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Bacterial phyla
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.[2]
It has been estimated that ~1,300 bacterial phyla exist.[2] As of May 2020, 41 bacterial phyla are formally accepted by the LPSN,[3] 89 bacterial phyla are recognized on the Silva database, dozens more have been proposed,[4][5] and hundreds likely remain to be discovered.[2] As of 2017, approximately 72% of widely recognized bacterial phyla were candidate phyla[6] (i.e. have no cultured representatives).
The rank of phylum has been included in the rules of the International Code of Nomenclature of Prokaryotes, using the ending –ota for phylum names that must be based on the name of a genus as its nomenclatural type.[7][8]
- ^ Hug, Laura A.; Baker, Brett J.; Anantharaman, Karthik; Brown, Christopher T.; Probst, Alexander J.; Castelle, Cindy J.; Butterfield, Cristina N.; Hernsdorf, Alex W.; Amano, Yuki; Ise, Kotaro; Suzuki, Yohey (11 April 2016). "A new view of the tree of life". Nature Microbiology. 1 (5): 16048. doi:10.1038/nmicrobiol.2016.48. ISSN 2058-5276. PMID 27572647.
- ^ a b c Yarza, Pablo; Yilmaz, Pelin; Pruesse, Elmar; Glöckner, Frank Oliver; Ludwig, Wolfgang; Schleifer, Karl-Heinz; Whitman, William B.; Euzéby, Jean; Amann, Rudolf; Rosselló-Móra, Ramon (September 2014). "Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences". Nature Reviews Microbiology. 12 (9): 635–645. doi:10.1038/nrmicro3330. ISSN 1740-1534. PMID 25118885. S2CID 21895693.
- ^ Bacterial phyla in LPSN; Parte, Aidan C.; Sardà Carbasse, Joaquim; Meier-Kolthoff, Jan P.; Reimer, Lorenz C.; Göker, Markus (1 November 2020). "List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ". International Journal of Systematic and Evolutionary Microbiology. 70 (11): 5607–5612. doi:10.1099/ijsem.0.004332.
- ^ Anantharaman, Karthik; Brown, Christopher T.; Hug, Laura A.; Sharon, Itai; Castelle, Cindy J.; Probst, Alexander J.; Thomas, Brian C.; Singh, Andrea; Wilkins, Michael J.; Karaoz, Ulas; Brodie, Eoin L. (24 October 2016). "Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system". Nature Communications. 7 (1): 13219. Bibcode:2016NatCo...713219A. doi:10.1038/ncomms13219. ISSN 2041-1723. PMC 5079060. PMID 27774985.
- ^ Cite error: The named reference
:12was invoked but never defined (see the help page). - ^ Dudek, Natasha K.; Sun, Christine L.; Burstein, David; Kantor, Rose S.; Aliaga Goltsman, Daniela S.; Bik, Elisabeth M.; Thomas, Brian C.; Banfield, Jillian F.; Relman, David A. (18 December 2017). "Novel Microbial Diversity and Functional Potential in the Marine Mammal Oral Microbiome". Current Biology. 27 (24): 3752–3762.e6. Bibcode:2017CBio...27E3752D. doi:10.1016/j.cub.2017.10.040. ISSN 1879-0445. PMID 29153320.
- ^ Oren, Aharon; Arahal, David R.; Rosselló-Móra, Ramon; Sutcliffe, Iain C.; Moore, Edward R. B. (23 June 2021). "Emendation of Rules 5b, 8, 15 and 22 of the International Code of Nomenclature of Prokaryotes to include the rank of phylum". International Journal of Systematic and Evolutionary Microbiology. 71 (6). doi:10.1099/ijsem.0.004851. PMID 34161220. S2CID 235625014.
- ^ Oren, Aharon; Garrity, George M. (20 October 2021). "Valid publication of the names of forty-two phyla of prokaryotes". International Journal of Systematic and Evolutionary Microbiology. 71 (10). doi:10.1099/ijsem.0.005056. PMID 34694987. S2CID 239887308.
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