Microbiome

Extracted Attributes

• Core Components

  Bacteria, archaea, fungi, algae, and small protists

• Functional Roles

  Pathogen protection, immune system development, food digestion, and vitamin production

• Definition Origin

  Whipps et al. (1988)

• Debated Components

  Phages, viruses, plasmids, and mobile genetic elements

• Primary Research Methods

  DNA sequencing, PCR, 16S rRNA typing, and shotgun metagenomics

• Microbe-to-Human Cell Ratio

  Estimated 10:1

• Human Body Weight Contribution

  Up to 5 pounds

Timeline

• Microbiome research originates in microbiology with the development of the first microscopes. (Source: Wikipedia)

  1600-01-01

• Whipps et al. provide the first precise definition of the microbiome as a microbial community and its theatre of activity. (Source: Wikipedia)

  1988-01-01

• Early 21st century paradigm shifts occur as sequencing technologies enable cultivation-independent investigation of microbial communities. (Source: Wikipedia)

  2000-01-01

• An international panel of experts publishes a refined definition of the microbiome to separate it from the term microbiota. (Source: Wikipedia)

  2020-01-01

• FDA Commissioner Marty Makary announces a shift in NIH funding toward researching the microbiome as a root cause for autism. (Source: Document 065d2e96-4d40-49bd-8511-d8d35f8b01f4)

  2024-01-01

Microbiome

A microbiome (from Ancient Greek μικρός (mikrós) 'small' and βίος (bíos) 'life') is the community of microorganisms that can usually be found living together in any given habitat. It was defined more precisely in 1988 by Whipps et al. as "a characteristic microbial community occupying a reasonably well-defined habitat which has distinct physio-chemical properties. The term thus not only refers to the microorganisms involved but also encompasses their theatre of activity". In 2020, an international panel of experts published the outcome of their discussions on the definition of the microbiome. They proposed a definition of the microbiome based on a revival of the "compact, clear, and comprehensive description of the term" as originally provided by Whipps et al., but supplemented with two explanatory paragraphs, the first pronouncing the dynamic character of the microbiome, and the second clearly separating the term microbiota from the term microbiome. The microbiota consists of all living members forming the microbiome. Most microbiome researchers agree bacteria, archaea, fungi, algae, and small protists should be considered as members of the microbiome. The integration of phages, viruses, plasmids, and mobile genetic elements is more controversial. Whipps's "theatre of activity" includes the essential role secondary metabolites play in mediating complex interspecies interactions and ensuring survival in competitive environments. Quorum sensing induced by small molecules allows bacteria to control cooperative activities and adapts their phenotypes to the biotic environment, resulting, e.g., in cell–cell adhesion or biofilm formation. All animals and plants form associations with microorganisms, including protists, bacteria, archaea, fungi, and viruses. In the ocean, animal–microbial relationships were historically explored in single host–symbiont systems. However, new explorations into the diversity of microorganisms associating with diverse marine animal hosts is moving the field into studies that address interactions between the animal host and the multi-member microbiome. The potential for microbiomes to influence the health, physiology, behaviour, and ecology of marine animals could alter current understandings of how marine animals adapt to change. This applies to especially the growing climate-related and anthropogenic-induced changes already impacting the ocean and the phytoplankton microbiome in it. The plant microbiome plays key roles in plant health and food production and has received significant attention in recent years. Plants live in association with diverse microbial consortia, referred to as the plant microbiota, living both inside (the endosphere) and outside (the episphere) plant tissues. They play important roles in the ecology and physiology of plants. The core plant microbiome is thought to contain keystone microbial taxa essential for plant health and for the fitness of the plant holobiont. Likewise, the mammalian gut microbiome has emerged as a key regulator of host physiology, and coevolution between host and microbial lineages has played a key role in the adaptation of mammals to their diverse lifestyles. Microbiome research originated in microbiology in the seventeenth century. The development of new techniques and equipment boosted microbiological research and caused paradigm shifts in understanding health and disease. The development of the first microscopes allowed the discovery of a new, unknown world and led to the identification of microorganisms. Infectious diseases became the earliest focus of interest and research. However, only a small proportion of microorganisms are associated with disease or pathogenicity. The overwhelming majority of microbes are essential for healthy ecosystem functioning and are known for beneficial interactions with other microbes and organisms. The concept that microorganisms exist as single cells began to change as it became increasingly obvious that microbes occur within complex assemblages in which species interactions and communication are critical. Discovery of DNA, the development of sequencing technologies, PCR, and cloning techniques enabled the investigation of microbial communities using cultivation-independent approaches. Further paradigm shifts occurred at the beginning of this century and still continue, as new sequencing technologies and accumulated sequence data have highlighted both the ubiquity of microbial communities in association within higher organisms and the critical roles of microbes in human, animal, and plant health. These have revolutionised microbial ecology. The analysis of genomes and metagenomes in a high-throughput manner now provides highly effective methods for researching the functioning of individual microorganisms as well as whole microbial communities in natural habitats.

