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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.
The Bacillota are a phylum of bacteria, most of which have gram-positive cell wall structure. The renaming of phyla such as Firmicutes in 2021 remains controversial among microbiologists, many of whom continue to use the earlier names of long standing in the literature.
The Clostridia are a highly polyphyletic class of Bacillota, including Clostridium and other similar genera. They are distinguished from the Bacilli by lacking aerobic respiration. They are obligate anaerobes and oxygen is toxic to them. Species of the class Clostridia are often but not always Gram-positive and have the ability to form spores. Studies show they are not a monophyletic group, and their relationships are not entirely certain. Currently, most are placed in a single order called Clostridiales, but this is not a natural group and is likely to be redefined in the future.
Enterobacter is a genus of common Gram-negative, facultatively anaerobic, rod-shaped, non-spore-forming bacteria of the family Enterobacteriaceae. Cultures are found in soil, water, sewage, feces and gut environments. It is the type genus of the order Enterobacterales. Several strains of these bacteria are pathogenic and cause opportunistic infections in immunocompromised hosts and in those who are on mechanical ventilation. The urinary and respiratory tracts are the most common sites of infection. The genus Enterobacter is a member of the coliform group of bacteria. It does not belong to the fecal coliforms group of bacteria, unlike Escherichia coli, because it is incapable of growth at 44.5 °C in the presence of bile salts. Some of them show quorum sensing properties.
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.
Bacteroides is a genus of Gram-negative, obligate anaerobic bacteria. Bacteroides species are non endospore-forming bacilli, and may be either motile or nonmotile, depending on the species. The DNA base composition is 40–48% GC. Unusual in bacterial organisms, Bacteroides membranes contain sphingolipids. They also contain meso-diaminopimelic acid in their peptidoglycan layer.
Dysbiosis is characterized by a disruption to the microbiome resulting in an imbalance in the microbiota, changes in their functional composition and metabolic activities, or a shift in their local distribution. For example, a part of the human microbiota such as the skin flora, gut flora, or vaginal flora, can become deranged, with normally dominating species underrepresented and normally outcompeted or contained species increasing to fill the void. Dysbiosis is most commonly reported as a condition in the gastrointestinal tract.
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.
Faecalibacterium is a genus of bacteria. The genus contains several species including Faecalibacterium prausnitzii, Faecalibacterium butyricigenerans, Faecalibacterium longum, Faecalibacterium duncaniae, Faecalibacterium hattorii, and Faecalibacterium gallinarum. Its first known species, Faecalibacterium prausnitzii is gram-positive, mesophilic, rod-shaped, and anaerobic, and is one of the most abundant and important commensal bacteria of the human gut microbiota. It is non-spore forming and non-motile. These bacteria produce butyrate and other short-chain fatty acids through the fermentation of dietary fiber. The production of butyrate makes them an important member of the gut microbiota, fighting against inflammation.
Oral ecology is the microbial ecology of the microorganisms found in mouths. Oral ecology, like all forms of ecology, involves the study of the living things found in oral cavities as well as their interactions with each other and with their environment. Oral ecology is frequently investigated from the perspective of oral disease prevention, often focusing on conditions such as dental caries, candidiasis ("thrush"), gingivitis, periodontal disease, and others. However, many of the interactions between the microbiota and oral environment protect from disease and support a healthy oral cavity. Interactions between microbes and their environment can result in the stabilization or destabilization of the oral microbiome, with destabilization believed to result in disease states. Destabilization of the microbiome can be influenced by several factors, including diet changes, drugs or immune system disorders.
Ruminococcus is a genus of bacteria in the class Clostridia. They are anaerobic, Gram-positive gut microbes. One or more species in this genus are found in significant numbers in the human gut microbiota. The type species is R. flavefaciens. As usual, bacteria taxonomy is in flux, with Clostridia being paraphyletic, and some erroneous members of Ruminococcus being reassigned to a new genus Blautia on the basis of 16S rRNA gene sequences.
