Synergistota Explained

The Synergistota is a phylum of anaerobic bacteria that show Gram-negative staining and have rod/vibrioid cell shape.[1] [2] Although Synergistota have a diderm cell envelope,[3] [4] the genes for various proteins involved in lipopolysaccharides biosynthesis have not yet been detected in Synergistota, indicating that they may have an atypical outer cell envelope.[3] [4] The Synergistota inhabit a majority of anaerobic environments including animal gastrointestinal tracts, soil, oil wells, and wastewater treatment plants and they are also present in sites of human diseases such as cysts, abscesses, and areas of periodontal disease.[5] [6] Due to their presence at illness related sites, the Synergistota are suggested to be opportunistic pathogens but they can also be found in healthy individuals in the microbiome of the umbilicus and in normal vaginal flora.[7] Species within this phylum have also been implicated in periodontal disease,[8] gastrointestinal infections and soft tissue infections.[6] Other species from this phylum have been identified as significant contributors in the degradation of sludge for production of biogas in anaerobic digesters and are potential candidates for use in renewable energy production through their production of hydrogen gas.[9] All of the known Synergistota species and genera are presently part of a single class (Synergistia), order (Synergistiales), and family (Synergistaceae).

Comparative genomics and molecular signatures

Recent comparative analyses of sequenced Synergistota genomes have led to identification of large numbers of conserved signature indels (CSIs) in protein sequences that are specific for either all sequenced Synergistota species or some of their sub-clades that are observed in phylogenetic trees.[10] Of the CSIs that were identified, 32 in widely distributed proteins such as RpoB, RpoC, UvrD, GyrA, PolA, PolC, MraW, NadD, PyrE, RpsA, RpsH, FtsA, RadA, etc., including a large >300 aa insert in the RpoC protein, are present in various Synergistota species, but except for isolated bacteria, these CSIs are not found in the protein homologues from all other organisms. These CSIs provide novel molecular markers for distinguishing Synergistota species from all other bacteria. Seven other CSIs in important proteins including a 13 aa in RpoB were found to be uniquely present in Jonquetella, Pyramidobacter and Dethiosulfovibrio species indicating a close and specific relationship among these bacteria, which is also strongly supported by phylogenetic trees. Fifteen addition CSIs that were only present in Jonquetella and Pyramidobacter indicate a close association between these two species. Lastly, a close relationship between the Aminomonas and Thermanaerovibrio species is also supported by 9 identified CSIs. The identified molecular markers provide reliable means for the division of species from the phylum Synergistota into intermediate taxonomic ranks such as families and orders.

Phylogeny

See also: Bacterial taxonomy.

Taxonomy

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LSPN)[17] and the National Center for Biotechnology Information (NCBI).[18]

See also

References

Notes and References

  1. Hugenholtz, P., Hooper, S.D., and Kyrpides, N.C. (2009). Focus: Synergistetes. Environ. Microbiol. 11, 1327–1329.
  2. Jumas-Bilak . E. . Roudiere . L. . Marchandin . H. . 2009 . Description of 'Synergistetes' phyl. nov. and emended description of the phylum 'Deferribacteres' and of the family Syntrophomonadaceae, phylum 'Firmicutes' . Int. J. Syst. Evol. Microbiol. . 59 . 1028–1035 . 10.1099/ijs.0.006718-0. free .
  3. Gupta, R. S. (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: 171–182
  4. Sutcliffe . I.C. . 2010 . A phylum level perspective on bacterial cell envelope architecture . Trends Microbiol . 18 . 464–470 . 10.1016/j.tim.2010.06.005 . 20637628.
  5. Jumas-Bilak . E. . Carlier . J.P. . Jean-Pierre . H. . Citron . D. . Bernard . K. . Damay . A. . Gay . B. . Teyssier . C. . Campos . J. . Marchandin . H. . 2007 . Jonquetella anthropi gen. nov., sp. nov., the first member of the candidate phylum 'Synergistetes' isolated from man . Int. J. Syst. Evol. Microbiol. . 57 . 2743–2748 . 10.1099/ijs.0.65213-0 . 18048718. free .
  6. Vartoukian, S.R., Palmer, R.M., and Wade, W.G. (2007). The division "Synergistes". Anaerobe. 13, 99–106.
  7. Marchandin, H., Damay, A., Roudiere, L., Teyssier, C., Zorgniotti, I., Dechaud, H., Jean-Pierre, H., and Jumas-Bilak, E. (2010). Phylogeny, diversity and host specialization in the phylum Synergistetes with emphasis on strains and clones of human origin. Res. Microbiol. 161, 91–100.
  8. Horz . H.P. . D.M. Citron . Y.A. Warren . E.J. Goldstein . G. Conrads . August 2006 . Synergistes Group Organisms of Human Origin . Journal of Clinical Microbiology . 44 . 8 . 2914–2920 . 16891512 . 10.1128/JCM.00568-06 . 1594628 .
  9. Riviere, D., Desvignes, V., Pelletier, E., Chaussonnerie, S., Guermazi, S., Weissenbach, J., Li, T., Camacho, P., and Sghir, A. (2009). Towards the definition of a core of microorganisms involved in anaerobic digestion of sludge. ISME. J. 3, 700–714.
  10. Bhandari . V. . Gupta . R. S. . 2012 . Molecular signatures for the phylum Synergistetes and some of its subclades . Antonie van Leeuwenhoek . 102. 517–40. 10.1007/s10482-012-9759-2 . 22711299 .
  11. Web site: The LTP . 20 November 2023.
  12. Web site: LTP_all tree in newick format. 20 November 2023.
  13. Web site: LTP_08_2023 Release Notes. 20 November 2023.
  14. Web site: GTDB release 08-RS214 . Genome Taxonomy Database. 10 May 2023.
  15. Web site: bac120_r214.sp_label . Genome Taxonomy Database. 10 May 2023.
  16. Web site: Taxon History . Genome Taxonomy Database. 10 May 2023.
  17. Web site: J.P. Euzéby . Synergistetes . List of Prokaryotic names with Standing in Nomenclature (LPSN). 2016-03-20.
  18. Web site: Sayers. Synergistetes . National Center for Biotechnology Information (NCBI) taxonomy database . 2016-03-20 . etal.

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