The number of bacterial phyla has greatly increased in the past decade. Among them, a candidate division named ‘’ was proposed in a phylogenetic study on the global diversity of bacteria. We previously described the genus and suggested that it belonged to this not yet well-delineated candidate phylum. 16S rRNA gene based-phylogeny studies were conducted using four reconstruction methods and 599 sequences forming five datasets were used in an alternative treeing approach. These analyses indicated that the genera , , , , , , , and should be grouped in the same high-level taxon. This taxon was shown to be a phylum-rank lineage in the domain and, because of the prior use of the name for a genus, the name ‘’ is proposed for this candidate phylum. We also propose an emended delineation of the phylum ‘’, which is now only represented by the family . The emended family is limited to the genera , , and .


Article metrics loading...

Loading full text...

Full text loading...



  1. Allison, M. J., Mayberry, W. R., McSweeney, C. S. & Stahl, D. A.(1992).Synergistes jonesii, gen. nov., sp. nov.: a rumen bacterium that degrades toxic pyridinediols. Syst Appl Microbiol 15, 522–529.[CrossRef] [Google Scholar]
  2. Baena, S., Fardeau, M. L., Ollivier, B., Labat, M., Thomas, P., Garcia, J. L. & Patel, B. K. C.(1999).Aminomonas paucivorans gen. nov., sp. nov., a mesophilic, anaerobic, amino-acid-utilizing bacterium. Int J Syst Bacteriol 49, 975–982.[CrossRef] [Google Scholar]
  3. Baena, S., Fardeau, M. L., Labat, M., Ollivier, B., Garcia, J. L. & Patel, B. K. C.(2000).Aminobacterium mobile sp. nov., a new anaerobic amino-acid degrading bacterium. Int J Syst Evol Microbiol 50, 259–264.[CrossRef] [Google Scholar]
  4. Caccavo, F., Jr, Coates, J. D., Rossello-Mora, R. A., Ludwig, W., Schleifer, K. H., Lovley, D. R. & McInerney, M. J.(1996).Geovibrio ferrireducens, a phylogenetically distinct dissimilatory Fe(III)-reducing bacterium. Arch Microbiol 165, 370–376.[CrossRef] [Google Scholar]
  5. Cavalier-Smith, T.(2002). The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification. Int J Syst Evol Microbiol 52, 7–76. [Google Scholar]
  6. Cayol, J. L., Ollivier, B., Patel, B. K. C., Ravot, G., Magot, M., Ageron, E., Grimont, P. A. D. & Garcia, J. L.(1995). Description of Thermoanaerobacter brockii subsp. lactiethylicus subsp. nov., isolated from a deep subsurface french oil well, a proposal to reclassify Thermoanaerobacter finnii as Thermoanaerobacter brockii subsp. finnii comb. nov., and an emended description of Thermoanaerobacter brockii. Int J Syst Bacteriol 45, 783–789.[CrossRef] [Google Scholar]
  7. Dahle, H. & Birkeland, N. K.(2006).Thermovirga lienii gen. nov., sp. nov., a novel moderately thermophilic, anaerobic, amino-acid-degrading bacterium isolated from a North Sea oil well. Int J Syst Evol Microbiol 56, 1539–1545.[CrossRef] [Google Scholar]
  8. Dalevi, D., Hugenholtz, P. & Blackall, L. L.(2001). A multiple-outgroup approach to resolving division-level phylogenetic relationships using 16S rDNA data. Int J Syst Evol Microbiol 51, 385–391. [Google Scholar]
  9. DeSantis, T. Z., Hugenholtz, P., Larsen, N., Rojas, M., Brodie, E. L., Keller, K., Huber, T., Dalevi, D., Hu, P. & Andersen, G. L.(2006). Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with arb. Appl Environ Microbiol 72, 5069–5072.[CrossRef] [Google Scholar]
  10. Díaz, C., Baena, S., Fardeau, M. L. & Patel, B. K.(2007).Aminiphilus circumscriptus gen. nov., sp. nov., an anaerobic amino-acid-degrading bacterium from an up-flow anaerobic sludge reactor. Int J Syst Evol Microbiol 57, 1914–1918.[CrossRef] [Google Scholar]
