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== Classification ==
== Classification ==
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 Pseudomonadota encompasses classes ''Acidithiobacilia, Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Hydrogenophilia'', and ''Zetaproteobacteria.''<ref name=":5">{{Citation |last=Kersters |first=Karel |title=Introduction to the Proteobacteria |date=2006 |work=The Prokaryotes: Volume 5: Proteobacteria: Alpha and Beta Subclasses |pages=3–37 |editor-last=Dworkin |editor-first=Martin |url=https://doi.org/10.1007/0-387-30745-1_1 |access-date=2024-04-07 |place=New York, NY |publisher=Springer |language=en |doi=10.1007/0-387-30745-1_1 |isbn=978-0-387-30745-9 |last2=De Vos |first2=Paul |last3=Gillis |first3=Monique |last4=Swings |first4=Jean |last5=Vandamme |first5=Peter |last6=Stackebrandt |first6=Erko |editor2-last=Falkow |editor2-first=Stanley |editor3-last=Rosenberg |editor3-first=Eugene |editor4-last=Schleifer |editor4-first=Karl-Heinz}}</ref> The phylum includes a wide variety of [[Pathogen|pathogenic]] genera, such as ''[[Escherichia]]'', ''[[Salmonella]]'', ''[[Vibrio]]'', ''[[Yersinia]]'', ''[[Legionella]]'', and many others. Others are free-living (non-[[Parasitism|parasitic]]) and include many of the [[bacteria]] responsible for [[nitrogen fixation]].
American microbiologist [[Carl Woese]] established this grouping in 1987, informally naming it the "purple bacteria and their relatives". The group was later formally named the 'Proteobacteria' after the Greek god Proteus, who was known to assume many forms.<ref>{{Cite journal |last=Moon |first=Christina D. |last2=Young |first2=Wayne |last3=Maclean |first3=Paul H. |last4=Cookson |first4=Adrian L. |last5=Bermingham |first5=Emma N. |date=2018-10 |title=Metagenomic insights into the roles of Proteobacteria in the gastrointestinal microbiomes of healthy dogs and cats |url=https://onlinelibrary.wiley.com/doi/10.1002/mbo3.677 |journal=MicrobiologyOpen |language=en |volume=7 |issue=5 |doi=10.1002/mbo3.677 |issn=2045-8827 |pmc=PMC6182564 |pmid=29911322}}</ref> In 2021 the [[International Committee on Systematics of Prokaryotes]] designated the synonym Pseudomonadota, and renamed many other prokaryotic phyla as well. This renaming of several phyla remains controversial among microbiologists. Many continue to use the earlier name Proteobacteria, of long standing in the literature. The phylum Pseudomonadota encompasses classes ''Acidithiobacilia, Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Hydrogenophilia'', and ''Zetaproteobacteria.''<ref name=":5">{{Citation |last=Kersters |first=Karel |title=Introduction to the Proteobacteria |date=2006 |work=The Prokaryotes: Volume 5: Proteobacteria: Alpha and Beta Subclasses |pages=3–37 |editor-last=Dworkin |editor-first=Martin |url=https://doi.org/10.1007/0-387-30745-1_1 |access-date=2024-04-07 |place=New York, NY |publisher=Springer |language=en |doi=10.1007/0-387-30745-1_1 |isbn=978-0-387-30745-9 |last2=De Vos |first2=Paul |last3=Gillis |first3=Monique |last4=Swings |first4=Jean |last5=Vandamme |first5=Peter |last6=Stackebrandt |first6=Erko |editor2-last=Falkow |editor2-first=Stanley |editor3-last=Rosenberg |editor3-first=Eugene |editor4-last=Schleifer |editor4-first=Karl-Heinz}}</ref> The phylum includes a wide variety of [[Pathogen|pathogenic]] genera, such as ''[[Escherichia]]'', ''[[Salmonella]]'', ''[[Vibrio]]'', ''[[Yersinia]]'', ''[[Legionella]]'', and many others. Others are free-living (non-[[Parasitism|parasitic]]) and include many of the [[bacteria]] responsible for [[nitrogen fixation]].


