Negativicoccus succinicivorans gen. nov., sp. nov., isolated from human clinical samples, emended description of the family Veillonellaceae and description of Negativicutes classis nov., Selenomonadales ord. nov. and Acidaminococcaceae fam. nov. in the bacterial phylum Firmicutes

International Journal of Systematic and Evolutionary Microbiology

Volumn 60, Issue 6, 2010, Pages 1271-1279

  Marchandin, Hélène ^a,b   Teyssier, Corinne ^a   Campos, Josiane ^b   Jean Pierre, Hélène ^a,b   Roger, Frédéric ^a   Gay, Bernard ^a   Carlier, Jean Philippe ^c   Jumas Bilak, Estelle ^a  

^a UNIV MONTPELLIER   (France)

^b HÔPITAL ARNAUD DE VILLENEUVE   (France)

^c INSTITUT PASTEUR   (France)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN DNAK; RNA 16S;

ACIDAMINOCOCCACEAE; ARTICLE; BACTERIAL CELL WALL; BACTERIAL GENE; BACTERIAL STRAIN; BACTERIUM ISOLATION; FIRMICUTES; GENE SEQUENCE; GENE STRUCTURE; GENOTYPE; GRAM NEGATIVE BACTERIUM; HUMAN; NEGATIVICOCCUS SUCCINICIVORANS; NEGATIVICUTES CLASSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; PHENOTYPE; PHYLOGENY; PRIORITY JOURNAL; SELENOMONADALES; SKIN; SOFT TISSUE; UNINDEXED SEQUENCE;

ACIDAMINOCOCCACEAE; BASE COMPOSITION; DNA, BACTERIAL; DNA, RIBOSOMAL; GRAM-NEGATIVE BACTERIA; HUMANS; MOLECULAR SEQUENCE DATA; PHYLOGENY; RNA, RIBOSOMAL, 16S;

ACIDAMINOCOCCACEAE; BACILLI (CLASS); BACTERIA (MICROORGANISMS); CLOSTRIDIA; DIALISTER MICRAEROPHILUS; FIRMICUTES; NEGIBACTERIA;

EID: 77953297034     PISSN: 14665026     EISSN: None     Source Type: Journal    
DOI: 10.1099/ijs.0.013102-0     Document Type: Article

References (40)

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.
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. (Pubitemid 24004393)
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. (Pubitemid 27359211)
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.
5. Carlier, J.-P. (1985). Gas chromatography of fermentation products: its application in diagnosis of anaerobic bacteria. Bull Inst Pasteur 83, 57-69.
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.
7. Castresana, J. (2000). Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 17, 540-552.
8. Cavalier-Smith, T. (2002). The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial mega-classification. Int J Syst Evol Microbiol 52, 7-76.
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. (Pubitemid 30167499)
10. Felsenstein, J. (1993). PHYLIP (phylogeny inference package), version 3.5c. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle, USA.
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.
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 D. R. Boone & R. W. Castenholz. New York: Springer.
13. Gibbons, N. E. & Murray, R. G. E. (1978). Proposals concerning the higher taxa of bacteria. Int J Syst Bacteriol 28, 1-6.
14. Grice, E. A., Kong, H. H., Conlan, S., Deming, C. B., Davis, J., Young, A. C., NISC Comparative Sequencing Program, Bouffard, G. G., Blakesley, R. W. & other authors (2009). Topographical and temporal diversity of the human skin microbiome. Science 324, 1190-1192.
15. Guindon, S. & Gascuel, O. (2003). A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52, 696-704.
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.
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.
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 J. G. Holt. Baltimore: Lippincott Williams & Wilkins.
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.
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.
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.
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. (Pubitemid 350031708)
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.
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.
25. Kamio, Y. & Takahashi, H. (1980). Outer membrane proteins and cell surface structure of Selenomonas ruminantium. J Bacteriol 141, 899-907.
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.
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 D. R. Boone, R. W. Castenholz & G. M. Garrity. New York: Springer.
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 J. Sapp. New York: Oxford University Press.
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 P. De Vos, G. Garrity, D. Jones, N. R. Krieg, W. Ludwig, F. A. Rainey, K.-H. Schleifer & W. B. Whitman. New York: Springer.
30. Males, B. M., Berthold, P., Dougherty, P. A. & Listgarten, M. A. (1984). Helical flagellation in Centipeda periodontii, a Gram-negative, anaerobic bacillus from periodontitis lesions. J Gen Microbiol 130, 185-191. (Pubitemid 14188296)
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.
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. (Pubitemid 36764072)
33. Prévot, A. R. (1933). Etude de systématique bactérienne. I. Lois générales. II. Cocci anaérobius. Ann Sci Nat Zool Biol Anim 15, 23-260.
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.
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.
36. Rogosa, M. (1984). Anaerobic Gram-negative cocci. In Bergey's Manual of Systematic Bacteriology, vol. 1, pp. 680-685. Edited by N. R. Krieg & J. G. Holt. Baltimore: Williams & Wilkins.
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.
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. (Pubitemid 32899215)
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.
40. Woese, C. R. (1987). Bacterial evolution. Microbiol Rev 51, 221-271.