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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.
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.
Atopobium is a genus of Actinomycetota, in the family Coriobacteriaceae. Atopobium species are anaerobic, Gram-positive rod-shaped or elliptical bacteria found as single elements or in pairs or short chains.
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.
The Peptostreptococcaceae are a family of Gram-positive bacteria in the class Clostridia.
Germ-free organisms are multi-cellular organisms that have no microorganisms living in or on them. Such organisms are raised using various methods to control their exposure to viral, bacterial or parasitic agents. When known microbiota are introduced to a germ-free organism, it usually is referred to as a gnotobiotic organism, however technically speaking, germ-free organisms are also gnotobiotic because the status of their microbial community is known. Due to lacking a microbiome, many germ-free organisms exhibit health deficits such as defects in the immune system and difficulties with energy acquisition. Typically germ-free organisms are used in the study of a microbiome where careful control of outside contaminants is required.
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.
Porphyromonadaceae 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 Porphyromonas genus, as compared to the larger taxonomic order Bacteroidales, are classified in this family.
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.
Free fatty acid receptor 2 (FFAR2), also termed G-protein coupled receptor 43 (GPR43), is a rhodopsin-like G-protein coupled receptor. It is coded by the FFAR2 gene. In humans, the FFAR2 gene is located on the long arm of chromosome 19 at position 13.12. Like other GPCRs, FFAR2s reside on the surface membrane of cells and when bond to one of their activating ligands regulate the function of their parent cells. FFAR2 is a member of a small family of structurally and functionally related GPRs termed free fatty acid receptors (FFARs). This family includes three other receptors which, like FFAR2, are activated by certain fatty acids: FFAR1, FFAR3 (GPR41), and FFAR4 (GPR120). FFAR2 and FFAR3 are activated by short-chain fatty acids whereas FFAR1 and FFAR4 are activated by long-chain fatty acids.
Long-term close-knit interactions between symbiotic microbes and their host can alter host immune system responses to other microorganisms, including pathogens, and are required to maintain proper homeostasis. The immune system is a host defense system consisting of anatomical physical barriers as well as physiological and cellular responses, which protect the host against harmful microorganisms while limiting host responses to harmless symbionts. Humans are home to 1013 to 1014 bacteria, roughly equivalent to the number of human cells, and while these bacteria can be pathogenic to their host most of them are mutually beneficial to both the host and bacteria.
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.
The Erysipelotrichia are a class of bacteria of the phylum Bacillota. Species of this class are known to be common in the gut microbiome, as they have been isolated from swine manure and increase in composition of the mouse gut microbiome for mice switched to diets high in fat.
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The gut–brain axis is the two-way biochemical signaling that takes place between the gastrointestinal tract and the central nervous system (CNS). The "microbiota–gut–brain axis" includes the role of gut microbiota in the biochemical signaling events that take place between the GI tract and the CNS. 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.
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Phocaeicola vulgatus,, is a mutualistic anaerobic Gram negative rod bacteria commonly found in the human gut microbiome and isolated from feces. P. vulgatus has medical relevance and has been notable in scientific research due to its production of fatty acids, potential use as a probiotic, and associations with protecting against and worsening some inflammatory diseases. Due to the difficulties in culturing anaerobic bacteria, P. vulgatus is still highly uncharacterised so efforts are being made to make use of multi-omic approaches to investigate the human gut microbiome more thoroughly in hopes to fully understand the role of this species in the development of and protection against diseases, as well as its potential uses in medicine and research. Generally, P. vulgatus is considered as a beneficial bacteria that contributes to digestion and a balanced microbiome, but it has been known to cause opportunistic infections and induce or worsen inflammatory responses. Due to its abundance in the microbiome, some researchers are investigating these species in hopes that it will be a suitable model organism for gut microbiome research, like Bacteroides thetaiotaomicron.
References
- 1 2 Krieg, Noel R. (14 September 2015). "Rikenellaceae fam. nov". Bergey's Manual of Systematics of Archaea and Bacteria : 1–2. doi:10.1002/9781118960608.fbm00062. ISBN 9781118960608.
- 1 2 Parte, Aidan C.; Carbasse, Joaquim Sardà; Meier-Kolthoff, Jan P.; Reimer, Lorenz C.; Göker, Markus (23 July 2020). "Family Rikenellaceae". List of Prokaryotic names with Standing in Nomenclature . Retrieved 8 April 2023.
- ↑ Graf, Joerg (2014). "The Family Rikenellaceae". In Rosenberg, Eugene; DeLong, Edward F.; Lory, Stephen; Stackebrandt, Erko; Thompson, Fabiano (eds.). The Prokaryotes (4th ed.). Springer Berlin. pp. 857–859. doi:10.1007/978-3-642-38954-2_134. ISBN 978-3-642-38953-5.
- ↑ Cani, Patrice D. (24 April 2013). "Gut Microbiota and Obesity: Lessons from the Microbiome". Briefings in Functional Genomics . 12 (4): 381–387. doi: 10.1093/bfgp/elt014 . PMID 23616309 – via Oxford Academic.
- ↑ Peters, Brandilyn A.; Shapiro, Jean A.; Church, Timothy R.; Miller, George; Trinh-Shevrin, Chau; Yuen, Elizabeth; Friedlander, Charles; Hayes, Richard B.; Ahn, Jiyoung (2018-06-27). "A taxonomic signature of obesity in a large study of American adults". Scientific Reports . 8 (1): 9749. doi:10.1038/s41598-018-28126-1. ISSN 2045-2322. PMC 6021409 . PMID 29950689.
- ↑ Wang, Hui; Wang, Gangduo; Banerjee, Nivedita; Liang, Yuejin; Du, Xiaotang; Boor, Paul J.; Hoffman, Kristi L.; Khan, M. Firoze (12 April 2021). "Aberrant Gut Microbiome Contributes to Intestinal Oxidative Stress, Barrier Dysfunction, Inflammation and Systemic Autoimmune Responses in MRL/lpr Mice". Frontiers in Immunology . 12: 651191. doi: 10.3389/fimmu.2021.651191 . ISSN 1664-3224. PMC 8071869 . PMID 33912174.
- ↑ Bello-Medina, Paola C.; Corona-Cervantes, Karina; Zavala Torres, Norma Gabriela; González, Antonio; Pérez-Morales, Marcel; González-Franco, Diego A.; Gómez, Astrid; García-Mena, Jaime; Díaz-Cintra, Sofía; Pacheco-López, Gustavo (26 July 2022). "Chronic-Antibiotics Induced Gut Microbiota Dysbiosis Rescues Memory Impairment and Reduces ß-Amyloid Aggregation in a Preclinical Alzheimer's Disease Model". International Journal of Molecular Sciences . 23 (15): 8209. doi: 10.3390/ijms23158209 . ISSN 1422-0067. PMC 9331718 . PMID 35897785.
- ↑ Hoang, Tung; Kim, Min Jung; Park, Ji Won; Jeong, Seung-Yong; Lee, Jeeyoo; Shin, Aesun (14 June 2022). "Nutrition-Wide Association Study of Microbiome Diversity and Composition in Colorectal Cancer Patients". BMC Cancer . 22 (1): 656. doi: 10.1186/s12885-022-09735-6 . ISSN 1471-2407. PMC 9199192 . PMID 35701733.
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