1887

Abstract

strains are lactic acid bacteria (LAB) that colonize diverse ecological niches, and have broad commercial applications. To probe their evolution and phylogeny, 40 strains were characterized; the strains included isolates from plant materials (=9), human gastrointestinal tracts (=7), human blood (=1), cheeses from different geographical locations (=22), and one strain of unknown origin. API biochemical testing identified niche-specific carbohydrate fermentation profiles. A multilocus sequence typing (MLST) scheme was developed for . Partial sequencing of six housekeeping genes (, , , , and ) revealed between 11 () and 20 () allelic types, as well as 36 sequence types. Phylogenetic analysis of MLST data by Reticulate and split decomposition analysis indicated frequent intra-species recombination. Purifying selection was detected, and is likely to have contributed to the evolution of certain genes. Pulsed-field gel electrophoresis (PFGE) using I was able to discriminate all the isolates, even those not differentiated by MLST. Phylogenetic trees reconstructed based on the MLST data using minimum evolution algorithm, and the I-PFGE restriction patterns using the unweighted-pair group method with arithmetic mean (UPGMA), revealed consensus clusters of strains specific to cheese and silage. Topological discrepancies between the MLST and PFGE trees were also observed, suggesting that intragenic point mutations have accumulated at a slower rate than indels and genome rearrangements in . The population analysed in this study demonstrated both a high level of phenotypic and genotypic diversity, as well as specificity to different ecological niches.

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2007-08-01
2019-11-19
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References

