfaces on the body (e.g. the skin, mouth, digestive and reproductive tracts) despite the frequent transfer of organisms between these sites; their characteristic composition reflects the significant differences in the biological and physical properties of each habitat (Wilson 2005 ). These properties determine which microorganisms are able to colonize successfully, and which will predominate or be only a minor component of the established Microbiome. These resident microorganisms function as an interactive microbial community
eBook - PDF- Kathleen A. Ireland(Author)
- 2018(Publication Date)
- Wiley(Publisher)
In this regard, your Microbiome is almost as personal as your DNA. Despite the incredible number of bacterial cells involved in the human Microbiome, very little is known about their influence on human health and wellness. Surely these bacterial cells are more than oppor- tunistic passengers. After all, bacteria have been shaping the world for billions of years! It stands to reason there must be some purpose to their presence in such numbers in the human Microbiome. The National Institutes of Health recognized this possibility and began the Human Microbiome Project in 2008. The initial goals of this federally and pri- vately funded program were to generate resources used to characterize the human Microbiome, and analyze its role in human health and disease. While it can be difficult and often impossible to isolate and culture many of the known species of bacterial cells in the laboratory, it is rela- tively easy to obtain samples of Microbiome DNA. The DNA pulled from a mixed sample of bacteria will include DNA from every species of bacte- ria present in that Microbiome. Analysis of that large mixed mass of DNA is referred to as metagenomics. The information obtained from this type of analysis does not identify individual bacteria, but rather shows the entire set of genes that are present in the bacterial community (Figure 11.8). Because bacteria within the Microbiome work as a single unit, sharing tasks and assisting one another with metabolic products, this analysis is perfect. It is the collection of functions the Microbiome is handling that are of most importance to us from a medical standpoint. The Human Microbiome Project’s first goal is to characterize the typical Microbiome found in and on the human body Scientists began this research by rec- ognizing five areas of the human body that may house slightly dif- ferent Microbiomes: the nasal passages, oral cavity, skin, GI tract, and urogenital tract (Figure 11.9).
eBook - PDFGenomics and Proteomics
Principles, Technologies, and Applications
- Devarajan Thangadurai, Jeyabalan Sangeetha, Devarajan Thangadurai, Jeyabalan Sangeetha(Authors)
- 2015(Publication Date)
- Apple Academic Press(Publisher)
The important points to note are that even though there are considerable intra- and interpersonal differences in the human Microbiome, this variation can be split into community types predic-tive of each other, and a particular type, or changing types, could be used to assess disease risk and to personalize antimicrobial treatment. The main sites studied so far in terms of their microbial constituents are the gut (Greenblum et al ., 2012), urinary tract (Nelson et al ., 2010; Wolfe et al ., 2012), lower and upper respiratory tract (Willner et al ., 2009), vagina (Oakley et al ., 2008; Hummelen et al ., 2010), skin (Grice et al ., 2009; Capone et al ., 2011; Fahlén et al ., 2012), gingiva (Lazarevic et al ., 2009), and wounds (Dowd et al ., 2008) in health and in disease (Pflughoeft and Versalovic, 2012). Studying the gut Microbiome has given us a better idea of how to classify disease processes such as inflammatory bowel disease, and sheds light on specific conditions such as Crohn’s disease or idiopathic bowel syndrome (Manichanh et al ., 2006). It will not be long before we are able to assess a range of diseases in this manner, giving us useful tools for improved clinical management. Indeed, studying the human Microbiome will eventually enable us to moni-tor its diversity during and in response to therapy, providing information that can be used to both predict prognosis and improve poor clinical outcomes. These advances will also extend far beyond bacterial infection, as the human Microbiome, while predominantly made up of bacteria, also contains eukaryotic microbes and viruses (both human viruses and bacteriophages). The human vi-rome is the collection of all viruses that are found in or on humans, and includes both eukaryotic and prokaryotic viruses, viruses causing acute, persistent, or latent infection, and viruses integrated into the human genome, such as en-dogenous retroviruses (Duerkop and Hooper, 2013; Minot et al ., 2013; Virgin, 2014).
