# Synergistota

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

| 16S rRNA based LTP_10_2024 | 120 marker proteins based GTDB 09-RS220 |
| Synergistota Aminithiophilaceae Aminithiophilus ramosus Pradel et al. 2023 Thermovirgaceae Thermovirga lienii Dahle and Birkeland 2006 Thermosynergistaceae Thermosynergistes pyruvativorans Yang et al. 2021 Acetomicrobaceae Acetomicrobium A. flavidum Soutschek et al. 1985 A. mobile (Menes & Muxi 2002) Ben Hania et al. 2016 A. hydrogeniformans (Maune & Tanner 2012) Ben Hania et al. 2016 A. thermoterrenum (Rees et al. 1997) Ben Hania et al. 2016 Aminiphilaceae Aminiphilus circumscriptus Díaz et al. 2007 Synergistaceae Aminomonas paucivorans Baena et al. 1999 Thermanaerovibrio T. acidaminovorans (Guangsheng et al. 1997) Baena et al. 1999 T. velox Zavarzina et al. 2000 Synergistes jonesii Allison et al. 1993 Cloacibacillus C. evryensis Ganesan et al. 2008 C. porcorum Looft et al. 2013 Aminivibrionaceae Lactivibrio alcoholicus Qiu et al. 2014 Aminivibrio pyruvatiphilus Honda et al. 2013 Fretibacterium fastidiosum Vartoukian et al. 2013 Aminobacterium A. thunnarium Hamdi et al. 2015 A. colombiense Baena et al. 1999 (type sp.) A. mobile Baena et al. 2000 Dethiosulfovibrionaceae Jonquetella anthropi Jumas-Bilak et al. 2007 Rarimicrobium hominis Jumas-Bilak et al. 2015 Pyramidobacter P. piscolens Downes et al. 2009 P. porci Wylensek et al. 2021 Dethiosulfovibrio D. salsuginis Díaz-Cárdenas et al. 2010 D. faecalis Grabowski et al. 2022 D. peptidovorans Magot et al. 1997 (type sp.) D. marinus Surkov et al. 2001 D. acidaminovorans Surkov et al. 2001 D. russensis Surkov et al. 2001 | Synergistota Thermosynergistaceae Thermosynergistes pyruvativorans Acetomicrobiaceae Acetomicrobium A. flavidum A. thermoterrenum [incl. A. hydrogeniformans] Thermovirgaceae Thermovirga lienii Aminiphilaceae Aminiphilus circumscriptus Aminithiophilaceae Aminithiophilus ramosus Synergistaceae Aminomonas paucivorans Thermanaerovibrio T. acidaminovorans T. velox Synergistes jonesii "Ca. Caccocola" "Ca. C. faecigallinarum" Gilroy et al. 2021 "Ca. C. faecipullorum" Gilroy et al. 2021 Cloacibacillus C. evryensis C. porcorum Aminobacteriaceae Aminivibrio pyruvatiphilus Fretibacterium fastidiosum Aminobacterium A. colombiense A. mobile Dethiosulfovibrionaceae Jonquetella anthropi Pyramidobacter P. piscolens P. porci Dethiosulfovibrio D. salsuginis D. faecalis D. peptidovorans D. russensis |

## 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 "Aminirod" Liu et al. 2021
****** Species ?"A. propionatiphilus" 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 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