  1. Adamberg, K., Antonsson, M., Vogensen, F. K., Nielsen, E. W., Kask, S., Moller, P. L. & Ardo, Y. ( 2005; ). Fermentation of carbohydrates from cheese sources by non-starter lactic acid bacteria isolated from semi-hard Danish cheese. Int Dairy J 15, 873–882.[CrossRef]
    [Google Scholar]
  2. Bandelt, H. J. & Dress, A. W. M. ( 1992; ). Split decomposition: a new and useful approach to phylogenetic analysis of distance data. Mol Phylogenet Evol 1, 242–252.[CrossRef]
    [Google Scholar]
  3. Broadbent, J. R., Houck, K., Johnson, M. E. & Oberg, C. J. ( 2003; ). Influence of adjunct use and cheese microenvironment on nonstarter lactic acid bacteria populations in Cheddar-type cheese. J Dairy Sci 86, 2773–2782.[CrossRef]
    [Google Scholar]
  4. Chen, H., Lim, C. K., Lee, Y. K. & Chan, Y. N. ( 2000; ). Comparative analysis of the genes encoding 23S–5S rRNA intergenic spacer regions of Lactobacillus casei-related strains. Int J Syst Evol Microbiol 50, 471–478.[CrossRef]
    [Google Scholar]
  5. Christiansen, P., Petersen, M. H., Kask, S., Moller, P. L., Petersen, M., Nielsen, E. W., Vogensen, F. K. & Ardo, Y. ( 2005; ). Anticlostridial activity of Lactobacillus isolated from semi-hard cheeses. Int Dairy J 15, 901–909.[CrossRef]
    [Google Scholar]
  6. de las Rivas, B., Marcobal, A. & Munoz, 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]
  7. de las Rivas, B., Marcobal, A. & Muñoz, R. ( 2006; ). Development of a multilocus sequence typing method for analysis of Lactobacillus plantarum strains. Microbiology 152, 85–93.[CrossRef]
    [Google Scholar]
  8. Doolittle, R. F., Feng, D., Tsang, S., Cho, G. & Little, E. ( 1996; ). Determining divergence times of the major kingdoms of living organisms with a protein clock. Science 271, 470–477.[CrossRef]
    [Google Scholar]
  9. Enright, M. C. & Spratt, B. G. ( 1999; ). Multilocus sequence typing. Trends Microbiol 7, 482–487.[CrossRef]
    [Google Scholar]
  10. Fitzsimons, N. A., Cogan, T. M., Condon, S. & Beresford, T. ( 1999; ). Phenotypic and genotypic characterization of non-starter lactic acid bacteria in mature cheddar cheese. Appl Environ Microbiol 65, 3418–3426.
    [Google Scholar]
  11. Fox, P. F. & McSweeney, P. L. H. ( 2004; ). Cheese: an overview. In Cheese Chemistry, Physics and Microbiology, pp. 1–37, vol. 1, 3rd edn. Edited by P. F. Fox, P. L. H. McSweeney, T. M. Cogan & T. P. Guinee. California: Elsevier.
  12. Germond, J. E., Lapierre, L., Delley, M., Mollet, B., Felis, G. E. & Dellaglio, F. ( 2003; ). Evolution of the bacterial species Lactobacillus delbrueckii: a partial genomic study with reflections on prokaryotic species concept. Mol Biol Evol 20, 93–104.[CrossRef]
    [Google Scholar]
  13. Hunter, P. R. & Gaston, M. A. ( 1988; ). Numerical index of the discriminatory ability of typing systems: an application of Simpson's index of diversity. J Clin Microbiol 26, 2465–2466.
    [Google Scholar]
  14. Huson, D. H. ( 1998; ). SplitsTree: analyzing and visualizing evolutionary data. Bioinformatics 14, 68–73.[CrossRef]
    [Google Scholar]
  15. Jakobsen, I. B. & Easteal, S. ( 1996; ). A program for calculating and displaying compatibility matrices as an aid in determining reticulate evolution in molecular sequences. Comput Appl Biosci 12, 291–295.
    [Google Scholar]
  16. Kandler, O. & Weiss, N. ( 1986; ). Genus Lactobacillus. In Bergey's Manual of Systematic Bacteriology, vol. 2, 9th edn, pp. 1063–1065. Edited by P. H. A. Sneath, N. S. Mair, M. E. Sharpe & J. G. Holt. Baltimore: Williams & Wilkins.
  17. Kumar, S., Tamura, K. & Nei, M. ( 2004; ). mega3: integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Brief Bioinform 5, 150–163.[CrossRef]
    [Google Scholar]
  18. Lacher, D. W., Steinsland, H., Blank, T. E., Donnenberg, M. S. & Whittam, T. S. ( 2007; ). Molecular evolution of typical enteropathogenic Escherichia coli: clonal analysis by multilocus sequence typing and virulence gene allelic profiling. J Bacteriol 189, 342–350.[CrossRef]
    [Google Scholar]
  19. Lawrence, J. G. & Ochman, H. ( 1998; ). Molecular archaeology of the Escherichia coli genome. Proc Natl Acad Sci U S A 95, 9413–9417.[CrossRef]
    [Google Scholar]
  20. Maiden, M. C., Bygraves, J. A., Feil, E., Morelli, G., Russell, J. E., Urwin, R., Zhang, Q., Zhou, J., Zurth, K. & other authors ( 1998; ). Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc Natl Acad Sci U S A 95, 3140–3145.[CrossRef]
    [Google Scholar]
  21. Makarova, K., Slesarev, A., Wolf, Y., Sorokin, A., Mirkin, B., Koonin, E., Pavlov, A., Pavlova, N., Karamychev, V. & other authors ( 2006; ). Comparative genomics of lactic acid bacteria. Proc Natl Acad Sci U S A 103, 15611–15616.[CrossRef]
    [Google Scholar]
  22. Mayra-Makinen, A. & Bigret, M. ( 1998; ). Industrial use and production of lactic acid bacteria. In Lactic Acid Bacteria – Microbiology and Functional Aspects, 2nd edn, pp. 73–102. Edited by S. Salminen & A. V. Wright. New York: Marcel Dekker.
  23. Michael, R. W., Rodolphe, B. & Philippe, H. ( 2006; ). Methods for typing Lactobacillus species in food products, dietary supplements or animal feed by PCR amplification of CRISPR repeats. PCT Int Appl 48 pp. CODEN: PIXXD2 WO 2006073445 A2 20060713 CAN 145:118272 AN 2006:681305 CAPLUS.
  24. Miragaia, M., Thomas, J. C., Couto, I., Enright, M. C. & de Lencastre, H. ( 2007; ). Inferring a population structure for Staphylococcus epidermidis from multilocus sequence typing (MLST) data. J Bacteriol 189, 2540–2552.[CrossRef]
    [Google Scholar]
  25. 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]
  26. Nightingale, K. K., Windham, K. & Wiedmann, M. ( 2005; ). Evolution and molecular phylogeny of Listeria monocytogenes isolated from human and animal listeriosis cases and foods. J Bacteriol 187, 5537–5551.[CrossRef]
    [Google Scholar]
  27. Olvera, A., Cerdà-Cuéllar, M. & Aragon, V. ( 2006; ). Study of the population structure of Haemophilus parasuis by multilocus sequence typing. Microbiology 152, 3683–3690.[CrossRef]
    [Google Scholar]
  28. 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]
  29. Rozas, J., Sánchez-DeLarrio, J. C., Messeguer, X. & Rozas, R. ( 2003; ). DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19, 2496–2497.[CrossRef]
    [Google Scholar]
  30. Siezen, R. J., Renckens, B., van Swam, I., Peters, S., van Kranenburg, R., Kleerebezem, M. & de Vos, W. M. ( 2005; ). Complete sequences of four plasmids of Lactococcus lactis subsp. cremoris SK11 reveal extensive adaptation to the dairy environment. Appl Environ Microbiol 71, 8371–8382.[CrossRef]
    [Google Scholar]
  31. Tajima, F. ( 1989; ). Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123, 585–595.
    [Google Scholar]
  32. Tynkkynen, S., Satokari, R., Saarela, M., Mattila-Sandholm, T. & Saxelin, M. ( 1999; ). Comparison of ribotyping, randomly amplified polymorphic DNA analysis, and pulsed-field gel electrophoresis in typing of Lactobacillus rhamnosus and L. casei strains. Appl Environ Microbiol 65, 3908–3914.
    [Google Scholar]
  33. Vasquez, A., Ahrne, S., Pettersson, B. & Molin, G. ( 2001; ). Temporal temperature gradient gel electrophoresis (TTGE) as a tool for identification of Lactobacillus casei, Lactobacillus paracasei, Lactobacillus zeae and Lactobacillus rhamnosus. Lett Appl Microbiol 32, 215–219.[CrossRef]
    [Google Scholar]
  34. Ventura, M., Canchaya, C., Bernini, V., Altermann, E., Barrangou, R., McGrath, S., Claesson, M. J., Li, Y., Leahy, S. & other authors ( 2006; ). Comparative genomics and transcriptional analysis of prophages identified in the genomes of Lactobacillus gasseri, Lactobacillus salivarius and Lactobacillus casei. Appl Environ Microbiol 72, 3130–3146.[CrossRef]
    [Google Scholar]
  35. Walter, J., Heng, N. C., Hammes, W. P., Loach, D. M., Tannock, G. W. & Hertel, C. ( 2003; ). Identification of Lactobacillus reuteri genes specifically induced in the mouse gastrointestinal tract. Appl Environ Microbiol 69, 2044–2051.[CrossRef]
    [Google Scholar]
  36. Zhang, B. & Dong, X. Z. ( 2005; ). Partial sequence homology of FtsZ in phylogenetics analysis of lactic acid bacteria. Wei Sheng Wu Xue Bao 45, 661–664.
    [Google Scholar]
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