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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; however, the term human metagenome has the same meaning.
Gut microbiota, gut microbiome, or gut flora, are the microorganisms, including bacteria, archaea, fungi, and viruses, that live in the digestive tracts of animals. The gastrointestinal metagenome is the aggregate of all the genomes of the gut microbiota. The gut is the main location of the human microbiome. The gut microbiota has broad impacts, including effects on colonization, resistance to pathogens, maintaining the intestinal epithelium, metabolizing dietary and pharmaceutical compounds, controlling immune function, and even behavior through the gut–brain axis.
In microbiology, the phyllosphere is the total above-ground surface of a plant when viewed as a habitat for microorganisms. The phyllosphere can be further subdivided into the caulosphere (stems), phylloplane (leaves), anthosphere (flowers), and carposphere (fruits). The below-ground microbial habitats are referred to as the rhizosphere and laimosphere. Most plants host diverse communities of microorganisms including bacteria, fungi, archaea, and protists. Some are beneficial to the plant, others function as plant pathogens and may damage the host plant or even kill it.
Bacteroidales is an order of bacteria. Notably it includes the genera Prevotella and Bacteroides, which are commonly found in the human gut microbiota.
Rikenellaceae is a family of Gram-negative bacteria described by Noel R. Krieg in 2015. It contains nine genera, five of which are validly published by the International Code of Nomenclature of Prokaryotes. Bacteria with 16S ribosomal RNA highly similar to the Rikenella genus, as compared to the larger taxonomic order Bacteroidales, are classified in this family.
The Human Microbiome Project (HMP) was a United States National Institutes of Health (NIH) research initiative to improve understanding of the microbiota involved in human health and disease. Launched in 2007, the first phase (HMP1) focused on identifying and characterizing human microbiota. The second phase, known as the Integrative Human Microbiome Project (iHMP) launched in 2014 with the aim of generating resources to characterize the microbiome and elucidating the roles of microbes in health and disease states. The program received $170 million in funding by the NIH Common Fund from 2007 to 2016.
Microbiota are the range of microorganisms that may be commensal, mutualistic, or pathogenic found in and on all multicellular organisms, including plants. Microbiota include bacteria, archaea, protists, fungi, and viruses, and have been found to be crucial for immunologic, hormonal, and metabolic homeostasis of their host.
Bacterial phyla constitute the major lineages of the domain Bacteria. While the exact definition of a bacterial phylum is debated, a popular definition is that a bacterial phylum is a monophyletic lineage of bacteria whose 16S rRNA genes share a pairwise sequence identity of ~75% or less with those of the members of other bacterial phyla.
An enterotype is a classification of living organisms based on the bacteriological composition of their gut microbiota. The discovery of three human enterotypes was announced in the April 2011 issue of Nature by Peer Bork and his associates. They found that enterotypes are not dictated by age, gender, body weight, or national divisions. There are indications that long-term diet influences enterotype. Type 1 is characterized by high levels of Bacteroides, type 2 has few Bacteroides but Prevotella are common, and type 3 has high levels of Ruminococcus.
CrAss-like phage are a bacteriophage family that was discovered in 2014 by cross assembling reads in human fecal metagenomes. In silico comparative genomics and taxonomic analysis have found that crAss-like phages represent a highly abundant and diverse family of viruses. CrAss-like phage were predicted to infect bacteria of the Bacteroidota phylum and the prediction was later confirmed when the first crAss-like phage (crAss001) was isolated on a Bacteroidota host in 2018. The presence of crAss-like phage in the human gut microbiota is not yet associated with any health condition.
A microbiome 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 explanatory paragraph pronounces the dynamic character of the microbiome, and the second explanatory paragraph clearly separates the term microbiota from the term microbiome.
Hologenomics is the omics study of hologenomes. A hologenome is the whole set of genomes of a holobiont, an organism together with all co-habitating microbes, other life forms, and viruses. While the term hologenome originated from the hologenome theory of evolution, which postulates that natural selection occurs on the holobiont level, hologenomics uses an integrative framework to investigate interactions between the host and its associated species. Examples include gut microbe or viral genomes linked to human or animal genomes for host-microbe interaction research. Hologenomics approaches have also been used to explain genetic diversity in the microbial communities of marine sponges.
