1887

Abstract

Three strains of a hitherto unknown, Gram-negative, tiny, anaerobic coccus were collected from human clinical samples originating from skin and soft tissues. The three isolates displayed at least 99.9 % identity in their 16S rRNA gene sequences and more than 99.8 % identity in their gene sequences. The isolates were affiliated to the family , the coccobacillus being the most closely related species, but there was no more than 91.1 % identity in the 16S rRNA gene sequence between this species and the three isolates. Phylogeny based on the 16S rRNA gene confirmed that the three strains represent a novel and robust lineage within the current family . A similar genomic structure was demonstrated for the three isolates by PFGE-based analysis. Morphology and metabolic end products, as well as genotypic and phylogenetic data supported the proposal of the novel genus gen. nov., with the novel species sp. nov. [type strain ADV 07/08/06-B-1388 (=AIP 149.07=CIP 109806=DSM 21255=CCUG 56017) as type species]. Phylogenetic analyses based on the 16S rRNA gene sequences of members of the phylum and other phyla indicated that the family forms a robust lineage clearly separated from those of the classes ‘’, ‘’, and ‘’ in the phylum . Therefore, we propose that this family is a class-level taxon in the phylum , for which the name classis nov. is proposed, based on the Gram-negative type of cell wall of its members, with the type order ord. nov. In this order, a novel family, fam. nov., is proposed and description of the family is emended.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.013102-0
2010-06-01
2024-03-28
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/60/6/1271.html?itemId=/content/journal/ijsem/10.1099/ijs.0.013102-0&mimeType=html&fmt=ahah

