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Negativicutes

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Negativicutes
Scientific classification Edit this classification
Domain: Bacteria
Phylum: Bacillota
Class: Negativicutes
Marchandin et al. 2010
Orders and families
Synonyms
  • "Selenomonadia" Oren, Parte & Garrity 2016
  • "Selenobacteria" Cavalier-Smith 1992 stat. nov. Cavalier-Smith 2006

The Negativicutes are a class of bacteria in the phylum Bacillota, whose members have a peculiar cell wall with a lipopolysaccharide outer membrane which stains gram-negative, unlike most other members of the Bacillota.[1] Although several neighbouring Clostridia species (firmicute bacteria) also stain gram-negative, the proteins responsible for the unusual diderm structure of the Negativicutes may have actually been laterally acquired from Pseudomonadota (formerly Proteobacteria).[1][2][3][4] Additional research is required to confirm the origin of the diderm cell envelope in the Negativicutes.

Most members of this class are obligate anaerobes, and occur in habitats such as rivers, lakes, and the intestines of vertebrates. They range from spherical forms, such as Megasphaera and Veillonella, to curved rods, as typified by the selenomonads. Selenomonas has a characteristic crescent shape, with flagella inserted on the concave side, while Sporomusa is similar, but nonmotile. Their names refer to this distinctive morphology: selene means moon, and musa means banana.[5]

Taxonomy

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The class currently consists of 32 validly named genera across three orders and four families.[6][7] The orders Veillonellales and Acidaminococcales each contain a single family, Veillonellaceae and Acidaminococcaceae, respectively, while the order Selenomonadales contains two families, Selenomonadaceae and Sporomusaceae.[7]

Molecular signatures

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Historically, the Negativicutes consisted of a single order, the Selenomonadales, and two families, Veillonellaceae and Acidaminococcaceae based on 16S rRNA gene sequence similarity.[8][5] However, these groupings did not include several members within the Negativicutes that branched outside of the two families. The current taxonomic view is inclusive of these members who have been validly assigned to the families Selenomonadaceae and Sporomusaceae within the emended Selenomonadales order.[7] Molecular markers in the form of conserved signature indels (CSIs) and proteins (CSPs) justify the present taxonomic divisions. These molecular markers are found at each taxonomic rank, and their distribution is in agreement with the observed phylogenetic branching.[9][10]

Many works have implicated that the Negativicutes should be reclassified as an order within the class Clostridia, based on close phylogenetic branching, and the observation that the spore-forming members of the Negativicutes share similar sporulation genes as the Clostridia, and that both stain gram-negative.[9][10] However, the heterogeneity of members within the Negativicutes, as well as the distribution of molecular signatures, supports the view that the Negativicutes are in fact an independent class within the Bacillota, with Clostridia as their closest phylogenetic neighbours.[5][10][11][12] Additionally, several CSIs and CSPs have been found to be uniquely shared among all Negativicutes, while no CSIs have been found to be shared by both Negativicutes and Clostridia.[7]

Phylogeny

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The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN)[13] and National Center for Biotechnology Information (NCBI)[14]

16S rRNA based LTP_08_2023[15][16][17] 120 single copy marker proteins based GTDB 08-RS214[18][19][20]
Acidaminococcales
"Succinispiraceae"

Succinispira Janssen and O'Farrell 1999

Acidaminococcaceae

"Ca. Avacidaminococcus" Gilroy et al. 2021

Acidaminococcus Rogosa 1969

Phascolarctobacterium Del Dot et al. 1994

Phascolarctobacterium succinatutens Watanabe et al. 2012

Succiniclasticum van Gylswyk 1995

Veillonellales
"Negativicoccaceae"

Negativicoccus Marchandin et al. 2010

"Dialisteraceae"

Dialister Bergey et al. 1923 ex Moore & Moore 1994 [incl. Allisonella]

"Megasphaeraceae"

Megasphaera paucivorans Juvonen & Suihko 2006

Anaeroglobus Carlier et al. 2002

"Caecibacter" Ricaboni et al. 2017

Megasphaera Rogosa 1971

Veillonellaceae

Veillonella Prévot 1933

Sporomusales_A
"Acetonemaceae"

Anaerosporomusa Choi et al. 2016

Acetonema Kane and Breznak 1992

Sporomusales C
DSM‑15969

Anaerospora Woo et al. 2005

"Thermosinaceae"

Thermosinus Sokolova et al. 2004 [Sporolituus Ogg and Patel 2009]

"Sporomusales"
"Luciferaceae"

Lucifera Sanchez-Andrea et al. 2018

Sporomusaceae

Methylomusa Amano et al. 2018

Sporomusa Möller et al. 1985

"Anaeromusales"
"Anaeromusaceae"

Anaeromusa Baena et al. 1999 (incl. Anaeroarcus Strömpl et al. 1999)

UMGS1260
UMGS1260

Pelorhabdus Grässle et al. 2022

"Propionisporales"
"Propionisporaceae"

Propionispora Biebl et al. 2001

"Pelosinaceae"

Pelosinus Shelobolina et al. 2007

"Dendrosporobacterales"
"Dendrosporobacteraceae"

Dendrosporobacter Strömpl et al. 2000

Selenomonadales
"Massilibacillaceae"

