1887

Abstract

Partial RNA polymerase -subunit gene () sequences (315 bp) were determined and used to differentiate the type strains of 23 species of the genus . The sequences were compared with those of the partial (604 bp) and 16S rRNA genes (1475 or 1495 bp). The gene sequences showed nucleotide sequence similarities ranging from 84.1 % to 99.0 %, while the similarities of the sequences ranged from 78.5 % to 99.7 % and the 16S rRNA gene sequence similarities ranged from 89.4 % to 99.2 %. The phylogenetic trees constructed from the sequences of these three genes showed similar clustering patterns, with the exception of several species. The , subsp. subsp. and groups were more clearly differentiated in the partial and gene sequence trees than they were in the 16S rRNA gene tree. Based on sequence similarities and tree topologies, the newly determined gene sequences are suitable molecular markers for the differentiation of species of the genus and support various other molecular tools used to determine the relationships among species of this genus.

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2010-12-01
2019-11-19
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References

  1. Adekambi, T., Drancourt, M. & Raoult, D. ( 2009; ). The rpoB gene as a tool for clinical microbiologists. Trends Microbiol 17, 37–45.[CrossRef]
    [Google Scholar]
  2. Bourget, N., Simonet, J. M. & Decaris, B. ( 1993; ). Analysis of the genome of the five Bifidobacterium breve strains: plasmid content, pulsed-field gel electrophoresis genome size estimation and rrn loci number. FEMS Microbiol Lett 110, 11–20.[CrossRef]
    [Google Scholar]
  3. Cunningham, C. W. ( 1997; ). Can three incongruence tests predict when data should be combined? Mol Biol Evol 14, 733–740.[CrossRef]
    [Google Scholar]
  4. Dahllof, I., Baillie, H. & Kjelleberg, S. ( 2000; ). rpoB-based microbial community analysis avoids limitations inherent in 16S rRNA gene intraspecies heterogeneity. Appl Environ Microbiol 66, 3376–3380.[CrossRef]
    [Google Scholar]
  5. De Dea Lindner, J., Canchaya, C., Zhang, Z., Neviani, E., Fitzgerald, G. F., van Sinderen, D. & Ventura, M. ( 2007; ). Exploiting Bifidobacterium genomes: the molecular basis of stress response. Int J Food Microbiol 120, 13–24.[CrossRef]
    [Google Scholar]
  6. Fox, G. E., Wisotzkey, J. D. & Jurtshuk, P., Jr ( 1992; ). How close is close: 16S rRNA sequence identity may not be sufficient to guarantee species identity. Int J Syst Bacteriol 42, 166–170.[CrossRef]
    [Google Scholar]
  7. Gavini, F., Pourcher, A. M., Neut, C., Monget, D., Romond, C., Oger, C. & Izard, D. ( 1991; ). Phenotypic differentiation of bifidobacteria of human and animal origins. Int J Syst Bacteriol 41, 548–557.[CrossRef]
    [Google Scholar]
  8. Guarner, F. & Malagelada, J. R. ( 2003; ). Gut flora in health and disease. Lancet 361, 512–519.[CrossRef]
    [Google Scholar]
  9. Holmes, E. C., Urwin, R. & Maiden, M. C. ( 1999; ). The influence of recombination on the population structure and evolution of the human pathogen Neisseria meningitidis. Mol Biol Evol 16, 741–749.[CrossRef]
    [Google Scholar]
  10. Iyer, L. M., Koonin, E. V. & Aravind, L. ( 2004; ). Evolution of bacterial RNA polymerase: implications for large-scale bacterial phylogeny, domain accretion, and horizontal gene transfer. Gene 335, 73–88.[CrossRef]
    [Google Scholar]
  11. Jian, W., Zhu, L. & Dong, X. ( 2001; ). New approach to phylogenetic analysis of the genus Bifidobacterium based on partial HSP60 gene sequences. Int J Syst Evol Microbiol 51, 1633–1638.[CrossRef]
    [Google Scholar]