References

  1. Alain K., Pignet P., Zbinden M., Quillevere M., Duchiron F., Donval J. P., Lesongeur F., Raguenes G., Crassous P. other authors 2002; Caminicella sporogenes gen. nov., sp. nov., a novel thermophilic spore-forming bacterium isolated from an East-Pacific Rise hydrothermal vent. Int J Syst Evol Microbiol 52:1621–1628 [CrossRef]
    [Google Scholar]
  2. Allardet-Servent A., Michaux-Charachon S., Jumas-Bilak E., Karayan L., Ramuz M. 1993; Presence of one linear and one circular chromosome in the Agrobacterium tumefaciens C58 genome. J Bacteriol 175:7869–7874
    [Google Scholar]
  3. Altschul S. F., Madden T. L., Schäffer A. A., Zhang J., Zhang Z., Miller W., Lipman D. J. 1997; Gapped blast and psi-blast: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402 [CrossRef]
    [Google Scholar]
  4. Bladen H. A., Mergenhagen S. E. 1964; Ultrastructures of Veillonella and morphological correlation of an outer membrane with particles associated with endotoxic activity. J Bacteriol 88:1482–1492
    [Google Scholar]
  5. Carlier J.-P. 1985; Gas chromatography of fermentation products: its application in diagnosis of anaerobic bacteria. Bull Inst Pasteur 83:57–69
    [Google Scholar]
  6. Carlier J.-P., Marchandin H., Jumas-Bilak E., Lorin V., Henry C., Carrière C., Jean-Pierre H. 2002; Anaeroglobus geminatus gen. nov., sp. nov., a novel member of the family Veillonellaceae . Int J Syst Evol Microbiol 52:983–986 [CrossRef]
    [Google Scholar]
  7. Castresana J. 2000; Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 17:540–552 [CrossRef]
    [Google Scholar]
  8. 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]
  9. Cayol J. L., Ducerf S., Patel B. K., Garcia J. L., Thomas P., Ollivier B. 2000; Thermohalobacter berrensis gen. nov., sp. nov., a thermophilic, strictly halophilic bacterium from a solar saltern. Int J Syst Evol Microbiol 50:559–564 [CrossRef]
    [Google Scholar]
  10. Felsenstein J. 1993 phylip (phylogeny inference package), version 3.5c. Distributed by the author. Department of Genome Sciences University of Washington; Seattle, USA:
    [Google Scholar]
  11. Garner M. R., Flint J. F., Russell J. B. 2002; Allisonella histaminiformans gen. nov., sp. nov. A novel bacterium that produces histamine, utilizes histidine as its sole energy source, and could play a role in bovine and equine laminitis. Syst Appl Microbiol 25:498–506 [CrossRef]
    [Google Scholar]
  12. Garrity G. M., Holt J. G. 2001; Taxonomic outline of the Archaea and Bacteria . In Bergey's Manual of Systematic Bacteriology , 2nd edn. vol 1 pp 155–166 Edited by Boone D. R., Castenholz R. W. New York: Springer;
    [Google Scholar]
  13. Gibbons N. E., Murray R. G. E. 1978; Proposals concerning the higher taxa of bacteria. Int J Syst Bacteriol 28:1–6 [CrossRef]
    [Google Scholar]
  14. Grice E. A., Kong H. H., Conlan S., Deming C. B., Davis J., Young A. C., NISC Comparative Sequencing ProgramBouffard G. G., Blakesley R. W. other authors 2009; Topographical and temporal diversity of the human skin microbiome. Science 324:1190–1192 [CrossRef]
    [Google Scholar]
  15. 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]
  16. 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]
  17. Holdeman L. V., Cato E. P., Moore W. E. C. 1977 Anaerobe Laboratory Manual , 4th edn. Blacksburg, VA: Virginia Polytechnic Institute and State University;
    [Google Scholar]
  18. Holt J. G., Krieg N. R., Sneath P. H. A., Staley J. T., Williams S. T. 1994; Anaerobic Gram-negative cocci. In Bergey's Manual of Determinative Bacteriology , 9th edn. pp 347–350 Edited by Holt J. G. Baltimore: Lippincott Williams & Wilkins;
    [Google Scholar]
  19. Jousimies-Somer H. R., Summanen P., Citron D. M., Baron E. J., Wexler H. M., Finegold S. M. 2002 Wadworth-KTL Anaerobic Bacteriology Manual , 6th edn. Belmont, CA, USA: Star Publishing Company;
    [Google Scholar]
  20. Jumas-Bilak E., Carlier J.-P., Jean-Pierre H., Teyssier C., Gay B., Campos J., Marchandin H. 2004; Veillonella montpellierensis sp. nov., a novel, anaerobic, Gram-negative coccus isolated from human clinical samples. Int J Syst Evol Microbiol 54:1311–1316 [CrossRef]
    [Google Scholar]
  21. Jumas-Bilak E., Jean-Pierre H., Carlier J.-P., Teyssier C., Bernard K., Gay B., Campos J., Morio F., Marchandin H. 2005; Dialister micraerophilus sp. nov. and Dialister propionicifaciens sp. nov., isolated from human clinical samples. Int J Syst Evol Microbiol 55:2471–2478 [CrossRef]
    [Google Scholar]
  22. Jumas-Bilak E., Carlier J.-P., Jean-Pierre H., Mory F., Teyssier C., Gay B., Campos J., Marchandin H. 2007; Acidaminococcus intestini sp. nov., isolated from human clinical samples. Int J Syst Evol Microbiol 57:2314–2319 [CrossRef]