Web Search Results

• Microbiome - Wikipedia

  The microbiome is defined as a characteristic microbial community occupying a reasonable well-defined habitat which has distinct physio-chemical properties. The microbiome not only refers to the microorganisms involved but also encompass their theatre of activity, which results in the formation of specific ecological niches. The microbiome, which forms a dynamic and interactive micro-ecosystem prone to change in time and scale, is integrated in macro-ecosystems including eukaryotic hosts, and here crucial for their functioning and health. [...] #### Human [edit] Main article: Human microbiome The human microbiome is the aggregate of all microbiota that reside on or within human tissues and biofluids along with the corresponding anatomical sites in which they reside, including the skin, mammary glands, seminal fluid, uterus, ovarian follicles, lung, saliva, oral mucosa, conjunctiva, biliary tract, and gastrointestinal tract. Types of human microbiota include bacteria, archaea, fungi, protists and viruses. Though micro-animals can also live on the human body, they are typically excluded from this definition. In the context of genomics, the term human microbiome is sometimes used to refer to the collective genomes of resident microorganisms; the term human metagenome has the same meaning. [...] | "A community of microorganisms (such as bacteria, fungi, and viruses) that inhabit a particular environment and especially the collection of microorganisms living in or on the human body". "Human Microbiome Project (HMP): [...] The Human Microbiome is the collection of all the microorganisms living in association with the human body. These communities consist of a variety of microorganisms including eukaryotes, archaea, bacteria and viruses". |

• Microbiome - National Institute of Environmental Health Sciences

  # Microbiome Close the left navigation The microbiome is the collection of all microbes, such as bacteria, fungi, viruses, and their genes, that naturally live on our bodies and inside us. Although microbes require a microscope to see them, they contribute to human health and wellness in many ways. Table of Contents What is NIEHS Doing? Further Reading ### Introduction The microbiome is the collection of all microbes, such as bacteria, fungi, viruses, and their genes, that naturally live on our bodies and inside us. Although microbes are so small that they require a microscope to see them, they contribute in big ways to human health and wellness. They protect us against pathogens, help our immune system develop, and enable us to digest food to produce energy. [...] Because the microbiome is a key interface between the body and the environment, these microbes can affect health in many ways and can even affect how we respond to certain environmental substances. Some microbes alter environmental substances in ways that make them more toxic, while others act as a buffer and make environmental substances less harmful. #### How can the microbiome affect health? The critical role of the microbiome is not surprising when considering that there are as many microbes as there are human cells in the body. The human microbiome is diverse, and each body site – for example, the gut, skin, and oral and nasal cavities – has a different community of microbes. [...] A person’s core microbiome is formed in the first years of life but can change over time in response to different factors including diet, medications, and environmental exposures.

