Editing Pseudomonadota (section)

== Classification ==
American microbiologist [[Carl Woese]] established this grouping in 1987, calling it informally the "purple bacteria and their relatives".<ref name="woese87">{{cite journal | vauthors = Woese CR | title = Bacterial evolution | journal = Microbiological Reviews | volume = 51 | issue = 2 | pages = 221–271 | date = June 1987 | pmid = 2439888 | pmc = 373105 | doi = 10.1128/MMBR.51.2.221-271.1987}}</ref> The group was later formally named the 'Proteobacteria' after the Greek god Proteus, who was known to assume many forms.<ref>{{cite journal | vauthors = Moon CD, Young W, Maclean PH, Cookson AL, Bermingham EN | title = Metagenomic insights into the roles of Proteobacteria in the gastrointestinal microbiomes of healthy dogs and cats | journal = MicrobiologyOpen | volume = 7 | issue = 5 | pages = e00677 | date = October 2018 | pmid = 29911322 | pmc = 6182564 | doi = 10.1002/mbo3.677}}</ref> In 2021 the [[International Committee on Systematics of Prokaryotes]] designated the synonym Pseudomonadota, and renamed many other prokaryotic phyla as well.<ref name="Phynally" /> This 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.<ref>{{cite web | vauthors = Robitzski D | date = 4 January 2022 | work = The Scientist | url=https://www.the-scientist.com/news-opinion/newly-renamed-prokaryote-phyla-cause-uproar-69578 | title=Newly Renamed Prokaryote Phyla Cause Uproar}}</ref> The phylum Pseudomonadota encompasses classes ''Acidithiobacillia, Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Hydrogenophilia'', and ''Zetaproteobacteria.''<ref name = "Kersters_2006" /> The phylum includes a wide variety of [[pathogen]]ic genera, such as ''[[Escherichia]]'', ''[[Salmonella]]'', ''[[Vibrio]]'', ''[[Yersinia]]'', ''[[Legionella]]'', and many others.<ref name="Slonczewski">{{cite book | vauthors = Slonczewski JL, Foster JW, Foster E | title = Microbiology: An Evolving Science | edition = 5th | publisher = WW Norton & Company | date = 2020}}</ref> Others are free-living (non-[[Parasitism|parasitic]]) and include many of the [[bacteria]] responsible for [[nitrogen fixation]].<ref>{{Cite journal |last1=Sah |first1=Stuti |last2=Krishnani |first2=Shweena |last3=Singh |first3=Rajni |date=December 2021 |title=Pseudomonas mediated nutritional and growth promotional activities for sustainable food security |journal=Current Research in Microbial Sciences |language=en |volume=2 |pages=100084 |doi=10.1016/j.crmicr.2021.100084 |pmc=8645841 |pmid=34917993}}</ref>

Previously, the Pseudomonadota phylum included two additional classes, namely ''Deltaproteobacteria'' and ''[[Oligoflexia]]''. However, further investigation into the phylogeny of these taxa through genomic marker analysis demonstrated their separation from the Pseudomonadota phylum.<ref name="Waite_2020">{{cite journal | vauthors = Waite DW, Chuvochina M, Pelikan C, Parks DH, Yilmaz P, Wagner M, Loy A, Naganuma T, Nakai R, Whitman WB, Hahn MW, Kuever J, Hugenholtz P | title = Proposal to reclassify the proteobacterial classes ''Deltaproteobacteria'' and ''Oligoflexia'', and the phylum ''Thermodesulfobacteria'' into four phyla reflecting major functional capabilities | journal = International Journal of Systematic and Evolutionary Microbiology | volume = 70 | issue = 11 | pages = 5972–6016 | date = November 2020 | pmid = 33151140 | doi = 10.1099/ijsem.0.004213 | doi-access = free}}</ref> ''Deltaproteobacteria'' has been identified as a diverse [[Taxonomy|taxonomic]] unit, leading to a proposal for its reclassification into distinct phyla: ''[[Desulfobacterota]]'' (encompassing ''[[Thermodesulfobacteriota|Thermodesulfobacteria]]''), ''[[Myxococcota]]'', and ''[[Bdellovibrionota]]'' (comprising ''Oligoflexia'').<ref name="Waite_2020" />

The class ''[[Epsilonproteobacteria]]'' was additionally identified within the Pseudomonadota phylum. This class is characterized by its significance as [[chemolithotrophic]] primary producers and its metabolic prowess in deep-sea [[hydrothermal vent]] ecosystems.<ref name="Waite_2017">{{cite journal | vauthors = Waite DW, Vanwonterghem I, Rinke C, Parks DH, Zhang Y, Takai K, Sievert SM, Simon J, Campbell BJ, Hanson TE, Woyke T, Klotz MG, Hugenholtz P | title = Comparative Genomic Analysis of the Class ''Epsilonproteobacteria'' and Proposed Reclassification to Epsilonbacteraeota (phyl. nov.) | journal = Frontiers in Microbiology | volume = 8 | pages = 682 | date = 2017 | pmid = 28484436 | pmc = 5401914 | doi = 10.3389/fmicb.2017.00682 | doi-access = free}}</ref> Noteworthy pathogenic genera within this class include ''[[Campylobacter]], [[Helicobacter]], and [[Arcobacter]]''. Analysis of phylogenetic tree topology and genetic markers revealed the direct divergence of ''Epsilonproteobacteria'' from the Pseudomonadota phylum.<ref name="Waite_2017" /> Limited [[Outgroup (cladistics)|outgroup]] data and low bootstrap values support these discoveries. Despite further investigations, consensus has not been reached regarding the [[Monophyly|monophyletic]] nature of ''Epsilonproteobacteria'' within Proteobacteria, prompting researchers to propose its taxonomic separation from the phylum. The proposed reclassification of the name ''Epsilonproteobacteria'' is ''Epsilonbacteraeota'',<ref name="Waite_2017" /> later revised to ''[[Campylobacterota]]'' in 2018.<ref>{{cite journal | vauthors = Oren A, Garrity GM | title = Valid publication of the names of forty-two phyla of prokaryotes | journal = Int J Syst Evol Microbiol | year = 2021 | volume = 71 | issue = 10 | pages = 5056 | doi = 10.1099/ijsem.0.005056 | pmid = 34694987 | s2cid = 239887308 | doi-access = free }}</ref>