1887

International Journal of Systematic and Evolutionary Microbiology

Volume 59, Issue 9

Partial sequence comparison of the , , and genes within the genus Free

Abstract

Phylogenetic analysis and species identification of members of the genus were carried out using partial sequence comparison of the 16S rRNA gene (1468–1478 bp), , encoding the subunit of RNA polymerase (659–680 bp), , encoding the manganese-dependent superoxide dismutase (435–462 bp), , encoding the 60 kDa heat-shock protein (757 bp), and , encoding the Β subunit of DNA gyrase (458–461 bp). For the first time, most species within the genus were represented in the study (65 strains, representing 58 species and nine subspecies). Phylogenies inferred from , , and sequence comparisons were more discriminative than those inferred from 16S rRNA gene sequence comparison, and showed common clusters. The minimal interspecies divergence was 0.3, 2.7, 0, 2.5 and 3.4 % for the 16S rRNA gene, , , and , respectively. In general, partial gene sequence comparison represented the best tool for identifying species and subspecies and for phylogenetic analysis.

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2009-09-01
2020-09-30
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References

  1. Bentley, R. W., Leigh, J. A. & Collins, M. D. ( 1991; ). Intrageneric structure of Streptococcus based on comparative analysis of small-subunit rRNA sequences. Int J Syst Bacteriol 41, 487–494.[CrossRef]
    [Google Scholar]
  2. Blaiotta, G., Fusco, V., Ercolini, D., Aponte, M., Pepe, O. & Villani, F. ( 2008; ). Lactobacillus strain diversity based on partial hsp60 gene sequences and design of PCR-restriction fragment length polymorphism assays for species identification and differentiation. Appl Environ Microbiol 74, 208–215.[CrossRef]
    [Google Scholar]
  3. Chang, Y. H., Shangkuan, Y. H., Lin, H. C. & Liu, H. W. ( 2003; ). PCR assay of the groEL gene for detection and differentiation of Bacillus cereus group cells. Appl Environ Microbiol 69, 4502–4510.[CrossRef]
    [Google Scholar]
  4. Drancourt, M., Roux, V., Fournier, P. E. & Raoult, D. ( 2004; ). rpoB gene sequence-based identification of aerobic Gram-positive cocci of the genera Streptococcus, Enterococcus, Gemella, Abiotrophia and Granulicatella. J Clin Microbiol 42, 497–504.[CrossRef]
    [Google Scholar]
  5. Facklam, R. ( 2002; ). What happened to the streptococci: overview of taxonomic and nomenclature changes. Clin Microbiol Rev 15, 613–630.[CrossRef]
    [Google Scholar]
  6. Farris, J. S. ( 1970; ). Methods for computing Wagner trees. Syst Zool 19, 83–92.[CrossRef]
    [Google Scholar]
  7. Felsenstein, J. ( 1989; ). phylip – phylogeny inference package (version 3.2). Cladistics 5, 164–166.
     [Google Scholar]
  8. Fukushima, M., Kakinuma, K. & Kawaguchi, R. ( 2002; ). Phylogenetic analysis of Salmonella, Shigella, and Escherichia coli strains on the basis of the gyrB gene sequence. J Clin Microbiol 40, 2779–2785.[CrossRef]
    [Google Scholar]
  9. Garnier, F., Gerbaud, G., Courvalin, P. & Galimand, M. ( 1997; ). Identification of clinically relevant viridans group streptococci to the species level by PCR. J Clin Microbiol 35, 2337–2341.
     [Google Scholar]
  10. Gil, R., Silva, F. J., Pereto, J. & Moya, A. ( 2004; ). Determination of the core of a minimal bacterial gene set. Microbiol Mol Biol Rev 68, 518–537.[CrossRef]
    [Google Scholar]
  11. Holmes, D. E., Nevin, K. P. & Lovley, D. R. ( 2004; ). Comparison of 16S rRNA, nifD, recA, gyrB, rpoB and fusA genes within the family Geobacteraceae fam. nov. Int J Syst Evol Microbiol 54, 1591–1599.[CrossRef]
    [Google Scholar]
  12. Hoshino, T., Fujiwara, T. & Kilian, M. ( 2005; ). Use of phylogenetic and phenotypic analyses to identify nonhemolytic streptococci isolated from bacteremic patients. J Clin Microbiol 43, 6073–6085.[CrossRef]
    [Google Scholar]
  13. Hung, W. C., Tsai, J. C., Hsueh, P. R., Chia, J. S. & Teng, L. J. ( 2005; ). Species identification of mutans streptococci by groESL gene sequence. J Med Microbiol 54, 857–862.[CrossRef]
    [Google Scholar]
  14. Igarashi, T., Ichikawa, K., Yamamoto, A. & Goto, N. ( 2001; ). Identification of mutans streptococcal species by the PCR products of the dex genes. J Microbiol Methods 46, 99–105.[CrossRef]
    [Google Scholar]
  15. Itoh, Y., Kawamura, Y., Kasai, H., Shah, M. M., Nhung, P. H., Yamada, M., Sun, X., Koyana, T., Hayashi, M. & other authors ( 2006; ). dnaJ and gyrB gene sequence relationship among species and strains of genus Streptococcus. Syst Appl Microbiol 29, 368–374.[CrossRef]
    [Google Scholar]
  16. Kärenlampi, R. I., Tolvanen, T. P. & Hänninen, M. L. ( 2004; ). Phylogenetic analysis and PCR-restriction fragment length polymorphism identification of Campylobacter species based on partial groEL gene sequences. J Clin Microbiol 42, 5731–5738.[CrossRef]
    [Google Scholar]