• Human microbiome - Wikipedia

  Microbiome This term refers to the entire habitat, including the microorganisms (bacteria, archaea, lower and higher eurkaryotes, and viruses), their genomes (i.e., genes), and the surrounding environmental conditions. This definition is based on that of "biome," the biotic and abiotic factors of given environments. Others in the field limit the definition of microbiome to the collection of genes and genomes of members of a microbiota. It is argued that this is the definition of metagenome, which combined with the environment constitutes the microbiome. [...] ## Disease and death [edit] Human bodies rely on the innumerable bacterial genes as the source of essential nutrients. Both metagenomic and epidemiological studies indicate vital roles for the human microbiome in preventing a wide range of diseases, from type 2 diabetes and obesity to inflammatory bowel disease, Parkinson's disease, and even mental health conditions like depression. A symbiotic relationship between the gut microbiota and different bacteria may influence an individual's immune response. Metabolites generated by gut microbes appear to be causative factors in type 2 diabetes. Although in its infancy, microbiome-based treatment is also showing promise, most notably for treating drug-resistant C. difficile infection and in diabetes treatment. [...] The problem of elucidating the human microbiome is essentially identifying the members of a microbial community, which includes bacteria, eukaryotes, and viruses. This is done primarily using deoxyribonucleic acid (DNA)-based studies, though ribonucleic acid (RNA), protein and metabolite based studies are also performed. DNA-based microbiome studies typically can be categorized as either targeted amplicon studies or, more recently, shotgun metagenomic studies. The former focuses on specific known marker genes and is primarily informative taxonomically, while the latter is an entire metagenomic approach which can also be used to study the functional potential of the community. One of the challenges that is present in human microbiome studies, but not in other metagenomic studies, is to

• Microbiome studies: an overview of applications - OHMX.bio

  Microbiome research has grown significantly in recent decades, gaining substantial interest in the scientific and public sectors. The microbiome is a diverse collection of microbial communities in the body, including archaea, bacteria, fungi, and viruses. It encompasses trillions of microorganisms and their diverse molecules, including nucleic acids, proteins, lipids, polysaccharides, and metabolites, all of which are influenced by the host and environment. Our internal microbiome has coevolved with its human host, resulting in these microbial communities playing a crucial role in supporting our health. As a result, disruptions in the balance of the microbiome can trigger or worsen a wide range of diseases1-5. Furthermore, the applications of microbiome research extend beyond human [...] Microbiome studies offer valuable insights across a wide range of fields, including human health, animal care, agriculture, and environmental biotechnology. The choice of sequencing method, whether 16S rRNA typing, metagenomics, or long-read sequencing, depends on the study’s objectives. 16S sequencing is ideal for community profiling, metagenomics provides deeper functional analysis, and long-read sequencing offers detailed genomic data for complex microbial communities. Understanding these methods and their applications is essential for advancing research and achieving specific industry goals. By embracing microbiome analysis, researchers can unlock new opportunities for innovation, health improvements, and sustainability. As microbiome research continues to evolve, these techniques

• The Human Microbiome | BCM - Baylor College of Medicine

  Media Component Credit CDC PHIL-Dr. Gilda Jones Content The human microbiome, or microbiota, is defined as the collection of microbes - bacteria, viruses, and single-cell eukaryotes - that inhabits the human body. Microbes in a healthy human adult are estimated to outnumber human cells by a ratio of ten to one, and the total number of genes in the microbiome may exceed the number of genes in the human genome by a factor of about 100. Even though microbial cells are only one-tenth to one-hundredth the size of a human cell, they may account for up to five pounds of adult body weight. [...] ### The Microbiota in Health and Disease The microbiome contributes to our health in diverse ways: by helping the body sense and respond to our environment, by harvesting nutrients from food, by playing a role in the development of our immune system, by preventing disease, and by controlling inflammation. The microbiota may also influence many disease states, including diabetes, irritable bowel syndrome, and cancer, among others. Furthermore, the community of microbes that colonize the human body provides protection from incoming disease-causing microorganisms. Through an understanding of how the microbiome impacts human health, researchers aim to translate this knowledge into new diagnostics and therapeutics. Heading ## The Research Content [...] Although bacteria are often associated with infections, the bacteria that colonize the surface and insides of our bodies are essential for life. We are dependent on these bacteria to help digest our food, produce certain vitamins, regulate our immune system, and keep us healthy by protecting us against disease-causing bacteria. The identity and degree of diversity of the microbiota in a single individual is variable from person to person. The specific composition of a person's microbiome is increasingly recognized as playing an important role in disease and disease susceptibility.

• Award

  DOAJ seal

• Country

  United Kingdom

• Instance Of

  Q737498