Synergistetes

The Synergistetes is a recently recognized phylum of anaerobic bacteria that show Gram-negative staining and have rod/vibrioid cell shape.[1][2] Although Synergistetes have a diderm cell envelope,[3][4] the genes for various proteins involved in lipopolysaccharides biosynthesis have not yet been detected in Synergistetes, indicating that they may have an atypical outer cell envelope.[3][4] The Synergistetes 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 Synergistetes 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.[6][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 Synergistetes species and genera are presently part of a single class (Synergistia), order (Synergistiales) and family (Synergistaceae).[2]

Synergistaceae
Scientific classification
Kingdom:	Bacteria
Phylum:	Firmicutes?
Subphylum:	Synergistetes Jumas-Bilak et al. 2009
Class:	Synergistia Jumas-Bilak et al. 2009
Order:	Synergistales Jumas-Bilak et al. 2009
Family:	Synergistaceae Jumas-Bilak et al. 2009
Genera
Acetomicrobium flavidum Soutschek et al. 1985 Aminiphilus Díaz et al. 2007 Aminobacterium Baena et al. 1999 Aminomonas Baena et al. 1999 Anaerobaculum Rees et al. 1997 emend. Maune and Tanner 2012 Candidatus Tammella Hongoh et al. 2007 Cloacibacillus Ganesan et al. 2008 Dethiosulfovibrio Magot et al. 1997 Fretibacterium fastidiosum Vartoukian et al. 2013 Jonquetella Jumas-Bilak et al. 2007 Pyramidobacter Downes et al. 2009 Synergistes Allison et al. 1993 Thermanaerovibrio Baena et al. 1999 emend. Zavarzina et al. 2000 Thermovirga Dahle and Birkeland 2006
Synonyms
Aminanaerobia Hugenholtz Synergistaeota Oren et al. 2015

Comparative genomics and molecular signatures

Recent comparative analyses of sequenced Synergistetes genomes have led to identification of large numbers of conserved signature indels (CSIs) in protein sequences that are specific for either all sequenced Synergistetes 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 Synergistetes 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 Synergistetes species from all other bacteria.[10] 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.[10] 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 Synergistetes into intermediate taxonomic ranks such as families and orders.[10]

Phylogeny

See also: Bacterial taxonomy

The phylogeny based on the work of the All-Species Living Tree Project.[11]

Acetomicrobium flavidum (type sp.) [was Bacteroideaceae]   Anaerobaculum   A. hydrogeniformans     A. thermoterrenum           Thermovirga lienii         Aminiphilus circumscriptus     Thermanaerovibrio   T. acidaminovorans (type sp.)     T. velox         Synergistes jonesii   Cloacibacillus   C. evryensis     C. porcorum                   Lactivibrio alcoholicus       Aminivibrio pyruvatiphilus     Fretibacterium fastidiosum       Aminobacterium   A. thunnarium       A. colombiense (type sp.)     A. mobile               Jonquetella anthropi     Pyramidobacter piscolens     Dethiosulfovibrio   D. salsuginis       D. peptidovorans (type sp.)       D. acidaminovorans     D. marinus     D. russensis

Taxonomy

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LSPN)[12] and the National Center for Biotechnology Information (NCBI).[13]

• Subphylum Synergistetes Jumas-Bilak et al. 2009 [Synergistaeota Oren et al. 2015 [Aminanaerobia Hugenholtz]
  • Class Synergistia Jumas-Bilak et al. 2009
    • Order Synergistales Jumas-Bilak et al. 2009
      • Family Synergistaceae Jumas-Bilak et al. 2009 [Clostridiales Family XV]
        • Genus Acetomicrobium Soutschek et al. 1985
          • Species Acetomicrobium flavidum Soutschek et al. 1985
        • Genus Aminiphilus Díaz et al. 2007
          • Species Aminiphilus circumscriptus Díaz et al. 2007
        • Genus Aminivibrio Honda et al. 2013
          • Species Aminivibrio pyruvatiphilus Honda et al. 2013
        • Genus Aminobacterium Baena et al. 1999
          • Species A. colombiense Baena et al. 1999 (type sp.)
          • Species A. mobile Baena et al. 2000
          • Species A. thunnarium Hamdi et al. 2015
        • Genus Aminomonas Baena et al. 1999
          • Species Aminomonas paucivorans Baena et al. 1999
        • Genus Anaerobaculum Rees et al. 1997 emend. Maune & Tanner 2012
          • Species A. hydrogeniformans Maune & Tanner 2012
          • Species A. mobile Menes & Muxí 2002
          • Species A. thermoterrenum Rees et al. 1997 (type sp.)
        • Genus Candidatus Tammella Hongoh et al. 2007
          • Species Candidatus Tammella caduceiae Hongoh et al. 2007
        • Genus Cloacibacillus Ganesan et al. 2008 emend. Looft et al. 2013
          • Species Cloacibacillus evryensis Ganesan et al. 2008
          • Species Cloacibacillus porcorum Looft et al. 2013
        • Genus Dethiosulfovibrio Magot et al. 1997
          • Species D. salsuginis Díaz-Cárdenas et al. 2010
          • Species D. peptidovorans Magot et al. 1997 (type sp.)
          • Species D. acidaminovorans Surkov et al. 2001
          • Species D. marinus Surkov et al. 2001
          • Species D. russensis Surkov et al. 2001
        • Genus Fretibacterium Vartoukian et al. 2013
          • Species Fretibacterium fastidiosum Vartoukian et al. 2013
        • Genus Jonquetella Jumas-Bilak et al. 2007
          • Species Jonquetella anthropi Jumas-Bilak et al. 2007
        • Genus Lactivibrio Qiu et al. 2014
          • Species Lactivibrio alcoholicus Qiu et al. 2014
        • Genus Pyramidobacter Downes et al. 2009
          • Species Pyramidobacter piscolens Downes et al. 2009
        • Genus Synergistes Allison et al. 1993
          • Species Synergistes 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 Thermovirga Dahle and Birkeland 2006
          • Species Thermovirga lienii Dahle and Birkeland 2006

Notes:
♠ Strain found at the National Center for Biotechnology Information (NCBI) but not listed in the List of Prokaryotic names with Standing in Nomenclature (LPSN)

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. doi:10.1099/ijs.0.006718-0.
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. doi:10.1016/j.tim.2010.06.005. PMID 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. doi:10.1099/ijs.0.65213-0. PMID 18048718.
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. doi:10.1128/JCM.00568-06. PMC 1594628. PMID 16891512.
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. doi:10.1007/s10482-012-9759-2. PMID 22711299.
11. "16S rRNA-based LTP release 123 (full tree)" (PDF). Silva Comprehensive Ribosomal RNA Database. Retrieved 2016-03-20.
12. J.P. Euzéby. "Synergistetes". List of Prokaryotic names with Standing in Nomenclature (LPSN). Retrieved 2016-03-20.
13. Sayers; et al. "Synergistetes". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2016-03-20.