1887

Abstract

The aim of this study was to evaluate the use of the phenylalanyl-tRNA synthase alpha subunit () and the RNA polymerase alpha subunit () partial gene sequences for species identification of members of the genus . Two hundred and one strains representing the 98 species and 17 subspecies were examined. The gene sequence analysis provided an interspecies gap, which in most cases exceeded 10 % divergence, and an intraspecies variation of up to 3 %. The gene sequences revealed a somewhat lower resolution, with an interspecies gap normally exceeding 5 % and an intraspecies variation of up to 2 %. The combined use of and gene sequences offers a reliable identification system for nearly all species of the genus . The and gene sequences provide a powerful tool for the detection of potential novel species and synonymous taxa. In conclusion, the and gene sequences can be used as alternative genomic markers to 16S rRNA gene sequences and have a higher discriminatory power for reliable identification of species of the genus .

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2007-12-01
2019-12-06
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References

  1. Christensen, H., Kuhnert, P., Olsen, J. E. & Bisgaard, M. ( 2004; ). Comparative phylogenies of the housekeeping genes atpD, infB, rpoB and the 16S rRNA gene within the Pasteurellaceae. Int J Syst Evol Microbiol 54, 1601–1609.[CrossRef]
    [Google Scholar]
  2. Coenye, T., Gevers, D., Van de Peer, Y., Vandamme, P. & Swings, J. ( 2005; ). Towards a prokaryotic genomic taxonomy. FEMS Microbiol Rev 29, 147–167.
    [Google Scholar]
  3. Collins, M. D., Rodrigues, U., Ash, C., Aguirre, M., Farrow, J. A. E., Martinez-Murcia, A., Phillips, B. A., Williams, A. M. & Wallbanks, S. ( 1991; ). Phylogenetic analysis of the genus Lactobacillus and related lactic acid bacteria as determined by reverse transcriptase sequencing of 16S rRNA. FEMS Microbiol Lett 77, 5–12.[CrossRef]
    [Google Scholar]
  4. Daud Khaled, D., Neilan, B. A., Henriksson, A. & Conway, P. L. ( 1997; ). Identification and phylogenetic analysis of Lactobacillus using multiplex RAPD-PCR. FEMS Microbiol Lett 153, 191–197.[CrossRef]
    [Google Scholar]
  5. De Vuyst, L., Schrijvers, V., Paramithiotis, S., Hoste, B., Vancanneyt, M., Swings, J., Kalantzopoulos, G., Tsakalidou, E. & Messens, W. ( 2002; ). The biodiversity of lactic acid bacteria in Greek traditional wheat sourdoughs is reflected in both composition and metabolite formation. Appl Environ Microbiol 68, 6059–6069.[CrossRef]
    [Google Scholar]
  6. Dellaglio, F., Felis, G. E. & Torriani, S. ( 2002; ). The status of the species Lactobacillus casei (Orla-Jensen 1916) Hansen and Lessel 1971 and Lactobacillus paracasei Collins et al. 1989. Request for an opinion. Int J Syst Evol Microbiol 52, 285–287.
    [Google Scholar]
  7. Dellaglio, F., Vancanneyt, M., Endo, A, Vandamme, P., Felis, G. E., Castioni, A., Fujimoto, J., Watanabe, K. & Okada, S. ( 2006; ). Lactobacillus durianis Leisner et al. 2002 is a later heterotypic synonym of Lactobacillus vaccinostercus Kozaki and Okada 1983. Int J Syst Evol Microbiol 56, 1721–1724.[CrossRef]
    [Google Scholar]
  8. Dicks, L. M., Du Plessis, E. M., Dellaglio, F. & Lauer, E. ( 1996; ). Reclassification of Lactobacillus casei subsp. casei ATCC 393 and Lactobacillus rhamnosus ATCC 15820 as Lactobacillus zeae nom. rev., designation of ATCC 334 as the neotype of L. casei subsp. casei, and rejection of the name Lactobacillus paracasei. Int J Syst Bacteriol 46, 337–340.[CrossRef]
    [Google Scholar]
  9. Felis, G. E., Dellaglio, F., Mizzi, L. & Torriani, S. ( 2001; ). Comparative sequence analysis of a recA gene fragment brings new evidence for a change in the taxonomy of the Lactobacillus casei group. Int J Syst Evol Microbiol 51, 2113–2117.[CrossRef]
    [Google Scholar]
