1887

Abstract

is a species of considerable industrial and medical interest. To date, the lack of reliable molecular methods for definite identification at strain level has hindered studies of the population biology of this organism. Here, a multilocus sequence typing (MLST) system for this organism is described, which exploits the genetic variation present in six housekeeping loci to determine the genetic relationship among isolates. The MLST system was established using 16 strains that were also characterized by ribotyping and restriction fragment length polymorphism (RFLP) analysis of the PCR-amplified 16S–23S rDNA intergenic spacer region (ISR). Ribotyping grouped the strains into four groups; however, RFLP analysis of the ISRs showed no differences in the strains analysed. In contrast, MLST had a good discriminatory ability. The sequence analysis of the six genes showed 14 different allelic combinations, with 12 of them represented by only one strain. By using this MLST approach we were able to confirm the identity of two strains deposited in the Spanish Type Culture Collection as different strains. Phylogenetic analysis indicated a panmictic population structure of and split decomposition analysis indicated that recombination plays a role in creating genetic heterogeneity in . As MLST allows precise identification, and easy comparison and exchange of results obtained in different laboratories, the future application of this new molecular method could be useful for the identification of valuable strains.

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2006-01-01
2019-10-24
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References

  1. Abazinge, M. D. A., Fontenot, J. P., Allen, V. G. & Flick, G. J. ( 1993; ). Ensiling characteristics of crab waste and wheat straw treated with different additives. J Agric Food Chem 41, 657–661.[CrossRef]
    [Google Scholar]
  2. De las Rivas, B., Marcobal, A. & Muñoz, R. ( 2004; ). Allelic diversity and population structure in Oenococcus oeni as determined from sequence analysis of housekeeping genes. Appl Environ Microbiol 70, 7210–7219.[CrossRef]
    [Google Scholar]
  3. Dingle, K. E., Colles, F. M., Wareing, D. R. A. & 7 other authors ( 2001; ). Multilocus sequence typing system for Campylobacter jejuni. J Clin Microbiol 39, 14–23.[CrossRef]
    [Google Scholar]
  4. Elegado, F. B., Guerra, M. A. R. V., Macayan, R. A., Mendoza, H. A. & Lizaran, M. B. ( 2004; ). Spectrum of bacteriocin activity of Lactobacillus plantarum BS and fingerprinting by RAPD-PCR. Int J Food Microbiol 95, 11–18.[CrossRef]
    [Google Scholar]
  5. Enright, M. C. & Spratt, B. G. ( 1998; ). A multilocus sequence typing scheme for Streptococcus pneumoniae: identification of clones associated with serious invasive disease. Microbiology 144, 3049–3060.[CrossRef]
    [Google Scholar]
  6. Farfán, M., Miñana-Galbis, D., Fusté, M. C. & Lorén, J. G. ( 2002; ). Allelic diversity and population structure in Vibrio cholerae O139 Bengal based on nucleotide sequence analysis. J Bacteriol 184, 1304–1313.[CrossRef]
    [Google Scholar]
  7. Feil, E. J., Enright, M. C. & Spratt, B. G. ( 2000; ). Estimating the relative contributions of mutation and recombination to clonal diversification: a comparison between Neisseria meningitidis and Streptococcus pneumoniae. Res Microbiol 151, 465–469.[CrossRef]
    [Google Scholar]
  8. Hall, T. A. ( 1999; ). BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98NT. Nucleic Acids Symp Ser 41, 95–98.
    [Google Scholar]
  9. Haubold, B. & Hudson, R. R. ( 2000; ). LIAN 3.0: detecting linkage disequilibrium in multilocus data. Bioinformatics 14, 68–73.
    [Google Scholar]
  10. Helgason, E., Tourasse, N. J., Meisal, R., Caugant, D. A. & Kolsto, A. B. ( 2004; ). Multilocus sequence typing scheme for bacteria of the Bacillus cereus group. Appl Environ Microbiol 70, 191–201.[CrossRef]
    [Google Scholar]
  11. Herias, M. V., Hessle, C., Telemo, E., Midtvedt, T., Hanson, L. A. & Wold, E. ( 1999; ). Immunomodulatory effects of Lactobacillus plantarum colonizing the intestine of gnotobiotic rats. Clin Exp Immunol 116, 283–290.[CrossRef]
    [Google Scholar]
  12. Huson, D. H. ( 1998; ). SplitsTree: analyzing and visualizing evolutionary data. Bioinformatics 14, 68–73.[CrossRef]
    [Google Scholar]
  13. Johansson, M.-L., Quednau, M., Molin, G. & Ahrné, S. ( 1995; ). Randomly amplified polymorphic DNA (RAPD) for rapid typing of Lactobacillus plantarum strains. Lett Appl Microbiol 21, 155–159.[CrossRef]