Pharmacomicrobiomics, proposed by Prof. Marco Candela for the ERC-2009-StG project call, and publicly coined for the first time in 2010 by Rizkallah et al., is defined as the effect of microbiome variations on drug disposition, action, and toxicity. Pharmacomicrobiomics is concerned with the interaction between xenobiotics, or foreign compounds, and the gut microbiome. It is estimated that over 100 trillion prokaryotes representing more than 1000 species reside in the gut. Within the gut, microbes help modulate developmental, immunological and nutrition host functions. The aggregate genome of microbes extends the metabolic capabilities of humans, allowing them to capture nutrients from diverse sources. Namely, through the secretion of enzymes that assist in the metabolism of chemicals foreign to the body, modification of liver and intestinal enzymes, and modulation of the expression of human metabolic genes, microbes can significantly impact the ingestion of xenobiotics.
Muribaculum is a genus from the family of Muribaculaceae, with one known species.
Muribaculum intestinale is a strictly anaerobic bacterium from the genus of Muribaculum which has been isolated from the caecal content of a mouse in Zurich in Switzerland.
Paludibacter is a Gram-negative, strictly anaerobic, chemoorganotrophic and non-motile genus from the phylum Bacteroidota.
Cuneatibacter is a rod-shaped bacterial genus from the family of Lachnospiraceae with one known species.
The plant microbiome, also known as the phytomicrobiome, plays roles in plant health and productivity and has received significant attention in recent years. The microbiome has been defined 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".
The Genome Taxonomy Database (GTDB) is an online database that maintains information on a proposed nomenclature of prokaryotes, following a phylogenomic approach based on a set of conserved single-copy proteins. In addition to resolving paraphyletic groups, this method also reassigns taxonomic ranks algorithmically, updating names in both cases. Information for archaea was added in 2020, along with a species classification based on average nucleotide identity. Each update incorporates new genomes as well as automated and manual curation of the taxonomy.
Tannerellaceae is a family of bacteria.
References
- 1 2 Lagkouvardos I, Lesker TR, Hitch TCA, Galvez EJC, Smit N, Neuhaus K, Wang J, Baines JF, Abt B, Stecher B, Overmann J, Strowig T, Clavel T. (2019). "Sequence and cultivation study of Muribaculaceae reveals novel species, host preference, and functional potential of this yet undescribed family". Microbiome. 7 (1): 28. doi: 10.1186/s40168-019-0637-2 . PMC 6381624 . PMID 30782206.
- ↑ Euzéby JP, Parte AC. "Muribaculaceae". List of Prokaryotic names with Standing in Nomenclature (LPSN). Retrieved June 27, 2021.
- ↑ Ormerod, Kate L.; Wood, David L. A.; Lachner, Nancy; Gellatly, Shaan L.; Daly, Joshua N.; Parsons, Jeremy D.; Dal’Molin, Cristiana G. O.; Palfreyman, Robin W.; Nielsen, Lars K.; Cooper, Matthew A.; Morrison, Mark; Hansbro, Philip M.; Hugenholtz, Philip (7 July 2016). "Genomic characterization of the uncultured Bacteroidales family S24-7 inhabiting the guts of homeothermic animals". Microbiome. 4 (1): 36. doi: 10.1186/s40168-016-0181-2 . PMC 4936053 . PMID 27388460.
- ↑ Lagkouvardos, I.; Pukall, R.; Abt, B.; Foesel, B. U.; Meier-Kolthoff, J. P.; Kumar, N.; Bresciani, A.; Martínez, I.; Just, S.; Ziegler, C.; Brugiroux, S.; Garzetti, D.; Wenning, M.; Bui, T. P.; Wang, J.; Hugenholtz, F.; Plugge, C. M.; Peterson, D. A.; Hornef, M. W.; Baines, J. F.; Smidt, H.; Walter, J.; Kristiansen, K.; Nielsen, H. B.; Haller, D.; Overmann, J.; Stecher, B.; Clavel, T. (2016). "miBC". Nature Microbiology. 1 (10): 16131. doi:10.1038/nmicrobiol.2016.131. hdl: 11858/00-001M-0000-002C-0BCC-0 . PMID 27670113.
- ↑ Pereira, Fátima C.; Wasmund, Kenneth; Cobankovic, Iva; Jehmlich, Nico; Herbold, Craig W.; Lee, Kang Soo; Sziranyi, Barbara; Vesely, Cornelia; Decker, Thomas; Stocker, Roman; Warth, Benedikt (December 2020). "Rational design of a microbial consortium of mucosal sugar utilizers reduces Clostridiodes difficile colonization". Nature Communications. 11 (1): 5104. Bibcode:2020NatCo..11.5104P. doi:10.1038/s41467-020-18928-1. ISSN 2041-1723. PMC 7547075 . PMID 33037214.
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