Synergistetes

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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
Synonyms
  • Aminanaerobia Hugenholtz
  • Synergistaeota Oren et al. 2015

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[edit]

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[edit]

The phylogeny based on the work of the All-Species Living Tree Project.[11]




Acetomicrobium flavidum (type sp.) [was Bacteroideaceae]


Anaerobaculum

A. hydrogeniformans



A. thermoterrenum






Thermovirga lienii





Aminiphilus circumscriptus



Thermanaerovibrio

T. acidaminovorans (type sp.)



T. velox





Synergistes jonesii


Cloacibacillus

C. evryensis



C. porcorum










Lactivibrio alcoholicus




Aminivibrio pyruvatiphilus



Fretibacterium fastidiosum




Aminobacterium

A. thunnarium




A. colombiense (type sp.)



A. mobile








Jonquetella anthropi



Pyramidobacter piscolens



Dethiosulfovibrio

D. salsuginis




D. peptidovorans (type sp.)




D. acidaminovorans



D. marinus



D. russensis










Taxonomy[edit]

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LSPN)[12] and the National Center for Biotechnology Information (NCBI).[13]

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[edit]

  1. ^ Hugenholtz, P., Hooper, S.D., and Kyrpides, N.C. (2009). Focus: Synergistetes. Environ. Microbiol. 11, 1327–1329.
  2. ^ a b 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. ^ a b 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. ^ a b Sutcliffe, I.C. (2010). "A phylum level perspective on bacterial cell envelope architecture". Trends Microbiol. 18: 464–470. PMID 20637628. doi:10.1016/j.tim.2010.06.005. 
  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. ^ a b c 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. PMC 1594628Freely accessible. PMID 16891512. doi:10.1128/JCM.00568-06. 
  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. ^ a b c d Bhandari, V.; Gupta, R. S. (2012). "Molecular signatures for the phylum Synergistetes and some of its subclades". Antonie Van Leeuwenhoek. 102: 517–40. PMID 22711299. doi:10.1007/s10482-012-9759-2. 
  11. ^ "16S rRNA-based LTP release 123 (full tree)" (PDF). Silva Comprehensive Ribosomal RNA Database. Retrieved 2016-03-20. 
  12. ^ J.P. Euzéby. "Synergistetes". List of Prokaryotic names with Standing in Nomenclature (LPSN). Retrieved 2016-03-20. 
  13. ^ Sayers; et al. "Synergistetes". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2016-03-20.