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Pseudomonadota is a major phylum of Gram-negative bacteria. The renaming of several prokaryote phyla in 2021, including Pseudomonadota, remains controversial among microbiologists, many of whom continue to use the earlier name Proteobacteria, of long standing in the literature. The phylum Proteobacteria includes a wide variety of pathogenic genera, such as Escherichia, Salmonella, Vibrio, Yersinia, Legionella, and many others. Others are free-living (non-parasitic) and include many of the bacteria responsible for nitrogen fixation.
The phylum Bacteroidota is composed of three large classes of Gram-negative, nonsporeforming, anaerobic or aerobic, and rod-shaped bacteria that are widely distributed in the environment, including in soil, sediments, and sea water, as well as in the guts and on the skin of animals.
Acidobacteriota is a phylum of Gram-negative bacteria. Its members are physiologically diverse and ubiquitous, especially in soils, but are under-represented in culture.
16S ribosomal RNA is the RNA component of the 30S subunit of a prokaryotic ribosome. It binds to the Shine-Dalgarno sequence and provides most of the SSU structure.
Terrabacteria is a taxon containing approximately two-thirds of prokaryote species, including those in the gram positive phyla as well as the phyla "Cyanobacteria", Chloroflexota, and Deinococcota.
Bacterial phyla constitute the major lineages of the domain Bacteria. While the exact definition of a bacterial phylum is debated, a popular definition is that a bacterial phylum is a monophyletic lineage of bacteria whose 16S rRNA genes share a pairwise sequence identity of ~75% or less with those of the members of other bacterial phyla.
Saccharibacteria, formerly known as TM7, is a major bacterial lineage. It was discovered through 16S rRNA sequencing.
Bacterial taxonomy is subfield of taxonomy devoted to the classification of bacteria specimens into taxonomic ranks.
'The All-Species Living Tree' Project is a collaboration between various academic groups/institutes, such as ARB, SILVA rRNA database project, and LPSN, with the aim of assembling a database of 16S rRNA sequences of all validly published species of Bacteria and Archaea. At one stage, 23S sequences were also collected, but this has since stopped.
DPANN is a superphylum of Archaea first proposed in 2013. Many members show novel signs of horizontal gene transfer from other domains of life. They are known as nanoarchaea or ultra-small archaea due to their smaller size (nanometric) compared to other archaea.
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.
TACK is a group of archaea, its name an acronym for Thaumarchaeota, Aigarchaeota, Crenarchaeota, and Korarchaeota, the first groups discovered. They are found in different environments ranging from acidophilic thermophiles to mesophiles and psychrophiles and with different types of metabolism, predominantly anaerobic and chemosynthetic. TACK is a clade that is sister to the Asgard branch that gave rise to the eukaryotes. It has been proposed that the TACK clade be classified as Crenarchaeota and that the traditional "Crenarchaeota" (Thermoproteota) be classified as a class called "Sulfolobia", along with the other phyla with class rank or order.
Atribacterota is a phylum of bacteria, which are common in anoxic sediments rich in methane. They are distributed worldwide and in some cases abundant in anaerobic marine sediments, geothermal springs, and oil deposits. Genetic analyzes suggest a heterotrophic metabolism that gives rise to fermentation products such as acetate, ethanol, and CO2. These products in turn can support methanogens within the sediment microbial community and explain the frequent occurrence of Atribacterota in methane-rich anoxic sediments. According to phylogenetic analysis, Atribacterota appears to be related to several thermophilic phyla within Terrabacteria or may be in the base of Gracilicutes. According to research, Atribacterota shows patterns of gene expressions which consists of fermentative, acetogenic metabolism. These expressions let Atribacterota to be able to create catabolic and anabolic functions which are necessary to generate cellular reproduction, even when the energy levels are limited due to the depletion of dissolved oxygen in the areas of sea waters, fresh waters, or ground waters.
The candidate phyla radiation is a large evolutionary radiation of bacterial lineages whose members are mostly uncultivated and only known from metagenomics and single cell sequencing. They have been described as nanobacteria or ultra-small bacteria due to their reduced size (nanometric) compared to other bacteria.