  11. Felsenstein, J.(1984). Distance methods for inferring phylogenies: a justification. Evolution 38, 16–24.[CrossRef] [Google Scholar]
  12. Fiala, G., Woese, C. R., Langworthy, T. A. & Stetter, K. O.(1990).Flexistipes sinusarabici a novel genus and species of eubacteria occurring in the Atlantis II Deep brines of the Red Sea. Arch Microbiol 154, 120–126.[CrossRef] [Google Scholar]
  13. Garrity, G. M., Bell, J. A. & Lilburn, T. G.(2004). Taxonomic outline of the Prokaryotes. Bergey's Manual of Systematic Bacteriology, 2nd edition, Release 5.0. New York: Springer
  14. Gorlenko, V., Tsapin, A., Namsaraev, Z., Teal, T., Tourova, T., Engler, D., Mielke, R. & Nealson, K.(2004).Anaerobranca californiensis sp. nov., an anaerobic, alkalithermophilic, fermentative bacterium isolated from a hot spring on Mono Lake. Int J Syst Evol Microbiol 54, 739–743.[CrossRef] [Google Scholar]
  15. Greene, A. C., Patel, B. K. & Sheehy, A. J.(1997).Deferribacter thermophilus gen. nov., sp. nov., a novel thermophilic manganese- and iron-reducing bacterium isolated from a petroleum reservoir. Int J Syst Bacteriol 47, 505–509.[CrossRef] [Google Scholar]
  16. Guindon, S. & Gascuel, O.(2003). A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52, 696–704.[CrossRef] [Google Scholar]
  17. Gupta, R. S.(1998). Protein phylogenies and signature sequences: a reappraisal of evolutionary relationships among archaebacteria, eubacteria, and eukaryotes. Microbiol Mol Biol Rev 62, 1435–1491. [Google Scholar]
  18. Huang, C. Y., Patel, B. K., Mah, R. A. & Baresi, L.(1998).Caldicellulosiruptor owensensis sp. nov., an anaerobic, extremely thermophilic, xylanolytic bacterium. Int J Syst Bacteriol 48, 91–97.[CrossRef] [Google Scholar]
  19. Hugenholtz, P., Goebel, B. M. & Pace, N. R.(1998). Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol 180, 4765–4774. [Google Scholar]
  20. Jumas-Bilak, E., Carlier, J. P., Jean-Pierre, H., Citron, D., Bernard, K. A., Damay, A., Gay, C., 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.[CrossRef] [Google Scholar]
  21. Ludwig, W., Strunk, O., Westram, R., Richter, L., Meier, H., Yadhukumar, Buchner, A., Lai, T., Steppi, S. & other authors(2004).arb: a software environment for sequence data. Nucleic Acids Res 32, 1363–1371.[CrossRef] [Google Scholar]
  22. Magot, M., Ravot, G., Campaignolle, X., Ollivier, B., Patel, B. K. C., Fardeau, M.-L., Thomas, P., Crolet, J.-L. & Garcia, J.-L.(1997).Dethiosulfovibrio peptidovorans gen. nov., sp. nov., a new anaerobic, slightly halophilic, thiosulfate-reducing bacterium from corroding offshore oil wells. Int J Syst Bacteriol 47, 818–824.[CrossRef] [Google Scholar]
  23. McInerney, M. J., Bryant, M. P., Hespell, R. B. & Costerton, J. W.(1981).Syntrophomonas wolfei gen. nov. sp. nov., an anaerobic, syntrophic, fatty acid-oxidizing bacterium. Appl Environ Microbiol 41, 1029–1039. [Google Scholar]
  24. Menes, R. J. & Muxi, L.(2002).Anaerobaculum mobile sp. nov., a novel anaerobic, moderately thermophilic, peptide-fermenting bacterium that uses crotonate as an electron acceptor, and emended description of the genus Anaerobaculum. Int J Syst Evol Microbiol 52, 157–164. [Google Scholar]
  25. Myhr, S. & Torsvik, T.(2000).Denitrovibrio acetophilus, a novel genus and species of dissimilatory nitrate-reducing bacterium isolated from an oil reservoir model column. Int J Syst Evol Microbiol 50, 1611–1619.[CrossRef] [Google Scholar]
  26. Posada, D. & Crandall, K. A.(1998).modeltest: testing the model of DNA substitution. Bioinformatics 14, 817–818.[CrossRef] [Google Scholar]