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=":0">{{Cite journal |last=Waite |first=David W |last2=Chuvochina |first2=Maria |last3=Pelikan |first3=Claus |last4=Parks |first4=Donovan H |last5=Yilmaz |first5=Pelin |last6=Wagner |first6=Michael |last7=Loy |first7=Alexander |last8=Naganuma |first8=Takeshi |last9=Nakai |first9=Ryosuke |last10=Whitman |first10=William B |last11=Hahn |first11=Martin W |last12=Kuever |first12=Jan |last13=Hugenholtz |first13=Philip |date=2020 |title=Proposal to reclassify the proteobacterial classes Deltaproteobacteria and Oligoflexia, and the phylum Thermodesulfobacteria into four phyla reflecting major functional capabilities |url=https://www.microbiologyresearch.org/content/journal/ijsem/10.1099/ijsem.0.004213 |journal=International Journal of Systematic and Evolutionary Microbiology |volume=70 |issue=11 |pages=5972–6016 |doi=10.1099/ijsem.0.004213 |issn=1466-5034}}</ref> 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).<ref name=":0" /> The proposed reclassification of the name ''Epsilonprotobacteria'' is ''Campylobacterota''.<ref name=":0" />
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=":0">{{Cite journal |last=Waite |first=David W |last2=Chuvochina |first2=Maria |last3=Pelikan |first3=Claus |last4=Parks |first4=Donovan H |last5=Yilmaz |first5=Pelin |last6=Wagner |first6=Michael |last7=Loy |first7=Alexander |last8=Naganuma |first8=Takeshi |last9=Nakai |first9=Ryosuke |last10=Whitman |first10=William B |last11=Hahn |first11=Martin W |last12=Kuever |first12=Jan |last13=Hugenholtz |first13=Philip |date=2020 |title=Proposal to reclassify the proteobacterial classes Deltaproteobacteria and Oligoflexia, and the phylum Thermodesulfobacteria into four phyla reflecting major functional capabilities |url=https://www.microbiologyresearch.org/content/journal/ijsem/10.1099/ijsem.0.004213 |journal=International Journal of Systematic and Evolutionary Microbiology |volume=70 |issue=11 |pages=5972–6016 |doi=10.1099/ijsem.0.004213 |issn=1466-5034}}</ref> 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).<ref name=":0" /> The proposed reclassification of the name ''Epsilonprotobacteria'' is ''Campylobacterota''.<ref name=":0" />

Revision as of 03:58, 17 April 2024

Lead

Pseudomonadota (synonym Proteobacteria) is a major phylum of Gram-negative bacteria.[1] At present, they are considered the predominant phylum within the realm of bacteria.[2] They are naturally found as pathogenic and free-living (non-parasitic) genera.[2] The phylum comprises six classes Acidithiobacilia, Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Hydrogenophilia, and Zetaproteobacteria.[3] The Pseudomonadota are widely diverse, with differences in morphology, metabolic processes, relevance to humans, and ecological influence.[2]

Classification

American microbiologist Carl Woese established this grouping in 1987, informally naming it the "purple bacteria and their relatives". The group was later formally named the 'Proteobacteria' after the Greek god Proteus, who was known to assume many forms.[4] In 2021 the International Committee on Systematics of Prokaryotes designated the synonym Pseudomonadota, and renamed many other prokaryotic phyla as well. This renaming of several phyla remains controversial among microbiologists. Many continue to use the earlier name Proteobacteria, of long standing in the literature. The phylum Pseudomonadota encompasses classes Acidithiobacilia, Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Hydrogenophilia, and Zetaproteobacteria.[3] The phylum 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.

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.[5] 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).[5] The proposed reclassification of the name Epsilonprotobacteria is Campylobacterota.[5]

Characteristics

Pseudomonadota are a diverse group. Though some species may stain Gram-positive or Gram-variable in the labortary, they are nominally Gram-negative. Their unique outer membrane is mainly composed of lipopolysaccharides, which helps differentiate them from the Gram-positive species[6]. Most Pseudomonadota are motile and move using flagella. Many move about using flagella, but some are nonmotile, or rely on bacterial gliding.[2]

Pseudomonadota have a wide variety of metabolism types. Most are facultatively or obligately anaerobic, chemolithoautotrophic, and heterotrophic, but numerous exceptions occur. A variety of genera, which are not closely related to each other, convert energy from light through conventional photosynthesis or anoxygenic photosynthesis.[citation needed]

