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 | |
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| Synonyms | |
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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
| 16S rRNA based LTP_12_2021[12][13][14] | 120 single copy marker proteins based GTDB 08-RS214[15][16][17] | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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
- Species ?A. ramosus 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]
- Species A. flavidum Soutschek et al. 1985
- Species A. hydrogeniformans (Maune & Tanner 2012) Ben Hania et al. 2016
- Species A. mobile (Menes & Muxi 2002) Ben Hania et al. 2016
- Species A. thermoterrenum (Rees et al. 1997) Ben Hania et al. 2016
- 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
- Species A. circumscriptus Díaz et al. 2007
- Genus "Aminirod" Liu et al. 2021
- Family Aminobacteriaceae Pradel et al. 2023
- Genus Aminobacterium Baena et al. 1999
- Genus Aminivibrio Honda et al. 2013
- Species A. pyruvatiphilus Honda et al. 2013
- Species A. colombiense Baena et al. 1999 (type sp.)
- Species A. mobile Baena et al. 2000
- Species ?A. thunnarium Hamdi et al. 2015
- Genus Fretibacterium Vartoukian et al. 2013
- Species F. fastidiosum Vartoukian et al. 2013
- Genus Lactivibrio Qiu et al. 2014
- Species ?L. alcoholicus Qiu et al. 2014
- Family Dethiosulfovibrionaceae Pradel et al. 2023
- Genus Dethiosulfovibrio Magot et al. 1997
- Species D. acidaminovorans Surkov et al. 2001
- Species D. faecalis Grabowski et al. 2022
- Species D. marinus Surkov et al. 2001
- Species D. peptidovorans Magot et al. 1997 (type sp.)
- Species D. russensis Surkov et al. 2001
- Species D. salsuginis Díaz-Cárdenas et al. 2010
- Genus Jonquetella Jumas-Bilak et al. 2007
- Species J. anthropi Jumas-Bilak et al. 2007
- Genus Pyramidobacter Downes et al. 2009
- Species P. piscolens Downes et al. 2009
- Species P. porci Wylensek et al. 2021
- Genus Rarimicrobium Jumas-Bilak et al. 2015
- Species ?R. hominis Jumas-Bilak et al. 2015
- Genus Dethiosulfovibrio Magot et al. 1997
- Family Synergistaceae Jumas-Bilak et al. 2009 [Clostridiales Family XV; Thermosynergistaceae Yang et al. 2021]
- Genus Aminomonas Baena et al. 1999
- Species A. paucivorans Baena et al. 1999
- Genus "Candidatus Caccocola" Gilroy et al. 2021
- Species "Ca. C. faecigallinarum" Gilroy et al. 2021
- Species "Ca. C. faecipullorum" Gilroy et al. 2021
- Genus Cloacibacillus Ganesan et al. 2008 emend. Looft et al. 2013
- Species C. evryensis Ganesan et al. 2008
- Species C. porcorum 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
- Species S. jonesii Allison et al. 1993
- Genus Thermanaerovibrio Baena et al. 1999 emend. Palaniappan et al. 2013
- Species T. acidaminovorans (Guangsheng et al. 1997) Baena et al. 1999 [Selenomonas acidaminovorans Guangsheng et al. 1997] (type sp.)
- Species T. velox Zavarzina et al. 2000
- Genus Aminomonas Baena et al. 1999
- Family Thermosynergistaceae Yang et al. 2021
- Genus Thermosynergistes Yang et al. 2021
- Species T. pyruvativorans Yang et al. 2021
- Genus Thermosynergistes Yang et al. 2021
- Family Thermovirgaceae Pradel et al. 2023
- Genus Thermovirga Dahle and Birkeland 2006
- Species T. lienii Dahle and Birkeland 2006
- Genus Thermovirga Dahle and Birkeland 2006
- Genus "Pacaella" Ndongo et al. 2017
- Order Synergistales Jumas-Bilak et al. 2009
- Class Synergistia Jumas-Bilak et al. 2009
References
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- Hugenholtz, P., Hooper, S.D., and Kyrpides, N.C. (2009). Focus: Synergistetes. Environ. Microbiol. 11, 1327–1329.
- 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.
- 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
- 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.
- 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.
- Vartoukian, S.R., Palmer, R.M., and Wade, W.G. (2007). The division "Synergistes". Anaerobe. 13, 99–106.
- 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.
- 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.
- 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.
- 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.
- "The LTP". Retrieved 23 February 2021.
- "LTP_all tree in newick format". Retrieved 23 February 2021.
- "LTP_12_2021 Release Notes" (PDF). Retrieved 23 February 2021.
- "GTDB release 08-RS214". Genome Taxonomy Database. Retrieved 10 May 2023.
- "bac120_r214.sp_label". Genome Taxonomy Database. Retrieved 10 May 2023.
- "Taxon History". Genome Taxonomy Database. Retrieved 10 May 2023.
- J.P. Euzéby. "Synergistetes". List of Prokaryotic names with Standing in Nomenclature (LPSN). Retrieved 2016-03-20.
- Sayers; et al. "Synergistetes". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2016-03-20.