Alistipes is a Gram-negative genus of rod-shaped anaerobic bacteria in the phylum Bacteroidota. When members of this genus colonize the human gastrointestinal (GI) tract, they provide protective effects against colitis, autism, and cirrhosis. However, this genus can also cause dysbiosis by contributing to anxiety, chronic fatigue syndrome, depression, and hypertension. Showcasing priority effects in microbiome assembly, when infant GI tracts have bacteria of the species Staphylococcus but not the species Faecalibacterium, Alistipes species become less capable of colonization.
Parasutterella is a genus of Gram-negative, circular/rod-shaped, obligate anaerobic, non-spore forming bacteria from the Pseudomonadota phylum, Betaproteobacteria class and the family Sutterellaceae. Previously, this genus was considered "unculturable," meaning that it could not be characterized through conventional laboratory techniques, such as grow in culture due its unique requirements of anaerobic environment. The genus was initially discovered through 16S rRNA sequencing and bioinformatics analysis. By analyzing the sequence similarity, Parasutterella was determined to be related most closely to the genus Sutterella and previously classified in the family Alcaligenaceae.
Sutterella is a genus of Gram-negative, rod-shaped, non-spore-forming, Betaproteobacteria whose species have been isolated from the human gastrointestinal tract as well as canine feces. The genus of the family Sutterellaceae currently encompasses 4 distinct species, though at least 5 additional species have been proposed that do not yet meet International Code of Nomenclature of Prokaryotes (ICNP) standards for classification. Sutterella are frequently referred to as commensal in the context of human hosts, but are associated with inflammation, which has implications for a number of diseases.
Akkermansia muciniphila is a human intestinal symbiont, isolated from human feces. It is a mucin-degrading bacterium belonging to the genus, Akkermansia, discovered in 2004 by Muriel Derrien and Willem de Vos at Wageningen University of the Netherlands. It belongs to the phylum Verrucomicrobiota and its type strain is MucT. It is under preliminary research for its potential association with metabolic disorders.
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.
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.
Anaerococcus is a genus of bacteria. Its type species is Anaerococcus prevotii. These bacteria are Gram-positive and strictly anaerobic. The genus Anaerococcus was proposed in 2001. Its genome was sequenced in August 2009. The genus Anaerococcus is one of six genera classified within the group GPAC. These six genera are found in the human body as part of the commensal human microbiota.
Christensenella hongkongensis is a species of clinically relevant gram-positive coccobacilli, first isolated from patients in Hong Kong and Canada in 2006. Although the species remains relatively rare, it has a high mortality rate of up to 50%. Christensenella is thought to be broadly distributed globally, as it has been isolated from patient blood cultures around the world including Hong Kong, South Korea, New Zealand, Canada, Sweden, France and Italy. Fewer than 15 cases of C. hongkongensis have been observed worldwide.
References
- ↑ Morotomi, Masami; Nagai, Fumiko; Watanabe, Yohei (2012). "Description of Christensenella minuta gen. nov., sp. nov., isolated from human faeces, which forms a distinct branch in the order Clostridiales, and proposal of Christensenellaceae fam. nov". International Journal of Systematic and Evolutionary Microbiology. 62 (1): 144–149. doi: 10.1099/ijs.0.026989-0 . ISSN 1466-5034.
- ↑ Waters, Jillian L.; Ley, Ruth E. (2019-10-28). "The human gut bacteria Christensenellaceae are widespread, heritable, and associated with health". BMC Biology. 17 (1): 83. doi: 10.1186/s12915-019-0699-4 . ISSN 1741-7007. PMC 6819567 . PMID 31660948.
This article incorporates textfrom this source, which is available under the CC BY 4.0 license. - ↑ Waters JL, Ley RE (October 2019). "The human gut bacteria Christensenellaceae are widespread, heritable, and associated with health". BMC Biology. 17 (1): 83. doi: 10.1186/s12915-019-0699-4 . PMC 6819567 . PMID 31660948.