Some Alphaproteobacteria can grow at very low levels of nutrients and have unusual morphology such as stalks and buds. Others include agriculturally important bacteria capable of inducing nitrogen fixation in symbiosis with plants. The type order is the Caulobacterales, comprising stalk-forming bacteria such as Caulobacter. The mitochondria of eukaryotes are thought to be descendants of an alphaproteobacterium.[7]

The Betaproteobacteria are highly metabolically diverse and contain chemolithoautotrophs, photoautotrophs, and generalist heterotrophs. The type order is the Burkholderiales, comprising an enormous range of metabolic diversity, including opportunistic pathogens.[citation needed]

The Gammaproteobacteria are one of the largest classes in terms of genera, containing approximately 250 validly published names[8]. The type order is the Pseudomonadales, which include the genera Pseudomonas and the nitrogen-fixing Azotobacter.[citation needed]

The Zetaproteobacteria are iron-oxidizing neutrophilic chemolithoautotrophs, distributed worldwide in estuaries and marine habitats. The type order is the Mariprofundales.[citation needed]

The Hydrogenophilalia are thermophilic chemoheterotrophs and autotrophs. The bacteria typically use hydrogen gas as an electron donor. The type order is the Hydrogenophilales which contains two genera, Hydrogenophilus and Tepidiphilus.[9]

The Acidithiobacillia contain only sulfur, iron, and uranium-oxidising autotrophs. The type order is the Acidithiobacillales, which includes economically important organisms used in the mining industry such as Acidithiobacillus spp.[citation needed]

Habitat

Due to the distinctive nature of each of the six classes of Pseudomonadota, this phylum occupies a multitude of habitats. These include:

  • Human oral cavity[10]
  • Microbial mats in the deep sea[11]
  • Marine sediments[12]
  • Thermal sulfur springs[13]
  • Agricultural soil[13]
  • Hydrothermal vents[14]
  • Stem nodules of legumes[15]
  • Within aphids as endosymbionts[15]
  • Gastrointestinal tract of warm-blooded species[15]
  • Brackish, estuary waters[15]
  • Microbiomes of shrimp and mollusks[15]
  • Human vaginal tract[1]

Significance

Human Health

Studies have suggested Pseudomonadota as a relevant signature of disease in the human gastrointestinal (GI) tract, by operating as a marker for microbiota instability.[1] The human gut microbiome consists mainly of four phyla: Firmicutes, Bacteroidetes, Actinobacteria, and Pseudomonadota.[1] Microorganism gut colonization is dynamic from birth to death, with stabilization at the first few years of life, to higher diversity in adults, to reduced diversity in the elderly.[1] The gut microbiome conducts processes like nutrient synthesis, chemical metabolism, and the formation of the gut barrier.[1] 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.[1] An example in Lambeth et al. found increased bacterial count in patients with type 2 diabetes (T2DM) in comparison to patients with pre-diabetes or other control groups.[16] Another study by Michail et al. showed a correlation of microbial composition in children with and without nonalcoholic fatty liver disease (NAFLD), wherein patients with NAFLD having a higher abundance of Gammproteobacteria than patients without the disease.[17]

Classes Betaproteobacteria and Gammaproteobacteria are prevalent within the human oral cavity, and are markers for good oral health.[10] The oral microbiome consists of 11 habitats, including the tongue dorsum, hard palate, tonsils, throat, saliva, and more.[18] Changes in the oral microbiome are due to endogenous and exogenous factors like host lifestyle, genotype, environment, immune system, and socioeconomic status.[18] Considering diet as a factor, high saturated fatty acid (SAF) content, achieved through poor diet, has been correlated to increased abundance of Betaproteobacteria in the oral cavity.[18]