    [Google Scholar]
  23. 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 [CrossRef]
    [Google Scholar]
  24. Kalmokoff M. L., Austin J. W., Whitford M. F., Teather R. M. 2000; Characterization of a major envelope protein from the rumen anaerobe Selenomonas ruminantium OB268. Can J Microbiol 46:295–303 [CrossRef]
    [Google Scholar]
  25. Kamio Y., Takahashi H. 1980; Outer membrane proteins and cell surface structure of Selenomonas ruminantium . J Bacteriol 141:899–907
    [Google Scholar]
  26. Liu S.-L., Schryvers A. B., Sanderson K. E., Johnston R. N. 1999; Bacterial phylogenetic clusters revealed by genome structure. J Bacteriol 181:6747–6755
    [Google Scholar]
  27. Ludwig W., Klenk H.-P. 2001; Overview: a phylogenetic backbone and taxonomic framework for procaryotic systematics. In Bergey's Manual of Systematic Bacteriology , 2nd edn. vol 1 pp 49–65 Edited by Boone D. R., Castenholz R. W., Garrity G. M. New York: Springer;
    [Google Scholar]
  28. Ludwig W., Schleifer K. H. 2005; Molecular phylogeny of bacteria based on comparative sequence analysis of conserved genes. In Microbial Phylogeny and Evolution , Concepts and Controversies pp 70–98 Edited by Sapp J. New York: Oxford University Press;
    [Google Scholar]
  29. Ludwig W., Schleifer K.-H., Whitman W. B. 2009; Revised road map to the phylum Firmicutes . In Bergey's Manual of Systematic Bacteriology , 2nd edn, vol. 3 (The Firmicutes ) pp 1–13 Edited by De Vos P., Garrity G., Jones D., Krieg N. R., Ludwig W., Rainey F. A., Schleifer K.-H., Whitman W. B. New York: Springer;
    [Google Scholar]
  30. Males B. M., Berthold P., Dougherty P. A., Listgarten M. A. 1984; Helical flflagellation in Centipeda periodontii , a Gram-negative, anaerobic bacillus from periodontitis lesions. J Gen Microbiol 130:185–191
    [Google Scholar]
  31. Marchandin H., Jumas-Bilak E., Gay B., Teyssier C., Jean-Pierre H., Siméon de Buochberg M., Carrière C., Carlier J.-P. 2003a; Phylogenetic analysis of some Sporomusa sub-branch members isolated from human clinical specimens: description of Megasphaera micronuciformis sp. nov. Int J Syst Evol Microbiol 53:547–553 [CrossRef]
    [Google Scholar]
  32. Marchandin H., Teyssier C., Siméon de Buochberg M., Jean-Pierre H., Carrière C., Jumas-Bilak E. 2003b; Intra-chromosomal heterogeneity between the four 16S rRNA gene copies in the genus Veillonella : implications for phylogeny and taxonomy. Microbiology 149:1493–1501 [CrossRef]
    [Google Scholar]
  33. Prévot A. R. 1933; Etude de systématique bactérienne. I. Lois générales. II. Cocci anaérobius. Ann Sci Nat Zool Biol Anim 15:23–260
    [Google Scholar]
  34. Rogosa M. 1969; Acidaminococcus gen. n., Acidaminococcus fermentans sp. n., anaerobic Gram-negative diplococci using amino acids as the sole energy source for growth. J Bacteriol 98:756–766
    [Google Scholar]
  35. Rogosa M. 1971; Transfer of Veillonella Prévot and Acidaminococcus Rogosa from Neisseriaceae to Veillonellaceae fam. nov. and the inclusion of Megasphaera Rogosa in Veillonellaceae . Int J Syst Bacteriol 21:231–233 [CrossRef]
    [Google Scholar]
  36. Rogosa M. 1984; Anaerobic Gram-negative cocci. In Bergey's Manual of Systematic Bacteriology vol 1 pp 680–685 Edited by Krieg N. R., Holt J. G. Baltimore: Williams & Wilkins;
    [Google Scholar]
  37. Sokolova T., Hanel J., Onyenwoke R. U., Reysenbach A. L., Banta A., Geyer R., Gonzalez J. M., Whitman W. B., Wiegel J. 2007; Novel chemolithotrophic, thermophilic, anaerobic bacteria Thermolithobacter ferrireducens gen.nov., sp. nov. and Thermolithobacter carboxydivorans sp. nov. Extremophiles 11:145–157 [CrossRef]
    [Google Scholar]
  38. Wery N., Moricet J. M., Cueff V., Jean J., Pignet P., Lesongeur F., Cambon-Bonavita M. A., Barbier G. 2001; Caloranaerobacter azorensis gen. nov., sp. nov., an anaerobic thermophilic bacterium isolated from a deep-sea hydrothermal vent. Int J Syst Evol Microbiol 51:1789–1796 [CrossRef]
    [Google Scholar]
  39. Willems A., Collins M. D. 1995; Phylogenetic placement of Dialister pneumosintes (formerly Bacteroides pneumosintes ) within the Sporomusa subbranch of the Clostridium subphylum of the Gram-positive bacteria. Int J Syst Bacteriol 45:403–405 [CrossRef]
    [Google Scholar]
  40. Woese C. R. 1987; Bacterial evolution. Microbiol Rev 51:221–271
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.013102-0
Loading
/content/journal/ijsem/10.1099/ijs.0.013102-0
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Supplementary material 2

PDF

Supplementary material 3

PDF
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