- ↑ Lim JM, Letchumanan V, Tan LT, Hong KW, Wong SH, Ab Mutalib NS, et al. (August 2022). "Ketogenic Diet: A Dietary Intervention via Gut Microbiome Modulation for the Treatment of Neurological and Nutritional Disorders (a Narrative Review)". Nutrients. 14 (17): 3566. doi: 10.3390/nu14173566 . PMC 9460077 . PMID 36079829.
- ↑ Goodrich JK, Waters JL, Poole AC, Sutter JL, Koren O, Blekhman R, et al. (November 2014). "Human genetics shape the gut microbiome". Cell. 159 (4): 789–799. doi:10.1016/j.cell.2014.09.053. PMC 4255478 . PMID 25417156.
- ↑ Liu X, Sutter JL, de la Cuesta-Zuluaga J, Waters JL, Youngblut ND, Ley RE (April 2021). "Reclassification of Catabacter hongkongensis as Christensenella hongkongensis comb. nov. based on whole genome analysis". International Journal of Systematic and Evolutionary Microbiology. 71 (4): 004774. doi:10.1099/ijsem.0.004774. PMC 8289216 . PMID 33881979.
- ↑ Morotomi M, Nagai F, Watanabe Y (January 2012). "Description of Christensenella minuta gen. nov., sp. nov., isolated from human faeces, which forms a distinct branch in the order Clostridiales, and proposal of Christensenellaceae fam. nov". International Journal of Systematic and Evolutionary Microbiology. 62 (Pt 1): 144–149. doi: 10.1099/ijs.0.026989-0 . PMID 21357455.
- 1 2 Pető Á, Kósa D, Szilvássy Z, Fehér P, Ujhelyi Z, Kovács G, Német I, Pócsi I, Bácskay I (August 2023). "Scientific and Pharmaceutical Aspects of Christensenella minuta, a Promising Next-Generation Probiotic". Fermentation. 9 (8): 767. doi: 10.3390/fermentation9080767 . ISSN 2311-5637.
- ↑ Waters JL, Goodrich JK, Ley RE. "The human gut bacterium Christensenella minuta reduces weight and adiposity gains in mice" (PDF). Department of Molecular Biology and Genetics, Department of Microbiology, Cornell University.
- ↑ Goodrich JK, Waters JL, Poole AC, Sutter JL, Koren O, Blekhman R, et al. (November 2014). "Human genetics shape the gut microbiome". Cell. 159 (4): 789–799. doi:10.1016/j.cell.2014.09.053. PMC 4255478 . PMID 25417156.
- ↑ Hamzelou J (6 November 2014). "Composition of your gut bacteria may be inherited". New Scientist. Retrieved 28 July 2016.
- 1 2 Stenman LK, Burcelin R, Lahtinen S (February 2016). "Establishing a causal link between gut microbes, body weight gain and glucose metabolism in humans - towards treatment with probiotics". Beneficial Microbes. 7 (1): 11–22. doi:10.3920/BM2015.0069. PMID 26565087.
- ↑ Alonso BL, Irigoyen von Sierakowski A, Sáez Nieto JA, Rosel AB (April 2017). "First report of human infection by Christensenella minuta, a gram-negative, strickly anaerobic rod that inhabits the human intestine". Anaerobe. 44: 124–125. doi:10.1016/j.anaerobe.2017.03.007. PMID 28286022.
- ↑ Zou Y, Xue W, Lin X, Hu T, Liu SW, Sun CH, et al. (2021-02-22). "Taxonomic Description and Genome Sequence of Christensenella intestinihominis sp. nov., a Novel Cholesterol-Lowering Bacterium Isolated From Human Gut". Frontiers in Microbiology. 12: 632361. doi: 10.3389/fmicb.2021.632361 . PMC 7937921 . PMID 33692769.
- ↑ Ndongo S, Dubourg G, Khelaifia S, Fournier PE, Raoult D (September 2016). "Christensenella timonensis, a new bacterial species isolated from the human gut". New Microbes and New Infections. 13: 32–33. doi:10.1016/j.nmni.2016.05.010. PMC 4925455 . PMID 27408737.
