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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 gastrointestinal tract, skin, mammary glands, seminal fluid, uterus, ovarian follicles, lung, saliva, oral mucosa, conjunctiva, and the biliary 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.
Inflammatory bowel disease (IBD) is a group of inflammatory conditions of the colon and small intestine, with Crohn's disease and ulcerative colitis (UC) being the principal types. Crohn's disease affects the small intestine and large intestine, as well as the mouth, esophagus, stomach and the anus, whereas UC primarily affects the colon and the rectum.
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.
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.
The Peptostreptococcaceae are a family of Gram-positive bacteria in the class Clostridia.
Prevotellaceae is a family of bacteria from the order Bacteroidales. As a member of the phylum Bacteroidota, its species are gram negative – meaning their outer cell wall contains lipopolysaccharides. Since they are anaerobes, members of Prevotellaceae can live in areas where there is little to no oxygen – such as the guts of mammals.
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.
Campylobacter concisus is a Gram-negative, highly fastidious, mesophilic bacterium that grows under both anaerobic and microaerobic conditions with the presence of hydrogen significantly aiding growth. Motile, with either unipolar or bipolar flagella, the organisms have a characteristic spiral/corkscrew appearance and are oxidase-positive. Although the human oral cavity is the natural colonization site of the bacterium, C. concisus may also colonize the intestinal tract of some individuals. In particular, several studies have reported higher intestinal prevalence of C. concisus in patients with IBD compared to healthy controls, which has led to current speculation of the bacterium's implication in the induction of Crohn's disease.
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.
The gut–brain axis is the two-way biochemical signaling that takes place between the gastrointestinal tract and the central nervous system (CNS). The term "microbiota–gut–brain axis" highlights the role of gut microbiota in these biochemical signaling. Broadly defined, the gut–brain axis includes the central nervous system, neuroendocrine system, neuroimmune systems, the hypothalamic–pituitary–adrenal axis, sympathetic and parasympathetic arms of the autonomic nervous system, the enteric nervous system, vagus nerve, and the gut microbiota.
Clostridium leptum is a bacterium species in the genus Clostridium.
Microbiota-accessible carbohydrates (MACs) are carbohydrates that are resistant to digestion by a host's metabolism, and are made available for gut microbes, as prebiotics, to ferment or metabolize into beneficial compounds, such as short chain fatty acids. The term, ‘‘microbiota-accessible carbohydrate’’ contributes to a conceptual framework for investigating and discussing the amount of metabolic activity that a specific food or carbohydrate can contribute to a host's microbiota.
Interspecies hydrogen transfer (IHT) is a form of interspecies electron transfer. It is a syntrophic process by which H2 is transferred from one organism to another, particularly in the rumen and other anaerobic environments.
Christensenella is a genus of non-spore-forming, anaerobic, and nonmotile bacteria from the family Christensenellaceae. They are also part of the order Clostridiales, the class Clostridia and the phylum Firmicutes. Phylogenetic analyzes of 16S rRNA gene sequences are used to describe this family. Due to the recent discovery of the Christensenellaceae family, it was not given importance until a few years ago. This is why very little is known about its ecology and how it may be associated with host factors and other microbiota. However, recent studies establish that members of this family, with exceptions, may be associated with a healthy phenotype for humans. The species C. minuta has been published and validated, and C. timonensis and C. massiliensis have been proposed as novel species of the genus Christensenella, all isolated from human feces.
Parabacteroides is a Gram-negative, anaerobic, non-spore-forming genus from the family Tannerellaceae.
The human milk microbiota, also known as human milk probiotics (HMP), encompasses the microbiota–the community of microorganisms–present within the human mammary glands and breast milk. Contrary to the traditional belief that human breast milk is sterile, advancements in both microbial culture and culture-independent methods have confirmed that human milk harbors diverse communities of bacteria. These communities are distinct in composition from other microbial populations found within the human body which constitute the human microbiome.
Bacteroides thetaiotaomicron is a Gram-negative, obligate anaerobic bacterium and a prominent member of the human gut microbiota, particularly within the large intestine. B. thetaiotaomicron belongs to the Bacteroides genus – a group that is known for its role in the complex microbial community of the gut microbiota. Its proteome, consisting of 4,779 members, includes a system for obtaining and breaking down dietary polysaccharides that would otherwise be difficult to digest for the human body.
