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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 60, Issue 1

Multilocus sequence analysis of the central clade of the genus by using the 16S rRNA, , , , , and genes Free

Abstract

The central clade of the genus , also called the core group, comprises six species that are tightly related (DNA–DNA reassociation values are very close to 70 % for most species pairs). Identification of novel strains to the species level within this group is troublesome and results are quite often dependent on the methodology employed. Therefore, this group represents an excellent framework to test the robustness of multilocus sequence analysis (MLSA) not only for inferring phylogeny but also as an identification tool without the need for DNA–DNA hybridization assays. The genes selected, 16S rRNA, , , , , and , were amplified by direct PCR from 44 core-group strains. Subsequent analysis allowed us to recognize and as the most resolving individual genes and showed that concatenated sequences of , and were more useful than concatenated sequences of all seven genes. To validate our conclusions, MLSA similarities have been correlated with DNA–DNA relatedness values obtained in this study and values taken from the literature. Although the seven concatenated genes gave the best correlation, the concatenated sequences of , and have the practical advantage of showing a considerable gap between the maximal interspecies similarity and the minimal intraspecies similarity recorded, meaning that they can be used quite conveniently for species identification of vibrios.

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Keyword(s): ML, maximum-likelihood , MLSA, multilocus sequence analysis , MP, maximum-parsimony and NJ, neighbour-joining
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2010-01-01
2024-04-19
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References