"Massilibacillus" Tidjani Alou et al. 2017

Selenomonadaceae

Propionispira arboris Schink et al. 1983

Megamonas Shah and Collins 1983

Pectinatus Lee et al. 1978

Selenomonas von Prowazek 1913

Anaerovibrio Hungate 1966

Schwartzia Gylswyk et al. 1997

Quinella Krumholz et al. 1993

Centipeda Lai et al. 1983

Selenomonas species-group 2

Selenomastix Woodcock & Lapage 1913

Mitsuokella Shah & Collins 1983

See also

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References

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  1. ^ a b Sutcliffe IC (2010). "A phylum level perspective on bacterial cell envelope architecture". Trends Microbiol. 18 (10): 464–470. doi:10.1016/j.tim.2010.06.005. PMID 20637628.
  2. ^ Gupta RS (2011). "Origin of diderm (Gram-negative) bacteria: antibiotic selection pressure rather than endosymbiosis likely led to the evolution of bacterial cells with two membranes". Antonie van Leeuwenhoek. 100 (2): 171–182. doi:10.1007/s10482-011-9616-8. PMC 3133647. PMID 21717204.
  3. ^ Campbell C, Sutcliffe IC, Gupta RS (2014). "Comparative proteome analysis of Acidaminococcus intestini supports a relationship between outer membrane biogenesis in Negativicutes and Proteobacteria" (PDF). Arch Microbiol. 196 (4): 307–310. doi:10.1007/s00203-014-0964-4. PMID 24535491. S2CID 253722630.
  4. ^ Tocheva EI, Matson EG, Morris DM, Moussavi F, Leadbetter JR, Jensen GJ (2011). "Peptidoglycan remodeling and conversion of an inner membrane into an outer membrane during sporulation". Cell. 146 (5): 799–812. doi:10.1016/j.cell.2011.07.029. PMC 3176627. PMID 21884938.
  5. ^ a b c Marchandin, H.; Teyssier, C.; Campos, J.; Jean-Pierre, H.; Roger, F.; Gay, B.; Carlier, J. -P.; Jumas-Bilak, E. (2009). "Negativicoccus succinicivorans gen. nov., sp. nov., isolated from human clinical samples, emended description of the family Veillonellaceae and description of Negativicutes classis nov., Selenomonadales ord. nov. and Acidaminococcaceae fam. nov. in the bacterial phylum Firmicutes". International Journal of Systematic and Evolutionary Microbiology. 60 (6): 1271–1279. doi:10.1099/ijs.0.013102-0. PMID 19667386.
  6. ^ Sayers; et al. "Negativicutes". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2013-03-20.
  7. ^ a b c d Campbell C, Adeolu M, Gupta RS (2015). "Genome-based taxonomic framework for the class Negativicutes: division of the class Negativicutes into the orders Selenomonadales emend., Acidaminococcales ord. nov. and Veillonellales ord. nov". Int J Syst Evol Microbiol. 65 (9): 3203–3215. doi:10.1099/ijs.0.000347. PMID 25999592.
  8. ^ Ludwig W, Schleifer K-H, Whitman, WB (2009) Revised road map to the phylum Firmicutes. In: Bergey’s Manual of Systematic Bacteriology, vol. 3, 2nd edn. pp. 1–13. Eds P. De Vos, G. M. Garrity, D. Jones, N. R. Krieg, W. Ludwig, F. A. Rainey, K. H. Schleifer & W. B. Whitman Springer-: New York.
  9. ^ a b Yutin N, Galperin MY (2013). "A genomic update on clostridial phylogeny: Gram-negative spore formers and other misplaced clostridia". Environ Microbiol. 15 (10): 2631–2641. doi:10.1111/1462-2920.12173. PMC 4056668. PMID 23834245.
  10. ^ a b c Vesth T, Ozen A, Andersen SC, Kaas RS, Lukjancenko O, Bohlin J, Nookaew I, Wassenaar TM, Ussery DW (2013). "Veillonella, Firmicutes: Microbes disguised as Gram negatives". Stand Genomic Sci. 9 (2): 431–448. doi:10.4056/sigs.2981345. PMC 4062629. PMID 24976898.
  11. ^ Merchandin H, Jumas-Bilak E (2014) The family Veillonellaceae. In: The Prokaryotes, vol. 7, 4th edn. pp. 433–453. Eds E. Rosenberg, E. DeLong, S. Lory, E. Stackebrandt & F. Thompson Springer-: Berlin, Heidelberg.
  12. ^ Yilmaz P, Parfrey LW, Yarza P, Gerken J, Pruesse E, Quast C, Schweer T, Peplies J, Ludwig W, Glöckner FO (2014). "The SILVA and "All-species Living Tree Project (LTP)" taxonomic frameworks". Nucleic Acids Res. 42 (Database issue): D643–8. doi:10.1093/nar/gkt1209. PMC 3965112. PMID 24293649.
  13. ^ J.P. Euzéby. "Negativicutes". List of Prokaryotic names with Standing in Nomenclature (LPSN). Retrieved 2022-09-09.
  14. ^ Sayers; et al. "Negativicutes". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2022-09-09.
  15. ^ "The LTP". Retrieved 20 November 2023.
  16. ^ "LTP_all tree in newick format". Retrieved 20 November 2023.
  17. ^ "LTP_08_2023 Release Notes" (PDF). Retrieved 20 November 2023.
  18. ^ "GTDB release 08-RS214". Genome Taxonomy Database. Retrieved 10 May 2023.
  19. ^ "bac120_r214.sp_label". Genome Taxonomy Database. Retrieved 10 May 2023.
  20. ^ "Taxon History". Genome Taxonomy Database. Retrieved 10 May 2023.
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