Economic Significance

Ecological Impact

  1. ^ a b c d e f g Rizzatti, G.; Lopetuso, L. R.; Gibiino, G.; Binda, C.; Gasbarrini, A. (2017). "Proteobacteria: A Common Factor in Human Diseases". BioMed Research International. 2017: 1–7. doi:10.1155/2017/9351507. ISSN 2314-6133. PMC 5688358. PMID 29230419.{{cite journal}}: CS1 maint: PMC format (link) CS1 maint: unflagged free DOI (link)
  2. ^ a b c d "Pseudomonadota Garrity et al., 2021". www.gbif.org. Retrieved 2024-04-11.
  3. ^ a b Kersters, Karel; De Vos, Paul; Gillis, Monique; Swings, Jean; Vandamme, Peter; Stackebrandt, Erko (2006), Dworkin, Martin; Falkow, Stanley; Rosenberg, Eugene; Schleifer, Karl-Heinz (eds.), "Introduction to the Proteobacteria", The Prokaryotes: Volume 5: Proteobacteria: Alpha and Beta Subclasses, New York, NY: Springer, pp. 3–37, doi:10.1007/0-387-30745-1_1, ISBN 978-0-387-30745-9, retrieved 2024-04-07
  4. ^ Moon, Christina D.; Young, Wayne; Maclean, Paul H.; Cookson, Adrian L.; Bermingham, Emma N. (2018-10). "Metagenomic insights into the roles of Proteobacteria in the gastrointestinal microbiomes of healthy dogs and cats". MicrobiologyOpen. 7 (5). doi:10.1002/mbo3.677. ISSN 2045-8827. PMC 6182564. PMID 29911322. {{cite journal}}: Check date values in: |date= (help)CS1 maint: PMC format (link)
  5. ^ a b c Waite, David W; Chuvochina, Maria; Pelikan, Claus; Parks, Donovan H; Yilmaz, Pelin; Wagner, Michael; Loy, Alexander; Naganuma, Takeshi; Nakai, Ryosuke; Whitman, William B; Hahn, Martin W; Kuever, Jan; Hugenholtz, Philip (2020). "Proposal to reclassify the proteobacterial classes Deltaproteobacteria and Oligoflexia, and the phylum Thermodesulfobacteria into four phyla reflecting major functional capabilities". International Journal of Systematic and Evolutionary Microbiology. 70 (11): 5972–6016. doi:10.1099/ijsem.0.004213. ISSN 1466-5034.
  6. ^ Silhavy, Thomas J.; Kahne, Daniel; Walker, Suzanne (2010-05-01). "The Bacterial Cell Envelope". Cold Spring Harbor Perspectives in Biology. 2 (5): a000414. doi:10.1101/cshperspect.a000414. ISSN 1943-0264. PMC 2857177. PMID 20452953.{{cite journal}}: CS1 maint: PMC format (link)
  7. ^ Roger, A.J.; Muñoz-Gómez, S.A.; Kamikawa, R. (2017). "The origin and diversification of mitochondria". Current Biology. 27 (21): R1177–R1192. doi:10.1016/j.cub.2017.09.015. PMID 29112874.
  8. ^ Williams, Kelly P.; Gillespie, Joseph J.; Sobral, Bruno W. S.; Nordberg, Eric K.; Snyder, Eric E.; Shallom, Joshua M.; Dickerman, Allan W. (2010-05). "Phylogeny of Gammaproteobacteria". Journal of Bacteriology. 192 (9): 2305–2314. doi:10.1128/JB.01480-09. ISSN 0021-9193. PMC 2863478. PMID 20207755. {{cite journal}}: Check date values in: |date= (help)CS1 maint: PMC format (link)
  9. ^ Boden, Rich; Hutt, Lee P; Rae, Alex W (2017). "Reclassification of Thiobacillus aquaesulis (Wood & Kelly, 1995) as Annwoodia aquaesulis gen. nov., comb. nov., transfer of Thiobacillus (Beijerinck, 1904) from the Hydrogenophilales to the Nitrosomonadales, proposal of Hydrogenophilalia class. nov. within the 'Proteobacteria', and four new families within the orders Nitrosomonadales and Rhodocyclales". International Journal of Systematic and Evolutionary Microbiology. 67 (5): 1191–1205. doi:10.1099/ijsem.0.001927. ISSN 1466-5034.
  10. ^ a b Leão, Inês; de Carvalho, Teresa Bento; Henriques, Valentina; Ferreira, Catarina; Sampaio-Maia, Benedita; Manaia, Célia M. (2023-02-01). "Pseudomonadota in the oral cavity: a glimpse into the environment-human nexus". Applied Microbiology and Biotechnology. 107 (2): 517–534. doi:10.1007/s00253-022-12333-y. ISSN 1432-0614. PMC 9842593. PMID 36567346.{{cite journal}}: CS1 maint: PMC format (link)