    [Google Scholar]
  14. Kleerebezem, M., Boekhorst, J., van Kranenburg, R. & 17 other authors ( 2003; ). Complete genome sequence of Lactobacillus plantarum WCFS1. Proc Natl Acad Sci U S A 100, 1990–1995.[CrossRef]
    [Google Scholar]
  15. Kumar, S., Tamura, K. & Nei, M. ( 1994; ). mega: molecular evolutionary genetics analysis software for microcomputers. Comput Appl Biosci 10, 189–191.
    [Google Scholar]
  16. Manfreda, G., de Cesare, A., Stella, S., Cozzi, M. & Cantoni, C. ( 2005; ). Occurrence and ribotypes of Listeria monocytogenes in Gorgonzola cheeses. Int J Food Microbiol 102, 287–293.[CrossRef]
    [Google Scholar]
  17. Marchesi, J. R., Sato, T., Weightman, A. J., Martin, T. A., Fry, J. C., Hiom, S. J. & Wade, W. G. ( 1998; ). Design and evaluation of useful bacterium-specific PCR primers that amplify genes coding for bacterial 16S rRNA. Appl Environ Microbiol 64, 795–799.
    [Google Scholar]
  18. Maynard Smith, J., Smith, N. H., O'Rourke, M. & Spratt, B. G. ( 1993; ). How clonal are bacteria? Proc Natl Acad Sci U S A 90, 4384–4388.[CrossRef]
    [Google Scholar]
  19. Merry, R. J., Dhanoa, M. S. & Theodorou, M. K. ( 1995; ). Use of freshly cultured lactic acid bacteria as silage inoculants. Grass For Sci 50, 112–123.[CrossRef]
    [Google Scholar]
  20. Molenaar, D., Bringel, F., Schuren, F. H., de Vos, W. M., Siezen, R. J. & Kleerebezem, M. ( 2005; ). Exploring Lactobacillus plantarum genome diversity by using microarrays. J Bacteriol 187, 6119–6127.[CrossRef]
    [Google Scholar]
  21. Nei, M. & Gojobori, T. ( 1986; ). Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol 3, 418–426.
    [Google Scholar]
  22. Oneca, M., Irigoyen, A., Ortigosa, M. & Torre, P. ( 2003; ). PCR and RAPD identification of L. plantarum strains isolated from ovine milk and cheese. Geographical distribution of strains. FEMS Microbiol Lett 227, 271–277.[CrossRef]
    [Google Scholar]
  23. Rodas, A. M., Ferrer, S. & Pardo, I. ( 2005; ). Polyphasic study of wine Lactobacillus strains: taxonomic implications. Int J Syst Evol Microbiol 55, 197–207.[CrossRef]
    [Google Scholar]
  24. Ruiz-Barba, J. L., Cathcart, D. P., Warner, P. J. & Jiménez-Díaz, R. ( 1994; ). Use of Lactobacillus plantarum LPCO10, a bacteriocin producer, as a starter culture in spanish-style green olive fermentations. Appl Environ Microbiol 60, 2059–2064.
    [Google Scholar]
  25. Sánchez, I., Seseña, S. & Palop, L. L. ( 2004; ). Polyphasic study of the genetic diversity of lactobacilli associated with ‘Almagro’ eggplants spontaneous fermentation, based on combined numerical analysis of randomly amplified polymorphic DNA and pulse-field gel electrophoresis patterns. J Appl Microbiol 97, 446–458.[CrossRef]
    [Google Scholar]
  26. Urlings, H. A. P., Bijker, P. G. H. & van Logtestijn, J. G. ( 1993; ). Fermentation of raw poultry by-products for animal nutrition. J Anim Sci 71, 2420–2426.
    [Google Scholar]
  27. Urwin, R. & Maiden, M. C. J. ( 2003; ). Multi-locus sequence typing: a tool for global epidemiology. Trends Microbiol 11, 479–487.[CrossRef]
    [Google Scholar]
  28. Vaquero, I., Marcobal, A. & Muñoz, R. ( 2004; ). Tannase activity by lactic acid bacteria isolated from grape must and wine. Int J Food Microbiol 96, 199–204.[CrossRef]
    [Google Scholar]
  29. Vescovo, M., Torriani, S., Dellaglio, F. & Bottazi, V. ( 1993; ). Basic characteristics, ecology and application of Lactobacillus plantarum: a review. Ann Microbiol Enzymol 43, 261–284.
    [Google Scholar]
  30. Yansanjav, A., Svec, P., Sedlacek, I., Hollerova, I. & Nemec, M. ( 2003; ). Ribotyping of lactobacilli isolated from spoiled beer. FEMS Microbiol Lett 229, 141–144.[CrossRef]
    [Google Scholar]
  31. Zadoks, R. N., Tikofsky, L. L. & Boor, K. J. ( 2005; ). Ribotyping of Streptococcus uberis from a dairy's environment, bovine feces and milk. Vet Microbiol 109, 257–265.[CrossRef]
    [Google Scholar]
  32. Zavaleta, A. I., Martínez-Murcia, A. J. & Rodríguez-Varela, F. ( 1996; ). 16S-23S rDNA intergenic sequences indicate that Leuconostoc oenos is phylogenetically homogeneous. Microbiology 142, 2105–2114.[CrossRef]
    [Google Scholar]
  33. Zhong, W., Millsap, K., Bialkowska-Hobrazanska, H. & Reid, G. ( 1998; ). Differentiation of Lactobacillus species by molecular typing. Appl Environ Microbiol 64, 2418–2423.
    [Google Scholar]
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