The Synergistota is a phylum of anaerobic bacteria that show Gram-negative staining and have rod/vibrioid cell shape. Although Synergistota have a diderm cell envelope, 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. 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. 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. 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
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 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 Family Acetomicrobiaceae Pradel et al. 2023 Genus Acetomicrobium Soutschek et al. 1985 [Anaerobaculum Rees et al. 1997] Family Aminiphilaceae Pradel et al. 2023 Genus "Aminirhabdus" corrig. Liu et al. 2021 ["Aminirod" (sic] Species ?"A. propionatiphilus" corrig. Liu et al. 2021 Genus Aminiphilus Díaz et al. 2007 Family Aminobacteriaceae Pradel et al. 2023 Genus Aminobacterium Baena et al. 1999 Genus Aminivibrio Honda et al. 2013 Genus Fretibacterium Vartoukian et al. 2013 Genus Lactivibrio Qiu et al. 2014 Family Dethiosulfovibrionaceae Pradel et al. 2023 Genus Dethiosulfovibrio Magot et al. 1997 Genus Jonquetella Jumas-Bilak et al. 2007 Genus Pyramidobacter Downes et al. 2009 Genus Rarimicrobium Jumas-Bilak et al. 2015 Family Synergistaceae Jumas-Bilak et al. 2009 [Clostridiales Family XV; Thermosynergistaceae Yang et al. 2021] Genus Aminomonas Baena et al. 1999 Genus "Candidatus Caccocola" Gilroy et al. 2021 Genus ?Caenicola El Houari et al. 2025 Genus Cloacibacillus Ganesan et al. 2008 emend. 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 Genus Thermanaerovibrio Baena et al. 1999 emend. Palaniappan et al. 2013 Family Thermosynergistaceae Yang et al. 2021 Genus Thermosynergistes Yang et al. 2021 Family Thermovirgaceae Pradel et al. 2023 Genus Thermovirga Dahle and Birkeland 2006
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