Synergistota

The Synergistota is a phylum of anaerobic bacteria that show Gram-negative staining and have rod/vibrioid cell shape.^[2][3] Although Synergistota have a diderm cell envelope,^[4][5] 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.^[4][5] 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.^[6][7] 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][8] Species within this phylum have also been implicated in periodontal disease,^[9] gastrointestinal infections and soft tissue infections.^[7] 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.^[10] All of the known Synergistota species and genera are presently part of a single class (Synergistia), order (Synergistiales), and family (Synergistaceae).^[3]

Synergistota
Scientific classification
Domain:	Bacteria Jumas-Bilak et al. 2021[1]
Phylum:	Synergistota Jumas-Bilak et al. 2009
Class:	Synergistia Jumas-Bilak et al. 2009
Order:	Synergistales Jumas-Bilak et al. 2009
Families
Acetomicrobiaceae Aminiphilaceae Aminithiophilaceae Aminobacteriaceae Dethiosulfovibrionaceae Synergistaceae Thermosynergistaceae Thermovirgaceae
Synonyms
"Synergistaeota" Oren et al. 2015 "Synergistetes" Jumas-Bilak et al. 2009 "Synergistota" Whitman et al. 2018

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.^[11] 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.^[11] 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.^[11] 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.^[11]

Phylogeny

See also: Bacterial taxonomy

16S rRNA based LTP_08_2023[12][13][14]

120 single copy marker proteins based GTDB 08-RS214[15][16][17]

Synergistota Thermosynergistes pyruvativorans Yang et al. 2021 Acetomicrobium A. flavidum Soutschek et al. 1985 A. mobile (Menes & Muxi 2002) Ben Hania et al. 2016 A. hydrogeniformans (Maune & Tanner 2012) Ben Hania et al. 2016 A. thermoterrenum (Rees et al. 1997) Ben Hania et al. 2016 Thermovirga lienii Dahle and Birkeland 2006 Aminithiophilus ramosus Pradel et al. 2023 Aminiphilus circumscriptus Díaz et al. 2007 Aminomonas paucivorans Baena et al. 1999 Thermanaerovibrio T. acidaminovorans (Guangsheng et al. 1997) Baena et al. 1999 T. velox Zavarzina et al. 2000 Synergistes jonesii Allison et al. 1993 Cloacibacillus C. evryensis Ganesan et al. 2008 C. porcorum Looft et al. 2013 Lactivibrio alcoholicus Qiu et al. 2014 Aminivibrio pyruvatiphilus Honda et al. 2013 Fretibacterium fastidiosum Vartoukian et al. 2013 Aminobacterium A. thunnarium Hamdi et al. 2015 A. colombiense Baena et al. 1999 (type sp.) A. mobile Baena et al. 2000 Jonquetella anthropi Jumas-Bilak et al. 2007 Rarimicrobium hominis Jumas-Bilak et al. 2015 Pyramidobacter P. piscolens Downes et al. 2009 P. porci Wylensek et al. 2021 Dethiosulfovibrio D. salsuginis Díaz-Cárdenas et al. 2010 D. faecalis Grabowski et al. 2022 D. peptidovorans Magot et al. 1997 (type sp.) D. marinus Surkov et al. 2001 D. acidaminovorans Surkov et al. 2001 D. russensis Surkov et al. 2001

Synergistota Thermosynergistaceae Thermosynergistes pyruvativorans Acetomicrobiaceae Acetomicrobium A. flavidum A. hydrogeniformans A. thermoterrenum Thermovirgaceae Thermovirga lienii Aminiphilaceae Aminiphilus circumscriptus Synergistaceae Aminomonas paucivorans Thermanaerovibrio T. acidaminovorans T. velox "Ca. Caccocola" "Ca. C. faecigallinarum" Gilroy et al. 2021 "Ca. C. faecipullorum" Gilroy et al. 2021 Synergistes jonesii Cloacibacillus C. evryensis C. porcorum Aminobacteriaceae Aminivibrio pyruvatiphilus Fretibacterium fastidiosum Aminobacterium A. colombiense A. mobile Dethiosulfovibrionaceae Jonquetella anthropi Pyramidobacter P. piscolens P. porci Dethiosulfovibrio D. salsuginis D. faecalis D. peptidovorans D. russensis

Taxonomy

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LSPN)^[18] and the National Center for Biotechnology Information (NCBI).^[19]

