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Synergistetes
The Synergistetes is a recently recognized 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 Synergistetes 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 Synergistetes, indicating that they may have an atypical outer cell envelope.〔〔 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.〔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 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.〔〔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 Synergistetes 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 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. 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.〔 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 Synergistetes into intermediate taxonomic ranks such as families and orders.〔
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