  10. Felis, G. E., Vancanneyt, M., Snauwaert, C., Swings, J., Torriani, S. & Castioni, A. and Dellaglio, F. ( 2006; ). Reclassification of Lactobacillus thermotolerans Niamsup et al. 2003 as a later synonym of Lactobacillus ingluviei Baele et al. 2003. Int J Syst Evol Microbiol 56, 793–795.[CrossRef]
    [Google Scholar]
  11. Gancheva, A., Pot, B., Vanhonacker, K., Hoste, B. & Kersters, K. ( 1999; ). A polyphasic approach towards the identification of strains belonging to Lactobacillus acidophilus and related species. Syst Appl Microbiol 22, 573–585.[CrossRef]
    [Google Scholar]
  12. Gevers, D., Huys, G. & Swings, J. ( 2001; ). Applicability of rep-PCR fingerprinting for identification of Lactobacillus species. FEMS Microbiol Lett 205, 31–36.[CrossRef]
    [Google Scholar]
  13. Gevers, D., Cohan, F. M., Lawrence, J. G., Spratt, B. G., Coenye, T., Feil, E. J., Stackebrandt, E., Van de Peer, Y., Vandamme, P. & other authors ( 2005; ). Opinion: re-evaluating prokaryotic species. Nat Rev Microbiol 3, 733–739.[CrossRef]
    [Google Scholar]
  14. Hammes, W. P. & Vogel, R. F. ( 1995; ). The genus Lactobacillus. In The Genera of Lactic Acid Bacteria, pp. 19–54. Edited by B. J. B. Wood & W. H. Holzapfel. London: Blackie Academic & Professional.
  15. Holzapfel, W. H., Haberer, P., Geisen, R., Bjorkroth, J. & Schillinger, U. ( 2001; ). Taxonomy and important features of probiotic microorganisms in food and nutrition. Am J Clin Nutr 73, 365S–373S.
    [Google Scholar]
  16. Kandler, O. & Weiss, N. ( 1986; ). Genus Lactobacillus Beijerinck 1901, 212. In Bergey's Manual of Systematic Bacteriology, vol. 2, pp. 1209−1234. Edited by P. H. A. Sneath, N. S. Mair & J. G. Holt. Baltimore, USA: The Williams and Wilkins Co.
  17. Klein, G., Pack, A., Bonaparte, C. & Reuter, G. ( 1998; ). Taxonomy and physiology of probiotic lactic acid bacteria. Int J Food Microbiol 41, 103–125.[CrossRef]
    [Google Scholar]
  18. Konstantinidis, K. T. & Tiedje, J. M. ( 2005; ). Towards a genome-based taxonomy for prokaryotes. J Bacteriol 187, 6258–6264.[CrossRef]
    [Google Scholar]
  19. Kostinek, M., Pukall, R., Rooney, A. P., Schillinger, U., Hertel, C., Holzapfel, W. H. & Franz, C. M. A. P. ( 2005; ). Lactobacillus arizonensis is a later heterotypic synonym of Lactobacillus plantarum. Int J Syst Evol Microbiol 55, 2485–2489.[CrossRef]
    [Google Scholar]
  20. Massi, M., Vitali, B., Federici, F., Matteuzzi, D. & Brigidi, P. ( 2004; ). Identification method based on PCR combined with automated ribotyping for tracking probiotic Lactobacillus strains colonizing the human gut and vagina. J Appl Microbiol 96, 777–786.[CrossRef]
    [Google Scholar]
  21. Meyer, C. P. & Paulay, G. ( 2005; ). DNA barcoding: error rates based on comprehensive sampling. PLoS Biol 3 (e422).
    [Google Scholar]
  22. Mori, K., Yamazaki, K., Ishiyama, T., Katsumata, M., Kobayashi, K., Kawai, Y., Inoue, N. & Shinano, H. ( 1997; ). Comparative sequence analyses of the genes coding for 16S rRNA of Lactobacillus casei-related taxa. Int J Syst Bacteriol 47, 54–57.[CrossRef]
    [Google Scholar]
  23. Nakamura, L. K. & Crowell, C. D. ( 1979; ). Lactobacillus amylophilus, a new starch-hydrolyzing species from swine waste-corn fermentation. Dev Ind Microbiol 20, 532–540.
    [Google Scholar]
  24. Naser, S., Thompson, F. L., Hoste, B., Gevers, D., Vandemeulebroecke, K., Cleenwerck, I., Thompson, C. C., Vancanneyt, M. & Swings, J. ( 2005a; ). Phylogeny and identification of enterococci using atpA gene sequence analysis. J Clin Microbiol 43, 2224–2230.[CrossRef]
    [Google Scholar]
  25. Naser, S. M., Thompson, F. L., Hoste, B., Gevers, D., Dawyndt, P., Vancanneyt, M. & Swings, J. ( 2005b; ). Application of multilocus sequence analysis (MLSA) for rapid identification of Enterococcus species based on rpoA and pheS genes. Microbiology 151, 2141–2150.[CrossRef]
    [Google Scholar]
  26. Naser, S. M., Hagen, K. E., Vancanneyt, M., Cleenwerck, I., Swings, J. & Tompkins, T. A. ( 2006a; ). 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]
