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Pseudomonadota is a major phylum of Gram-negative bacteria. Currently, they are considered the predominant phylum within the realm of bacteria. They are naturally found as pathogenic and free-living (non-parasitic) genera. The phylum comprises six classes Acidithiobacilia, Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Hydrogenophilia, and Zetaproteobacteria. The Pseudomonadota are widely diverse, with differences in morphology, metabolic processes, relevance to humans, and ecological influence.
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 Actinomycetota are a diverse phylum of Gram-positive bacteria with high GC content. They can be terrestrial or aquatic. They are of great economic importance to humans because agriculture and forests depend on their contributions to soil systems. In soil they help to decompose the organic matter of dead organisms so the molecules can be taken up anew by plants. While this role is also played by fungi, Actinomycetota are much smaller and likely do not occupy the same ecological niche. In this role the colonies often grow extensive mycelia, like a fungus would, and the name of an important order of the phylum, Actinomycetales, reflects that they were long believed to be fungi. Some soil actinomycetota live symbiotically with the plants whose roots pervade the soil, fixing nitrogen for the plants in exchange for access to some of the plant's saccharides. Other species, such as many members of the genus Mycobacterium, are important pathogens.
Geobacter is a genus of bacteria. Geobacter species are anaerobic respiration bacterial species which have capabilities that make them useful in bioremediation. Geobacter was found to be the first organism with the ability to oxidize organic compounds and metals, including iron, radioactive metals, and petroleum compounds into environmentally benign carbon dioxide while using iron oxide or other available metals as electron acceptors. Geobacter species are also found to be able to respire upon a graphite electrode. They have been found in anaerobic conditions in soils and aquatic sediment.
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.
The Actinomycetales is an order of Actinomycetota. A member of the order is often called an actinomycete. Actinomycetales are generally gram-positive and anaerobic and have mycelia in a filamentous and branching growth pattern. Some actinomycetes can form rod- or coccoid-shaped forms, while others can form spores on aerial hyphae. Actinomycetales bacteria can be infected by bacteriophages, which are called actinophages. Actinomycetales can range from harmless bacteria to pathogens with resistance to antibiotics.
Treponema is a genus of spiral-shaped bacteria. The major treponeme species of human pathogens is Treponema pallidum, whose subspecies are responsible for diseases such as syphilis, bejel, and yaws. Treponema carateum is the cause of pinta. Treponema paraluiscuniculi is associated with syphilis in rabbits. Treponema succinifaciens has been found in the gut microbiome of traditional rural human populations.
The Spirochaetales are an order of spirochete bacteria. Some species within this order are known to causes syphilis, Lyme disease, relapsing fever, and other illnesses.
The Coriobacteriaceae is a family of Actinomycetota. The family Coriobacteriaceae has been shown to increase significantly in the ceca of mice in response to stress.
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.
Fibrobacterota is a small bacterial phylum which includes many of the major rumen bacteria, allowing for the degradation of plant-based cellulose in ruminant animals. Members of this phylum were categorized in other phyla. The genus Fibrobacter was removed from the genus Bacteroides in 1988.
Bacteroidales is an order of bacteria. Notably it includes the genera Prevotella and Bacteroides, which are commonly found in the human gut microbiota.
Nitrospirota is a phylum of bacteria. It includes multiple genera, such as Nitrospira, the largest. The first member of this phylum, Nitrospira marina, was discovered in 1985. The second member, Nitrospira moscoviensis, was discovered in 1995.
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.
The Selenomonadales are an order of bacteria within the class Negativicutes; unlike most other members of Bacillota, they are Gram-negative. The phylogeny of this order was initially determined by 16S rRNA comparisons. More recently, molecular markers in the form of conserved signature indels (CSIs) have been found specific for all Selenomonadales species. On the basis of these markers, the Selenomonadales are inclusive of two distinct families, and are no longer the sole order within the Negativicutes. Several CSIs have also been found specific for both families, Sporomusaceae and Selenomonadceae. Samples of bacterial strains within this order have been isolated from the root canals of healthy human teeth.
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.
Tumebacillus is a genus of Gram-positive, rod-shaped, spore-forming bacteria. Members of the genus can be motile or non-motile, and form white or yellow colonies on R2A agar.
The Propionibacteriales are an order of bacteria.
The Micrococcales are an order of bacteria in the phylum Actinomycetota.
Jatrophihabitans is a genus of Actinomycetota.
References
- ↑ Egert, Markus; Stingl, Ulrich; Dyhrberg Bruun, Lars; Pommerenke, Bianca; Brune, Andreas; Friedrich, Michael W. (August 2005). "Structure and Topology of Microbial Communities in the Major Gut Compartments of Melolontha melolontha Larvae (Coleoptera: Scarabaeidae)". Applied and Environmental Microbiology. 71 (8): 4556–4566. doi:10.1128/AEM.71.8.4556-4566.2005. ISSN 0099-2240. PMC 1183286 . PMID 16085849.
- ↑ Hong-Xia Fan, Shuo Sheng, Feng Zhang (2022). "New hope for Parkinson's disease treatment: Targeting gut microbiota". CNS Neuroscience & Therapeutics . 28 (11): 1675–1688. doi:10.1111/cns.13916. PMC 9532916 . PMID 35822696.
{{cite journal}}: CS1 maint: multiple names: authors list (link) - ↑ Li, Zhe; Liang, Hongfeng; Hu, Yingyu (2023). "Gut bacterial profiles in Parkinson's disease: A systematic review". CNS Neuroscience & Therapeutics. 29 (1): 140–157. doi:10.1111/cns.13990. PMC 9804059 . PMID 36284437.
{{cite journal}}: CS1 maint: multiple names: authors list (link) - ↑ Chen, Jiewen, and Xiyuan Liu, Yi Zou, Junli Gong, Zhenhuang Ge, Xiaorong Lin, Wei Zhang, Hongyan Huang, Jianli Zhao, Phei Er Saw, Yongjun Lu, Hai Hu, and Erwei Song (2024). "A high-fat diet promotes cancer progression by inducing gut microbiota–mediated leucine production and PMN-MDSC differentiation". Proceedings of the National Academy of Sciences. 121 (20). doi:10.1073/pnas.2306776121. PMC 11098111 . PMID 38709933.
{{cite journal}}: CS1 maint: multiple names: authors list (link) - ↑ Lovley, Derek R.; Phillips, Elizabeth J. P. (November 1992). "Bioremediation of uranium contamination with enzymatic uranium reduction". Environmental Science & Technology. 26 (11): 2228–2234. Bibcode:1992EnST...26.2228L. doi:10.1021/es00035a023. ISSN 0013-936X.
- ↑ J.P. Euzéby. "Desulfovibrio". List of Prokaryotic names with Standing in Nomenclature (LPSN). Retrieved 2022-09-09.
- ↑ Sayers; et al. "Desulfovibrio". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2022-09-09.
- ↑ "The LTP" . Retrieved 20 November 2023.
- ↑ "LTP_all tree in newick format" . Retrieved 20 November 2023.
- ↑ "LTP_08_2023 Release Notes" (PDF). Retrieved 20 November 2023.
- ↑ "GTDB release 08-RS214". Genome Taxonomy Database . Retrieved 10 May 2023.
- ↑ "bac120_r214.sp_label". Genome Taxonomy Database . Retrieved 10 May 2023.
- ↑ "Taxon History". Genome Taxonomy Database . Retrieved 10 May 2023.
- Madigan M; Martinko J, eds. (2005). Brock Biology of Microorganisms (11th ed.). Prentice Hall. ISBN 0-13-144329-1.