eBook - ePubEden'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.”12Microbes 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
- Jyoti Prakash Tamang(Author)
- 2015(Publication Date)
- CRC Press(Publisher)
The gut Microbiome (gut microbiota and its collective genomes) plays a key role in homeostasis in humans and a strong relationship exists between diet, microbiota, and our health (Nicholson et al. 2012, Martin et al. 2014). Dietary components and dietary metabolites have roles beyond basic nutri-tion, and the modulation of the gut Microbiome composition by the alteration of food habits has potentialities in health improvement and even disease prevention (Holmes et al. 2012, Guzman et al. 2013). Understanding the complex interaction between diet and the composition and func-tion of human gut microbiota is critical in advancing our knowledge in the formulation of ways of manipulation of microbiota to prevent various health conditions and to improve our health. A growing body of evidence suggests that reprogramming the gut Microbiome or its function has beneficial effects on the host metabolism (de Vos and de Vos 2012, Goldsmith and Sartor 2014). The current knowledge of the complex and bidirectional interaction between the gut Microbiome and dietary components in relation to human health and disease is reviewed in this chapter. Virtually every surface of the human body is colonized by microorganisms. The human intes-tine is the habitat of many species of bacteria along with viruses, unicellular eukaryotes, and other organisms which have evolved and adapted to live, colonize, and grow there, forming a huge ecosystem, the gut microbiota (Bäckhed et al. 2005, Holmes et al. 2011). With an average length of 1.50 m and diameter of 6.4 cm, the human large intestine (colon) represents one of the largest interfaces where host–microbe interactions occur (Cummings and Macfarlane 1991). The intestine is home to an estimated 10 14 microbial cells (Lepage et al. 2012). The microbes that we carry outnumber us 10:1 in terms of total human body cell (somatic and germ cells) counts.
eBook - ePubBacterial 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 BEYONDTImportance of the Normal Resident Microbial Populations (Microbiota) of the Human Bodyhe 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.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.
- Chandra, Ram(Authors)
- 2021(Publication Date)
- Daya Publishing House(Publisher)
Chapter 13 Biodiversity of Microorganism in Different Area and its Ecological Importance Shika Jain 1 , Yogesh Franklin 1 * , Dinesh K. Kumawat 1 and B.M. Meena 2 1 Department of Food Microbiology, College of Dairy and Food Science Technology , 2 Department of Entomology, Rajasthan College of Agriculture, Maharana Pratap University of Agriculture and Technology, Udaipur, Rajasthan Introduction The overwhelming majority of biological diversity is microbial. Microorganisms span all three domains of life and are typically defined as unicellular life forms that can only be observed with a microscope, including bacteria, archaea, viruses, and many unicellular eukaryotes (e.g ., some fungi and protists). Although it might not be immediately obvious, our world is a microbial one. Biodiversity is usually discussed in terms of large organisms, but no organisms are more ubiquitous, abundant, or diverse than microorganisms. Microorganisms were the first cellular life forms and were active more than 3 billion years prior to the appearance of macro-organisms. The metabolic activities that they carried out during this time were critical for creating the conditions for the evolution of multicellular forms. The universal tree of life ( Figure 13.1 ) emphasizes this point; multicellular eukaryote is crown groups compared with the deeply rooted Bacteria and Archaea. Microbes force us to stretch our imagination about the limits of metabolic lifestyles, the geography of life, and the roles that organisms play in our lives. This ebook is exclusively for this university only. Cannot be resold/distributed. Figure 13.1 : The Universal Tree of Life Showing the Position of Archaea and Bacteria Relative to Eucarya. The placement of organisms on this phylogenetic tree is based on the analyses of SSU rRNA sequences of organisms from within each domain.
eBook - PDF- 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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