[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.
[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).
Analysis of phylogenetic tree topology and genetic markers revealed the direct divergence of Epsilonproteobacteria from the Pseudomonadota phylum.
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.
[19] The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LSPN)[20] and the National Center for Biotechnology Information (NCBI).
[22][23][24] 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.
[42] Transformation, a process in which genetic material passes from one bacterium to another,[43] has been reported in at least 30 species of Pseudomonadota distributed in the classes alpha, beta, and gamma.
[45] Natural genetic transformation is a sexual process involving DNA transfer from one bacterial cell to another through the intervening medium and the integration of the donor sequence into the recipient genome.
These include: Studies have suggested Pseudomonadota as a relevant signature of disease in the human gastrointestinal (GI) tract, by operating as a marker for microbiota instability.
[10] Additionally, the gut microbiome facilitates host interactions with its surrounding environment through regulation of nutrient absorption and bacterial intake.
In 16s rRNA and metagenome sequencing studies, Proteobacteria have been identified as bacteria that prompts endotoxemia (an inflammatory gut response) and metabolic disorders in human GI tracts.
[52] Changes in the oral microbiome are due to endogenous and exogenous factors like host lifestyle, genotype, environment, immune system, and socioeconomic status.
[50] Healthier root systems can lead to better nutrient uptake, improved water retention, increased resistance to diseases and pests, and ultimately higher crop yields per acre.
[53] Increased agricultural output can spark economic growth, contribute to food security, and lead to job creation in rural areas.
[54] As briefly mentioned in previous sections, members of Pseudomonadota have vast metabolic abilities that allow them to utilize and produce a variety of compounds.
[55] Any iron and sulfur oxidizing species has the potential to uncover metals and low-grade ores that conventional mining techniques were unable to extract.
[56] Additionally, photolithotrophs within the phylum are able to perform photosynthesis using sulfide or elemental sulfur as electron donors, which enables them to participate in carbon fixation and oxygen production even in anaerobic conditions.
[56] Because this phylum are able to form a symbiotic relationship with plant roots, incorporating Pseudomonadota into agricultural practices aligns with principles of sustainable farming.
[57][50] These bacteria contribute to soil health and fertility, promote natural pest management, and enhance the resilience of crops to environmental stressors.