  17. Kawamura, Y., Whiley, R. A., Shu, S. E., Ezaki, T. & Hardie, J. M. ( 1999; ). Genetic approaches to the identification of the mitis group within the genus Streptococcus. Microbiology 145, 2605–2613.
     [Google Scholar]
  18. Kawamura, Y., Itoh, Y., Mishima, N., Ohkusu, K., Kasai, H. & Ezaki, T. ( 2005; ). High genetic similarity of Streptococcus agalactiae and Streptococcus difficilis: S. difficilis Eldar et al. 1995 is a later synonym of S. agalactiae Lehmann and Neumann 1896 (Approved Lists 1980). Int J Syst Evol Microbiol 55, 961–965.[CrossRef]
    [Google Scholar]
  19. Kimura, M. ( 1980; ). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16, 111–120.[CrossRef]
    [Google Scholar]
  20. Küpfer, M., Kuhnert, P., Korczak, B. M., Peduzzi, R. & Demarta, A. ( 2006; ). Genetic relationships of Aeromonas strains inferred from 16S rRNA, gyrB and rpoB gene sequences. Int J Syst Evol Microbiol 56, 2743–2751.[CrossRef]
    [Google Scholar]
  21. Lee, J. H., Park, H. S., Jang, W. J., Koh, S. E., Kim, J. M., Shim, S. K., Park, M. Y., Kim, Y. W., Kim, B. J. & other authors ( 2003; ). Differentiation of rickettsiae by groEL gene analysis. J Clin Microbiol 41, 2952–2960.[CrossRef]
    [Google Scholar]
  22. 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]
  23. Naser, S. M., Dawyndt, P., Hoste, B., Gevers, D., Vandemeulebroecke, K., Cleenwerck, L., Vancanneyt, M. & Swings, J. ( 2007; ). Identification of lactobacilli by pheS and rpoA gene sequence analyses. Int J Syst Evol Microbiol 57, 2777–2789.[CrossRef]
    [Google Scholar]
  24. Picard, F. J., Ke, D., Boudreau, D. K., Boissinot, M., Huletsky, A., Richard, D., Ouellette, M., Roy, P. H. & Bergeron, M. G. ( 2004; ). Use of tuf sequences for genus-specific PCR detection and phylogenetic analysis of 28 streptococcal species. J Clin Microbiol 42, 3686–3695.[CrossRef]
    [Google Scholar]
  25. Poyart, C., Quesne, G., Coulon, S., Berche, P. & Trieu-Cuot, P. ( 1998; ). Identification of streptococci to species level by sequencing the gene encoding the manganese-dependent superoxide dismutase. J Clin Microbiol 36, 41–47.
     [Google Scholar]
  26. Radice, F., Orlandi, V., Massa, V., Cavalca, L., Demarta, A., Wood, T. K. & Barbieri, P. ( 2006; ). Genotypic characterization and phylogenetic relations of Pseudomonas sp. (formerly P. stutzeri) OX1. Curr Microbiol 52, 395–399.[CrossRef]
    [Google Scholar]
  27. Saitou, N. & Nei, M. ( 1987; ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425.
     [Google Scholar]
  28. Schlegel, L., Grimont, F., Ageron, E., Grimont, P. A. D. & Bouvet, A. ( 2003; ). Reappraisal of the taxonomy of the Streptococcus bovis/Streptococcus equinus complex and related species: description of Streptococcus gallolyticus subsp. gallolyticus subsp. nov., S. gallolyticus subsp. macedonicus subsp. nov. and S. gallolyticus subsp. pasteurianus subsp. nov. Int J Syst Evol Microbiol 53, 631–645.[CrossRef]
    [Google Scholar]
  29. 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]
  30. 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]
  31. Tapp, J., Thollesson, M. & Herrmann, B. ( 2003; ). Phylogenetic relationships and genotyping of the genus Streptococcus by sequence determination of the RNase P RNA gene, rnpB. Int J Syst Evol Microbiol 53, 1861–1871.[CrossRef]
    [Google Scholar]
  32. Teng, L. J., Hsueh, P. R., Tsai, J. C., Chen, P. W., Hsu, J. C., Lai, H. C., Lee, C. N. & Ho, S. W. ( 2002; ). groESL sequence determination, phylogenetic analysis, and species differentiation for viridans group streptococci. J Clin Microbiol 40, 3172–3178.[CrossRef]
    [Google Scholar]
  33. 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]
  34. Weisburg, W. G., Barns, S. M., Pelletier, D. A. & Lane, D. J. ( 1991; ). 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173, 697–703.
     [Google Scholar]
  35. Zeigler, D. R. ( 2003; ). Gene sequences useful for predicting relatedness of whole genomes in bacteria. Int J Syst Evol Microbiol 53, 1893–1900.[CrossRef]
    [Google Scholar]
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Partial sequence comparison of the rpoB, sodA, groEL and gyrB genes within the genus Streptococcus
Int J Syst Evol Microbiol 59, 2317 (2009); https://doi.org/10.1099/ijs.0.005488-0
/content/journal/ijsem/10.1099/ijs.0.005488-0
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Supplements

vol. , part 9, pp. 2317 - 2322

Strains used in this study and nucleotide sequence accession numbers.

Primers for PCR and sequencing of and genes.

Phylogenetic tree of members of the genus inferred from comparison of 16S rRNA gene sequences using the neighbour-joining method.

Phylogenetic trees of members of the genus inferred from comparison of partial , and gene sequences using the neighbour-joining method.

Schematic representation of similarity between different species for each gene studied.

[PDF file of Supplementary Tables and Figures](233 KB)

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