The Microgenomatota or Microgenomates are a proposed supergroup of bacterial candidate phyla in the Candidate Phyla Radiation.
Zixibacteria is a bacterial phylum with candidate status, meaning it had no cultured representatives. It is a member of the FCB group
Katanobacteria is a bacterial phylum formerly known as WWE3. It has candidate status, meaning there are no cultured representatives, and is a member of the Candidate Phyla Radiation (CPR).
Berkelbacteria is a bacterial phylum with candidate status, meaning there are no cultured representatives for this group. It is part of the Candidate Phyla Radiation.
Fertabacteria is a candidate bacterial phylum of the Candidate Phyla Radiation, first proposed in 2017 after analysis of a genome from the mouth of a bottlenose dolphin. Members of this phylum are predicted to have been widely under-detected in 16S rRNA gene-based surveys of community composition due to mismatches between commonly used primers and the corresponding primer site. Fertabacteria have been retroactively detected in a variety of environments.
Modulibacteria(Moduliflexota) is a bacterial phylum formerly known as KS3B3 or GN06. It is a candidate phylum, meaning there are no cultured representatives of this group. Members of the Modulibacteria phylum are known to cause fatal filament overgrowth (bulking) in high-rate industrial anaerobic wastewater treatment bioreactors.
References
- ↑ Li, Lina; Kato, Chiaki; Horikoshi, Koki (1999-05-01). "Bacterial diversity in deep-sea sediments from different depths". Biodiversity & Conservation. 8 (5): 659–677. doi:10.1023/A:1008848203739. ISSN 1572-9710. S2CID 25820840.
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- 1 2 Sieber, Christian M. K.; Paul, Blair G.; Castelle, Cindy J.; Hu, Ping; Tringe, Susannah G.; Valentine, David L.; Andersen, Gary L.; Banfield, Jillian F. (2019-11-12). "Unusual Metabolism and Hypervariation in the Genome of a Gracilibacterium (BD1-5) from an Oil-Degrading Community". mBio. 10 (6). doi:10.1128/mbio.02128-19. ISSN 2150-7511. PMC 6851277 . PMID 31719174.
- ↑ Rinke, Christian; Schwientek, Patrick; Sczyrba, Alexander; Ivanova, Natalia N.; Anderson, Iain J.; Cheng, Jan-Fang; Darling, Aaron; Malfatti, Stephanie; Swan, Brandon K.; Gies, Esther A.; Dodsworth, Jeremy A. (July 2013). "Insights into the phylogeny and coding potential of microbial dark matter". Nature. 499 (7459): 431–437. Bibcode:2013Natur.499..431R. doi: 10.1038/nature12352 . hdl: 10453/27467 . ISSN 1476-4687. PMID 23851394.
- ↑ Wrighton, K. C.; Thomas, B. C.; Sharon, I.; Miller, C. S.; Castelle, C. J.; VerBerkmoes, N. C.; Wilkins, M. J.; Hettich, R. L.; Lipton, M. S.; Williams, K. H.; Long, P. E. (2012-09-27). "Fermentation, Hydrogen, and Sulfur Metabolism in Multiple Uncultivated Bacterial Phyla". Science. 337 (6102): 1661–1665. Bibcode:2012Sci...337.1661W. doi:10.1126/science.1224041. ISSN 0036-8075. PMID 23019650. S2CID 10362580.
- ↑ Hanke, Anna; Hamann, Emmo; Sharma, Ritin; Geelhoed, Jeanine S.; Hargesheimer, Theresa; Kraft, Beate; Meyer, Volker; Lenk, Sabine; Osmers, Harald; Wu, Rong; Makinwa, Kofi (2014-05-16). "Recoding of the stop codon UGA to glycine by a BD1-5/SN-2 bacterium and niche partitioning between Alpha- and Gammaproteobacteria in a tidal sediment microbial community naturally selected in a laboratory chemostat". Frontiers in Microbiology. 5: 231. doi: 10.3389/fmicb.2014.00231 . ISSN 1664-302X. PMC 4032931 . PMID 24904545.