Synergistota

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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]

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

The phylogeny based on the work of the All-Species Living Tree Project.^[12]

Taxonomy

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LSPN)^[13] and the National Center for Biotechnology Information (NCBI).^[14]

• 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)

References