Pseudomonadota
Escherichia coli
Scientific classification
Domain:	Bacteria
Phylum:	Pseudomonadota Garrity et al. 2021[1]
Classes
Acidithiobacillia[2] Alphaproteobacteria[3] Betaproteobacteria[4] Gammaproteobacteria[2] Hydrogenophilalia[4] Zetaproteobacteria[5]
Synonyms
"Proteobacteria" Stackebrandt et al. 1988[6] "Proteobacteria" Gray and Herwig 1996[7] "Proteobacteria" Garrity et al. 2005[8] "Proteobacteria" Cavalier-Smith 2002[9] Alphaproteobacteraeota Oren et al. 2015 "Alphaproteobacteriota" Whitman et al. 2018 "Caulobacterota" corrig. Garrity et al. 2021 "Neoprotei" Pelletier 2012 Rhodobacteria Cavalier-Smith 2002

Pseudomonadota (synonym Proteobacteria) is a major phylum of Gram-negative bacteria.^[10] Currently, they are considered the predominant phylum within the realm of bacteria.^[11] They are naturally found as pathogenic and free-living (non-parasitic) genera.^[11] The phylum comprises six classes Acidithiobacilia, Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Hydrogenophilia, and Zetaproteobacteria.^[11] The Pseudomonadota are widely diverse, with differences in morphology, metabolic processes, relevance to humans, and ecological influence.^[11]

Classification

American microbiologist Carl Woese established this grouping in 1987, calling it informally the "purple bacteria and their relatives".^[12] The group was later formally named the 'Proteobacteria' after the Greek god Proteus, who was known to assume many forms.^[13] In 2021 the International Committee on Systematics of Prokaryotes designated the synonym Pseudomonadota, and renamed many other prokaryotic phyla as well.^[1] 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.^[14] The phylum Pseudomonadota encompasses classes Acidithiobacilia, Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Hydrogenophilia, and Zetaproteobacteria.^[11] The phylum includes a wide variety of pathogenic genera, such as Escherichia, Salmonella, Vibrio, Yersinia, Legionella, and many others.^[15] Others are free-living (non-parasitic) and include many of the bacteria responsible for nitrogen fixation.^[16]

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.^[17] Deltaproteobacteria has been identified as a diverse taxonomic unit, leading to a proposal for its reclassification into distinct phyla: Desulfobacterota (encompassing Thermodesulfobacteria), Myxococcota, and Bdellovibrionota (comprising Oligoflexia).^[17]

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.^[18] 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.^[18] Limited outgroup data and low bootstrap values support these discoveries. Despite further investigations, consensus has not been reached regarding the monophyletic nature of Epsilonproteobacteria within Proteobacteria, prompting researchers to propose its taxonomic separation from the phylum. The proposed reclassification of the name Epsilonproteobacteria is Campylobacterota.^[18]

Taxonomy

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LSPN)^[19] and the National Center for Biotechnology Information (NCBI).^[20]

The group Pseudomonadota is defined based on ribosomal RNA (rRNA) sequencing, and are divided into several subclasses. These subclasses were regarded as such for many years, but are now treated as various classes of the phylum. These classes are monophyletic.^[21][22][23] The genus Acidithiobacillus, part of the Gammaproteobacteria until it was transferred to class Acidithiobacillia in 2013,^[2] was previously regarded as paraphyletic to the Betaproteobacteria according to multigenome alignment studies.^[24] In 2017, the Betaproteobacteria was subject to major revisions and the class Hydrogenophilalia was created to contain the order Hydrogenophilales^[4]

Pseudomonadota classes with validly published names include some prominent genera:^[25] e.g.:

• Acidithiobacillia: Acidithiobacillus, Thermithiobacillus
• Alphaproteobacteria: Brucella, Rhizobium, Agrobacterium, Caulobacter, Rickettsia, Wolbachia, etc.
• Betaproteobacteria: Bordetella, Ralstonia, Neisseria, Nitrosomonas, etc.
• Gammaproteobacteria: Escherichia, Shigella, Salmonella, Yersinia, Buchnera, Haemophilus, Vibrio, Pseudomonas, Pasteurella, etc.
• Zetaproteobacteria: Mariprofundus