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Bacillota is 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.
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. Similar to the human gut microbiome, diverse microbes colonize the plant rhizosphere, and dysbiosis in the rhizosphere, can negatively impact plant health. Dysbiosis is most commonly reported as a condition in the gastrointestinal tract or plant rhizosphere.
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.
Prevotella is a genus of Gram-negative bacteria.
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, and cirrhosis [citations needed]. 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. Alistipes, typically benign in the gut, can sometimes trigger infections like intra-abdominal abscesses and bloodstream infections, emphasizing the fine line between symbiosis and disease. This underscores the significance of comprehending their impact on human health within microbial ecosystems.
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.
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 pronouncing the dynamic character of the microbiome, and the second clearly separating the term microbiota from the term microbiome.
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.
Gabonibacter is a genus from the family of Porphyromonadaceae which have been isolated from human sources.
Brachybacterium is a genus of Gram positive, nonmotile bacteria. The cells are coccoid during the stationary phase, and irregular rods during the exponential phase. The genus name comes from Greek word brachy, meaning short, and Latin bacterium, meaning rods, referencing the short rods noted during the exponential phase.
Sediminibacillus is a genus of bacteria from the family of Bacillaceae. Sediminibacillus species are halophilic bacteria and found in salty human stools and marine sponges. Sediminibacillus species are identified from Plakortis dariae sponge of the Saint Martin's island of the Bay of Bengal, Bangladesh.
Treponema succinifaciens is an anaerobic spirochete bacterium first discovered in the intestines of swine in 1981. The helical cells of T. succinifaciens grow to 16 μm in length and often form chains of cells when cultured. T. succinifaciens is gram-negative and non spore-forming.
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.
Mordavella is a Gram-negative bacterial genus from the family of Clostridiaceae with one known species. Mordavella massiliensis has been isolated from human feces
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. PMID 21357455.
- ↑ 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. (This paper currently has an expression of concern, see doi:10.1016/j.nmni.2024.101277, PMID 38799867, Retraction Watch )