References
- ↑ taxonomy. "Taxonomy browser (Ruminococcus)". www.ncbi.nlm.nih.gov. Retrieved 2016-04-05.
- ↑ Liu C, Finegold SM, Song Y, Lawson PA (August 2008). "Reclassification of Clostridium coccoides, Ruminococcus hansenii, Ruminococcus hydrogenotrophicus, Ruminococcus luti, Ruminococcus productus and Ruminococcus schinkii as Blautia coccoides gen. nov., comb. nov., Blautia hansenii comb. nov., Blautia hydrogenotrophica comb. nov., Blautia luti comb. nov., Blautia producta comb. nov., Blautia schinkii comb. nov. and description of Blautia wexlerae sp. nov., isolated from human faeces". International Journal of Systematic and Evolutionary Microbiology. 58 (Pt 8). Society for General Microbiology: 1896–902. doi: 10.1099/ijs.0.65208-0 . PMID 18676476.
- ↑ Iannotti EL, Kafkewitz D, Wolin MJ, Bryant MP (June 1973). "Glucose fermentation products in Ruminococcus albus grown in continuous culture with Vibrio succinogenes: changes caused by interspecies transfer of H 2". Journal of Bacteriology. 114 (3): 1231–40. doi:10.1128/JB.114.3.1231-1240.1973. PMC 285387 . PMID 4351387.
- ↑ Rajilić-Stojanović M, de Vos WM (September 2014). "The first 1000 cultured species of the human gastrointestinal microbiota". FEMS Microbiology Reviews. 38 (5): 996–1047. doi:10.1111/1574-6976.12075. PMC 4262072 . PMID 24861948.
- ↑ Ze, Xiaolei; Duncan, Sylvia H.; Louis, Petra; Flint, Harry J. (2012). "Ruminococcus bromii is a keystone species for the degradation of resistant starch in the human colon". The ISME Journal. 6 (8): 1535–1543. Bibcode:2012ISMEJ...6.1535Z. doi: 10.1038/ismej.2012.4 . PMC 3400402 . PMID 22343308.
- ↑ Nagao-Kitamoto H, Kamada N (February 2017). "Host-microbial Cross-talk in Inflammatory Bowel Disease". Immune Network. 17 (1): 1–12. doi:10.4110/in.2017.17.1.1. PMC 5334117 . PMID 28261015.
- ↑ Hill-Burns, EM; Debelius, JW; Morton, JT; Wissemann, WT; Lewis, MR; Wallen, ZD; Peddada, SD; Factor, SA; Molho, E; Zabetian, CP; Knight, R; Payami, H (May 2017). "Parkinson's disease and Parkinson's disease medications have distinct signatures of the gut microbiome". Movement Disorders. 32 (5): 739–749. doi:10.1002/mds.26942. PMC 5469442 . PMID 28195358.
- ↑ Brenner, D; Hiergeist, A; Adis, C; Mayer, B; Gessner, A; Ludolph, AC; Weishaupt, JH (Jan 2018). "The fecal microbiome of ALS patients". Neurobiol Aging. 61: 132–137. doi:10.1016/j.neurobiolaging.2017.09.023. PMID 29065369. S2CID 296116.
- ↑ Rowin, J; Xia, Y; Jung, B; Sun, J (Sep 2017). "Gut inflammation and dysbiosis in human motor neuron disease". Physiol Rep. 5 (18): e13443. doi:10.14814/phy2.13443. PMC 5617930 . PMID 28947596.
- ↑ Henke, Matthew T.; Kenny, Douglas J.; Cassilly, Chelsi D.; Vlamakis, Hera; Xavier, Ramnik J.; Clardy, Jon (2019-06-25). "Ruminococcus gnavus, a member of the human gut microbiome associated with Crohn's disease, produces an inflammatory polysaccharide". Proceedings of the National Academy of Sciences. 116 (26): 12672–12677. Bibcode:2019PNAS..11612672H. doi: 10.1073/pnas.1904099116 . ISSN 0027-8424. PMC 6601261 . PMID 31182571.
- ↑ https://www.ncbi.nlm.nih.gov/datasets/taxonomy/1263/