  27. Naser, S. M., Vancanneyt, M., Snauwaert, C., Vrancken, G., Hoste, B., De Vuyst, L. & Swings, J. ( 2006b; ). Reclassification of Lactobacillus amylophilus LMG 11400 and NRRL B-4435 as Lactobacillus amylotrophicus sp. nov. Int J Syst Evol Microbiol 56, 2523–2527.[CrossRef]
    [Google Scholar]
  28. Naser, S. M., Vancanneyt, M., Hoste, B., Snauwaert, C. & Swings, J. ( 2006c; ). Lactobacillus cypricasei Lawson et al. 2001 is a later synonym of Lactobacillus acidipiscis Tanasupawat et al. 2000. Int J Syst Evol Microbiol 56, 1681–1683.[CrossRef]
    [Google Scholar]
  29. Niemann, S., Puhler, A., Tichy, H. V., Simon, R. & Selbitschka, W. ( 1997; ). Evaluation of the resolving power of three different DNA fingerprinting methods to discriminate among isolates of a natural Rhizobium meliloti population. J Appl Microbiol 82, 477–484.[CrossRef]
    [Google Scholar]
  30. Pot, B., Hertel, C., Ludwig, W., Descheemaeker, P., Kersters, K. & Schleifer, K. H. ( 1993; ). Identification and classification of Lactobacillus acidophilus, L. gasseri and L. johnsonii strains by SDS-PAGE and rRNA-targeted oligonucleotide probe hybridization. J Gen Microbiol 139, 513–517.[CrossRef]
    [Google Scholar]
  31. Reid, G. ( 1999; ). The scientific basis for probiotic strains of Lactobacillus. Appl Environ Microbiol 65, 3763–3766.
    [Google Scholar]
  32. Saitou, N. & Nei, M. ( 1987; ). The neighbour-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425.
    [Google Scholar]
  33. Santos, S. R. & Ochman, H. ( 2004; ). Identification and phylogenetic sorting of bacterial lineages with universally conserved genes and proteins. Environ Microbiol 6, 754–759.[CrossRef]
    [Google Scholar]
  34. Schleifer, K. H. & Ludwig, W. ( 1995; ). Phylogeny of the genus Lactobacillus and related genera. Syst Appl Microbiol 18, 461–467.[CrossRef]
    [Google Scholar]
  35. Sneath, P. H. A. & Sokal, R. R. ( 1973; ). Numerical Taxonomy. The Principles and Practice of Numerical Classification. San Francisco: W. H. Freeman and Co.
  36. Stackebrandt, E., Frederiksen, W., Garrity, G. M., Grimont, P. A., Kämpfer, P., Maiden, M. C., Nesme, X., Rossello-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]
  37. Stiles, M. E. & Holzapfel, W. H. ( 1997; ). Lactic acid bacteria of foods and their current taxonomy. Int J Food Microbiol 36, 1–29.[CrossRef]
    [Google Scholar]
  38. 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]
  39. Torriani, S., Felis, G. E. & Dellaglio, F. ( 2001; ). Differentiation of Lactobacillus plantarum, L. pentosus, and L. paraplantarum by recA gene sequence analysis and multiplex PCR assay with recA gene-derived primers. Appl Environ Microbiol 67, 3450–3454.[CrossRef]
    [Google Scholar]
  40. 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]
  41. Vancanneyt, M., Engelbeen, K., De Wachter, M., Vandemeulebroecke, K., Cleenwerck, I. & Swings, J. ( 2005; ). Reclassification of Lactobacillus ferintoshensis as a later heterotypic synonym of Lactobacillus parabuchneri. Int J Syst Evol Microbiol 55, 2195–2198.[CrossRef]
    [Google Scholar]
  42. Vancanneyt, M., Naser, S. M., Engelbeen, K., De Wachter, M., Van der Meulen, R., Cleenwerck, I., Hoste, B., De Vuyst, L. & Swings, J. ( 2006; ). Reclassification of Lactobacillus brevis LMG 11494 and LMG 11984 as Lactobacillus parabrevis sp. nov. Int J Syst Evol Microbiol 56, 1553–1557.[CrossRef]
    [Google Scholar]
  43. 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]
  44. 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]
  45. Zhong, W., Millsap, K., Bialkowska-Hobrzanska, H. & Reid, G. ( 1998; ). Differentiation of Lactobacillus species by molecular typing. Appl Environ Microbiol 64, 2418–2423.
    [Google Scholar]
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vol. , part 12, pp. 2777 - 2789

Neighbour-joining tree based on the gene sequences of type strains.

Neighbour-joining tree based on the gene sequences of type strains.

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