  11. ^ Williams, Kelly P.; Kelly, Donovan P. (2013). "Proposal for a new class within the phylum Proteobacteria, Acidithiobacillia classis nov., with the type order Acidithiobacillales, and emended description of the class Gammaproteobacteria". International Journal of Systematic and Evolutionary Microbiology. 63 (Pt_8): 2901–2906. doi:10.1099/ijs.0.049270-0. ISSN 1466-5034.
  12. ^ Gray, J P; Herwig, R P (1996-11). "Phylogenetic analysis of the bacterial communities in marine sediments". Applied and Environmental Microbiology. 62 (11): 4049–4059. doi:10.1128/aem.62.11.4049-4059.1996. ISSN 0099-2240. PMC 168226. PMID 8899989. {{cite journal}}: Check date values in: |date= (help)CS1 maint: PMC format (link)
  13. ^ a b Boden, Rich; Hutt, Lee P; Rae, Alex W (2017). "Reclassification of Thiobacillus aquaesulis (Wood & Kelly, 1995) as Annwoodia aquaesulis gen. nov., comb. nov., transfer of Thiobacillus (Beijerinck, 1904) from the Hydrogenophilales to the Nitrosomonadales, proposal of Hydrogenophilalia class. nov. within the 'Proteobacteria', and four new families within the orders Nitrosomonadales and Rhodocyclales". International Journal of Systematic and Evolutionary Microbiology. 67 (5): 1191–1205. doi:10.1099/ijsem.0.001927. ISSN 1466-5034.
  14. ^ Emerson, David; Rentz, Jeremy A.; Lilburn, Timothy G.; Davis, Richard E.; Aldrich, Henry; Chan, Clara; Moyer, Craig L. (2007-08-01). "A Novel Lineage of Proteobacteria Involved in Formation of Marine Fe-Oxidizing Microbial Mat Communities". PLOS ONE. 2 (8): e667. doi:10.1371/journal.pone.0000667. ISSN 1932-6203. PMC 1930151. PMID 17668050.{{cite journal}}: CS1 maint: PMC format (link) CS1 maint: unflagged free DOI (link)
  15. ^ a b c d e Kersters, Karel; De Vos, Paul; Gillis, Monique; Swings, Jean; Vandamme, Peter; Stackebrandt, Erko (2006), Dworkin, Martin; Falkow, Stanley; Rosenberg, Eugene; Schleifer, Karl-Heinz (eds.), "Introduction to the Proteobacteria", The Prokaryotes: Volume 5: Proteobacteria: Alpha and Beta Subclasses, New York, NY: Springer, pp. 3–37, doi:10.1007/0-387-30745-1_1#sec3_0-387-30745-1_1, ISBN 978-0-387-30745-9, retrieved 2024-04-11
  16. ^ Sr Fellow New Mexico Center for the Advancement of Research, Engagement, & Science on Health Disparities (NM CARES HD), School of Medicine, University of New Mexico Albuquerque, NM, 87131, USA; Shah, Vallabh; Lambeth, Stacey M; Carson, Trechelle; Lowe, Janae; Ramaraj, Thiruvarangan; Leff, Jonathan W.; Luo, Li; Bell, Callum J (2015-12-26). "Composition Diversity and Abundance of Gut Microbiome in Prediabetes and Type 2 Diabetes". Journal of Diabetes and Obesity. 2 (2): 108–114. doi:10.15436/2376-0949.15.031. PMC 4705851. PMID 26756039.{{cite journal}}: CS1 maint: PMC format (link) CS1 maint: multiple names: authors list (link) CS1 maint: numeric names: authors list (link)
  17. ^ Michail, Sonia; Lin, Malinda; Frey, Mark R.; Fanter, Rob; Paliy, Oleg; Hilbush, Brian; Reo, Nicholas V. (2015-02-01). "Altered gut microbial energy and metabolism in children with non-alcoholic fatty liver disease". FEMS Microbiology Ecology. 91 (2): 1–9. doi:10.1093/femsec/fiu002. ISSN 1574-6941. PMC 4358749. PMID 25764541.{{cite journal}}: CS1 maint: PMC format (link)
  18. ^ a b c Jia, G.; Zhi, A.; Lai, P. F. H.; Wang, G.; Xia, Y.; Xiong, Z.; Zhang, H.; Che, N.; Ai, L. (2018-03). "The oral microbiota – a mechanistic role for systemic diseases". British Dental Journal. 224 (6): 447–455. doi:10.1038/sj.bdj.2018.217. ISSN 0007-0610. {{cite journal}}: Check date values in: |date= (help)
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