  27. Ronquist, F. & Huelsenbeck, J. P.(2003). MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19, 1572–1574.[CrossRef] [Google Scholar]
  28. Sekiguchi, Y., Kamagata, Y., Nakamura, K., Ohashi, A. & Harada, H.(2000).Syntrophothermus lipocalidus gen. nov., sp. nov., a novel thermophilic, syntrophic, fatty-acid-oxidizing anaerobe which utilizes isobutyrate. Int J Syst Evol Microbiol 50, 771–779.[CrossRef] [Google Scholar]
  29. Sokolova, T. G., Kostrikina, N. A., Chernyh, N. A., Tourova, T. P., Kolganova, T. V. & Bonch-Osmolovskaya, E. A.(2002).Carboxydocella thermautotrophica gen. nov., sp. nov., a novel anaerobic, CO-utilizing thermophile from a Kamchatkan hot spring. Int J Syst Evol Microbiol 52, 1961–1967.[CrossRef] [Google Scholar]
  30. Surkov, A. V., Dubinina, G. A., Lysenko, A. M., Glöckner, F. O. & Kuever, J.(2001).Dethiosulfovibrio russensis sp. nov., Dethiosulfovibrio marinus sp. nov., and Dethiosulfovibrio acidaminovorans sp. nov., novel anaerobic thiosulfate- and sulfur-reducing bacteria isolated from “Thidendron” sulfur mats in different saline environments. Int J Syst Evol Microbiol 51, 327–337. [Google Scholar]
  31. Svetlitshnyi, V., Rainey, F. & Wiegel, J.(1996).Thermosyntropha lipolytica gen. nov., sp. nov., a lipolytic, anaerobic, alkalitolerant, thermophilic bacterium utilizing short- and long-chain fatty acids in syntrophic coculture with a methanogenic archaeum. Int J Syst Bacteriol 46, 1131–1137.[CrossRef] [Google Scholar]
  32. Takai, K., Inoue, A. & Horikoshi, K.(1999).Thermaerobacter marianensis gen. nov., sp. nov., an aerobic extremely thermophilic marine bacterium from the 11,000 m deep Mariana Trench. Int J Syst Bacteriol 49, 619–628.[CrossRef] [Google Scholar]
  33. Tamura, K., Dudley, J., Nei, M. & Kumar, S.(2007).mega4: Molecular Evolutionary Genetics Analysis (mega) software version 4.0. Mol Biol Evol 24, 1596–1599.[CrossRef] [Google Scholar]
  34. Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F. & Higgins, D. G.(1997). The clustal_x windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25, 4876–4882.[CrossRef] [Google Scholar]
  35. Wu, C., Liu, X. & Dong, X.(2006a).Syntrophomonas erecta subsp. sporosyntropha subsp. nov., a spore-forming bacterium that degrades short chain fatty acids in co-culture with methanogens. Syst Appl Microbiol 29, 457–462.[CrossRef] [Google Scholar]
  36. Wu, C., Liu, X. & Dong, X.(2006b).Syntrophomonas cellicola sp. nov., a spore-forming syntrophic bacterium isolated from a distilled-spirit-fermenting cellar, and assignment of Syntrophospora bryantii to Syntrophomonas bryantii comb. nov. Int J Syst Evol Microbiol 56, 2331–2335.[CrossRef] [Google Scholar]
  37. Zavarzina, D. G., Zhilina, T. N., Tourova, T. P., Kuznetsov, B. B., Kostrikina, N. A. & Bonch-Osmolovskaya, E. A.(2000).Thermanaerovibrio velox sp. nov., a new anaerobic, thermophilic, organotrophic bacterium that reduces elemental sulfur, and emended description of the genus Thermanaerovibrio. Int J Syst Evol Microbiol 50, 1287–1295.[CrossRef] [Google Scholar]
  38. Zhao, H., Yang, D., Woese, C. R. & Bryant, M. P.(1993). Assignment of fatty acid-β-oxidizing syntrophic bacteria to Syntrophomonadaceae fam. nov. on the basis of 16S rRNA sequence analyses. Int J Syst Bacteriol 43, 278–286.[CrossRef] [Google Scholar]

Data & Media loading...


ML 16S rRNA gene-based phylogenetic trees reconstructed from the five datasets described in Supplementary Table S1. [PDF](653 KB)


Composition of the datasets. 1, 2, 3, 4 and 5 are the five datasets. (+) indicates that a sequence is a member of the corresponding dataset. [excel]


Most cited this month Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error