Synergistetes

Synergistaceae
Scientific classification
Kingdom:	Bacteria
Phylum:	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

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]

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

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LSPN)^[11] and the phylogeny is based on 16S rRNA-based LTP release 111 by The All-Species Living Tree Project.^[12]

?Candidatus Tammella caduceiae Hongoh et al. 2007 ?Aminomonas paucivorans Baena et al. 1999 ?Fretibacterium fastidiosum Vartoukian et al. 2013 Acetomicrobium flavidum Soutschek et al. 1985 (type sp.) [was Bacteroideaceae]   Anaerobaculum ?A. mobile Menes and Muxí 2002 A. hydrogeniformans Maune and Tanner 2012 A. thermoterrenum Rees et al. 1997 (type sp.) Thermovirga lienii Dahle and Birkeland 2006 Aminiphilus circumscriptus Díaz et al. 2007   Thermanaerovibrio T. acidaminovorans (Guangsheng et al. 1997) Baena et al. 1999 (type sp.) T. velox Zavarzina et al. 2000 Cloacibacillus evryensis Ganesan et al. 2008 Synergistes jonesii Allison et al. 1993   Aminobacterium A. colombiense Baena et al. 1999 (type sp.) A. mobile Baena et al. 2000 Jonquetella anthropi Jumas-Bilak et al. 2007 Pyramidobacter piscolens Downes et al. 2009   Dethiosulfovibrio D. salsuginis Díaz-Cárdenas et al. 2010 D. peptidovorans Magot et al. 1997 (type sp.) D. acidaminovorans Surkov et al. 2001 D. marinus Surkov et al. 2001 D. russensis Surkov et al. 2001

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.
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. See the List of Prokaryotic names with Standing in Nomenclature. Data extracted from the "Synergistetes". Retrieved 2011-11-17.
12. See the All-Species Living Tree Project here. Data extracted from the "16S rRNA-based LTP release 111 (full tree)" (PDF). Silva Comprehensive Ribosomal RNA Database. Retrieved 2013-03-20.