• Phylum Synergistota Jumas-Bilak et al. 2021
  • Class Synergistia Jumas-Bilak et al. 2009
    • Order Synergistales Jumas-Bilak et al. 2009
      • Genus "Pacaella" Ndongo et al. 2017
        • Species ?"P. massiliensis" Ndongo et al. 2017
      • Genus "Candidatus Tammella" Hongoh et al. 2007
        • Species ?"Ca. T. caduceiae" Hongoh et al. 2007
      • Family Aminithiophilaceae Pradel et al. 2023
        • Genus Aminithiophilus Pradel et al. 2023
      • Family Acetomicrobiaceae Pradel et al. 2023
        • Genus Acetomicrobium Soutschek et al. 1985 [Anaerobaculum Rees et al. 1997]
      • Family Aminiphilaceae Pradel et al. 2023
        • Genus "Aminirod" Liu et al. 2021
          • Species ?"A. propionatiphilus" Liu et al. 2021
        • Genus Aminiphilus Díaz et al. 2007
      • Family Aminobacteriaceae Pradel et al. 2023
        • Genus Aminobacterium Baena et al. 1999
        • Genus Aminivibrio Honda et al. 2013
        • Genus Fretibacterium Vartoukian et al. 2013
        • Genus Lactivibrio Qiu et al. 2014
      • Family Dethiosulfovibrionaceae Pradel et al. 2023
        • Genus Dethiosulfovibrio Magot et al. 1997
        • Genus Jonquetella Jumas-Bilak et al. 2007
        • Genus Pyramidobacter Downes et al. 2009
        • Genus Rarimicrobium Jumas-Bilak et al. 2015
      • Family Synergistaceae Jumas-Bilak et al. 2009 [Clostridiales Family XV; Thermosynergistaceae Yang et al. 2021]
        • Genus Aminomonas Baena et al. 1999
        • Genus "Candidatus Caccocola" Gilroy et al. 2021
        • Genus Cloacibacillus Ganesan et al. 2008 emend. Looft et al. 2013
        • Genus "Candidatus Equadaptatus" Gilroy et al. 2022
          • Species ?"Ca. E. faecalis" Gilroy et al. 2022
        • Genus Synergistes Allison et al. 1993
        • Genus Thermanaerovibrio Baena et al. 1999 emend. Palaniappan et al. 2013
      • Family Thermosynergistaceae Yang et al. 2021
        • Genus Thermosynergistes Yang et al. 2021
      • Family Thermovirgaceae Pradel et al. 2023
        • Genus Thermovirga Dahle and Birkeland 2006

See also

• List of bacteria genera
• List of bacterial orders

References

1. Oren A, Garrity GM (2021). "Valid publication of the names of forty-two phyla of prokaryotes". Int J Syst Evol Microbiol. 71 (10): 5056. doi:10.1099/ijsem.0.005056. PMID 34694987.
2. Hugenholtz, P., Hooper, S.D., and Kyrpides, N.C. (2009). Focus: Synergistetes. Environ. Microbiol. 11, 1327–1329.
3. 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. doi:10.1099/ijs.0.006718-0.
4. 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
5. Sutcliffe, I.C. (2010). "A phylum level perspective on bacterial cell envelope architecture". Trends Microbiol. 18: 464–470. doi:10.1016/j.tim.2010.06.005. PMID 20637628.
6. 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. doi:10.1099/ijs.0.65213-0. PMID 18048718.
7. Vartoukian, S.R., Palmer, R.M., and Wade, W.G. (2007). The division "Synergistes". Anaerobe. 13, 99–106.
8. 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.
9. 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. doi:10.1128/JCM.00568-06. PMC 1594628. PMID 16891512.
10. 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.
11. Bhandari, V.; Gupta, R. S. (2012). "Molecular signatures for the phylum Synergistetes and some of its subclades". Antonie van Leeuwenhoek. 102: 517–40. doi:10.1007/s10482-012-9759-2. PMID 22711299.
12. "The LTP". Retrieved 20 November 2023.
13. "LTP_all tree in newick format". Retrieved 20 November 2023.
14. "LTP_08_2023 Release Notes" (PDF). Retrieved 20 November 2023.
15. "GTDB release 08-RS214". Genome Taxonomy Database. Retrieved 10 May 2023.
16. "bac120_r214.sp_label". Genome Taxonomy Database. Retrieved 10 May 2023.
17. "Taxon History". Genome Taxonomy Database. Retrieved 10 May 2023.
18. J.P. Euzéby. "Synergistetes". List of Prokaryotic names with Standing in Nomenclature (LPSN). Retrieved 2016-03-20.
19. Sayers; et al. "Synergistetes". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2016-03-20.