  1. Adékambi T., Shinnick T. M., Raoult D., Drancourt M. 2008; Complete rpoB gene sequencing as a suitable supplement to DNA–DNA hybridization for bacterial species and genus delineation. Int J Syst Evol Microbiol 58:1807–1814 [CrossRef]
     [Google Scholar]
  2. Brenner D. J., Fanning G. R., Hickman-Brenner F. W., Steigerwalt A. G., Davis B. R., Farmer J. J. III 1983; DNA relatedness among Vibrionaceae, with emphasis on the Vibrio species associated with human infection. Colloq INSERM 114:175–184
     [Google Scholar]
  3. Dorsch M., Lane D., Stackebrandt E. 1992; Towards a phylogeny of the genus Vibrio based on 16S rRNA sequences. Int J Syst Bacteriol 42:58–63 [CrossRef]
     [Google Scholar]
  4. Goarant C., Reynaud Y., Ansquer D., Decker S. D., Saulnier D., Roux F. l. 2006; Molecular epidemiology of Vibrio nigripulchritudo , a pathogen of cultured penaeid shrimp ( Litopenaeus stylirostris ) in New Caledonia. Syst Appl Microbiol 29:570–580 [CrossRef]
     [Google Scholar]
  5. Gomez-Gil B., Thompson F. L., Thompson C. C., Swings J. 2003; Vibrio rotiferianus sp. nov., isolated from cultures of the rotifer Brachionus plicatilis . Int J Syst Evol Microbiol 53:239–243 [CrossRef]
     [Google Scholar]
  6. Gomez-Gil B., Soto-Rodríguez S., García-Gasca A., Roque A., Vazquez-Juarez R., Thompson F. L., Swings J. 2004; Molecular identification of Vibrio harveyi -related isolates associated with diseased aquatic organisms. Microbiology 150:1769–1777 [CrossRef]
     [Google Scholar]
  7. Le Roux F., Goubet A., Thompson F. L., Faury N., Gay M., Swings J., Saulnier D. 2005; Vibrio gigantis sp. nov., isolated from the haemolymph of cultured oysters ( Crassostrea gigas ). Int J Syst Evol Microbiol 55:2251–2255 [CrossRef]
     [Google Scholar]
  8. Martens M., Delaere M., Coopman R., De Vos P., Gillis M., Willems A. 2007; Multilocus sequence analysis of Ensifer and related taxa. Int J Syst Evol Microbiol 57:489–503 [CrossRef]
     [Google Scholar]
  9. Martens M., Dawyndt P., Coopman R., Gillis M., De Vos P., Willems A. 2008; Advantages of multilocus sequence analysis for taxonomic studies: a case study using 10 housekeeping genes in the genus Ensifer (including former Sinorhizobium ). Int J Syst Evol Microbiol 58:200–214 [CrossRef]
     [Google Scholar]
  10. Martin D. P., Williamson C., Posada D. 2005; RDP2: recombination detection and analysis from sequence alignments. Bioinformatics 21:260–262 [CrossRef]
     [Google Scholar]
  11. Mignard S., Flandrois J. P. 2008; A seven-gene, multilocus, genus-wide approach to the phylogeny of mycobacteria using supertrees. Int J Syst Evol Microbiol 58:1432–1441 [CrossRef]
     [Google Scholar]
  12. Naser S. M., Hagen K. E., Vancanneyt M., Cleenwerck I., Swings J., Tompkins T. A. 2006; Lactobacillus suntoryeus Cachat and Priest 2005 is a later synonym of Lactobacillus helveticus (Orla-Jensen 1919) Bergey et al. 1925 (Approved Lists 1980). Int J Syst Evol Microbiol 56:355–360 [CrossRef]
     [Google Scholar]
  13. Pitcher D. G., Saunders N. A., Owen R. J. 1989; Rapid extraction of bacterial genomic DNA with guanidium thiocyanate. Lett Appl Microbiol 8:151–156 [CrossRef]
     [Google Scholar]
  14. Posada D., Buckley T. R. 2004; Model selection and model averaging in phylogenetics: advantages of the AIC and Bayesian approaches over likelihood ratio tests. Syst Biol 53:793–808 [CrossRef]
     [Google Scholar]
  15. Posada D., Crandall K. A. 1998; Modeltest: testing the model of DNA substitution. Bioinformatics 14:817–818 [CrossRef]
     [Google Scholar]
  16. Pujalte M. J., Sitjà-Bobadilla A., Macián M. C., Belloch C., Álvarez-Pellitero P., Pérez-Sánchez J., Uruburu F., Garay E. 2003; Virulence and molecular typing of Vibrio harveyi strains isolated from cultured dentex, gilthead sea bream and European sea bass. Syst Appl Microbiol 26:284–292 [CrossRef]
     [Google Scholar]
  17. Rameshkumar N., Fukui Y., Sawabe T., Nair S. 2008; Vibrio porteresiae sp. nov., a diazotrophic bacterium isolated from a mangrove-associated wild rice ( Porteresia coarctata Tateoka). Int J Syst Evol Microbiol 58:1608–1615 [CrossRef]
     [Google Scholar]
  18. Reichelt J. L., Baumann P., Baumann L. 1976; Study of genetic relationships among marine species of the genera Beneckea and Photobacterium by means of in vitro DNA/DNA hybridization. Arch Microbiol 110:101–120 [CrossRef]
     [Google Scholar]
  19. Richter D., Postic D., Sertour N., Livey I., Matuschka F. R., Baranton G. 2006; Delineation of Borrelia burgdorferi sensu lato species by multilocus sequence analysis and confirmation of the delineation of Borrelia spielmanii sp. nov. Int J Syst Evol Microbiol 56:873–881 [CrossRef]
     [Google Scholar]
  20. Sawabe T., Kita-Tsukamoto K., Thompson F. L. 2007; Inferring the evolutionary history of vibrios by means of multilocus sequence analysis. J Bacteriol 189:7932–7936 [CrossRef]
     [Google Scholar]
  21. Stackebrandt E., Frederiksen W., Garrity G. M., Grimont P. A. D., Kämpfer P., Maiden M. C. J., Nesme X., Rosselló-Mora R., Swings J. other authors 2002; Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Microbiol 52:1043–1047 [CrossRef]
     [Google Scholar]
  22. Swofford D. L. 2002 paup*: Phylogenetic Analysis Using Parsimony (* and other methods), version 4 Sunderland, MA: Sinauer Associates;
     [Google Scholar]
  23. 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]
  24. Thompson F. L., Gevers D., Thompson C. C., Dawyndt P., Naser S., Hoste B., Munn C. B., Swings J. 2005; Phylogeny and molecular identification of vibrios on the basis of multilocus sequence analysis. Appl Environ Microbiol 71:5107–5115 [CrossRef]
     [Google Scholar]
  25. Thompson F. L., Gomez-Gil B., Ribeiro-Vasconcelos A. T., Sawabe T. 2007; Multilocus sequence analysis reveals that Vibrio harveyi and Vibrio campbellii form distinct species. Appl Environ Microbiol 73:4279–4285 [CrossRef]
     [Google Scholar]
  26. Thompson C. C., Thompson F. L., Vicente A. C. P. 2008; Identification of Vibrio cholerae and Vibrio mimicus by multilocus sequence analysis (MLSA). Int J Syst Evol Microbiol 58:617–621 [CrossRef]
     [Google Scholar]
  27. Urbanczyk H., Ast J. C., Higgins M. J., Carson J., Dunlap P. V. 2007; Reclassification of Vibrio fischeri , Vibrio logei , Vibrio salmonicida and Vibrio wodanis as Aliivibrio fischeri gen.nov., comb. nov., Aliivibrio logei comb. nov., Aliivibrio salmonicida comb. nov. and Aliivibrio wodanis comb. nov. Int J Syst Evol Microbiol 57:2823–2829 [CrossRef]
     [Google Scholar]
  28. Young J. M., Park D. C. 2007; Probable synonymy of the nitrogen-fixing genus Azotobacter and the genus Pseudomonas . Int J Syst Evol Microbiol 57:2894–2901 [CrossRef]
     [Google Scholar]
  29. Ziemke F., Höfle M. G., Lalucat J., Rosselló-Mora R. 1998; Reclassification of Shewanella putrefaciens Owen's genomic group II as Shewanella baltica sp. nov. Int J Syst Bacteriol 48:179–186 [CrossRef]
     [Google Scholar]
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Multilocus sequence analysis of the central clade of the genus Vibrio by using the 16S rRNA, recA, pyrH, rpoD, gyrB, rctB and toxR genes
Int J Syst Evol Microbiol 60, 154 (2010); https://doi.org/10.1099/ijs.0.010702-0
/content/journal/ijsem/10.1099/ijs.0.010702-0
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