Synergistaceae Jumas-Bilak et al., 2009
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Abstract
The Synergistota is a phylum of anaerobic bacteria that show Gram-negative staining and have rod/vibrioid cell shape.Hugenholtz, P., Hooper, S.D., and Kyrpides, N.C. (2009). Focus: Synergistetes. Environ. Microbiol. 11, 1327–1329. Although Synergistota have a diderm cell envelope,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 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. 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.Vartoukian, S.R., Palmer, R.M., and Wade, W.G. (2007). The division "Synergistes". Anaerobe. 13, 99–106. 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.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. Species within this phylum have also been implicated in periodontal disease, gastrointestinal infections and soft tissue infections. 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.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. 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. 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
The phylogeny based on the work of the All-Species Living Tree Project.
Taxonomy
The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LSPN) and the National Center for Biotechnology Information (NCBI).
Phylum Synergistota Jumas-Bilak et al. 2021 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)
Phylum Synergistota Jumas-Bilak et al. 2021 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)