  12. Kim, B. J., Lee, S. H., Lyu, M. A., Kim, S. J., Bai, G. H., Chae, G. T., Kim, E. C., Cha, C. Y. & Kook, Y. H. ( 1999; ). Identification of mycobacterial species by comparative sequence analysis of the RNA polymerase gene (rpoB). J Clin Microbiol 37, 1714–1720.
    [Google Scholar]
  13. Kim, J. F., Jeong, H., Yu, D. S., Choi, S. H., Hur, C. G., Park, M. S., Yoon, S. H., Kim, D. W., Ji, G. E. & other authors ( 2009; ). Genome sequence of the probiotic bacterium Bifidobacterium animalis subsp. lactis AD011. J Bacteriol 191, 678–679.[CrossRef]
    [Google Scholar]
  14. Ko, K. S., Lee, H. K., Park, M. Y., Lee, K. H., Yun, Y. J., Woo, S. Y., Miyamoto, H. & Kook, Y. H. ( 2002; ). Application of RNA polymerase beta-subunit gene (rpoB) sequences for the molecular differentiation of Legionella species. J Clin Microbiol 40, 2653–2658.[CrossRef]
    [Google Scholar]
  15. Ko, K. S., Kuwahara, T., Haehwa, L., Yoon, Y. J., Kim, B. J., Lee, K. H., Ohnishi, Y. & Kook, Y. H. ( 2007; ). RNA polymerase beta-subunit gene (rpoB) sequence analysis for the identification of Bacteroides spp. Clin Microbiol Infect 13, 48–54.[CrossRef]
    [Google Scholar]
  16. Leblond-Bourget, N., Philippe, H., Mangin, I. & Decaris, B. ( 1996; ). 16S rRNA and 16S to 23S internal transcribed spacer sequence analyses reveal inter- and intraspecific Bifidobacterium phylogeny. Int J Syst Bacteriol 46, 102–111.[CrossRef]
    [Google Scholar]
  17. Lee, S. H., Kim, B. J., Kim, J. H., Park, K. H., Kim, S. J. & Kook, Y. H. ( 2000; ). Differentiation of Borrelia burgdorferi sensu lato on the basis of RNA polymerase gene (rpoB) sequences. J Clin Microbiol 38, 2557–2562.
    [Google Scholar]
  18. Lee, J. H., Karamychev, V. N., Kozyavkin, S. A., Mills, D., Pavlov, A. R., Pavlova, N. V., Polouchine, N. N., Richardson, P. M., Shakhova, V. V. & other authors ( 2008; ). Comparative genomic analysis of the gut bacterium Bifidobacterium longum reveals loci susceptible to deletion during pure culture growth. BMC Genomics 9, 247.[CrossRef]
    [Google Scholar]
  19. Lim, C. Y., Lee, K. H., Cho, M. J., Chang, M. W., Kim, S. Y., Myong, N. H., Lee, W. K., Rhee, K. H. & Kook, Y. H. ( 2003; ). Detection of Helicobacter pylori in gastric mucosa of patients with gastroduodenal diseases by PCR-restriction analysis using the RNA polymerase gene (rpoB). J Clin Microbiol 41, 3387–3391.[CrossRef]
    [Google Scholar]
  20. Mitsuoka, T. & Kaneuchi, C. ( 1977; ). Ecology of the bifidobacteria. Am J Clin Nutr 30, 1799–1810.
    [Google Scholar]
  21. Miyake, T., Watanabe, K., Watanabe, T. & Oyaizu, H. ( 1998; ). Phylogenetic analysis of the genus Bifidobacterium and related genera based on 16S rDNA sequences. Microbiol Immunol 42, 661–667.[CrossRef]
    [Google Scholar]
  22. Orla-Jensen, S. ( 1924; ). Classification des bactéries lactiques. Lait 4, 468–474 (in French).[CrossRef]
    [Google Scholar]
  23. Palys, T., Nakamura, L. K. & Cohan, F. M. ( 1997; ). Discovery and classification of ecological diversity in the bacterial world: the role of DNA sequence data. Int J Syst Bacteriol 47, 1145–1156.[CrossRef]
    [Google Scholar]
  24. Renesto, P., Gautheret, D., Drancourt, M. & Raoult, D. ( 2000; ). Determination of the rpoB gene sequences of Bartonella henselae and Bartonella quintana for phylogenic analysis. Res Microbiol 151, 831–836.[CrossRef]
    [Google Scholar]
  25. Requena, T., Burton, J., Matsuki, T., Munro, K., Simon, M. A., Tanaka, R., Watanabe, K. & Tannock, G. W. ( 2002; ). Identification, detection, and enumeration of human Bifidobacterium species by PCR targeting the transaldolase gene. Appl Environ Microbiol 68, 2420–2427.[CrossRef]
    [Google Scholar]
  26. Roy, D., Ward, P. & Champagne, G. ( 1996; ). Differentiation of bifidobacteria by use of pulsed-field gel electrophoresis and polymerase chain reaction. Int J Food Microbiol 29, 11–29.[CrossRef]
    [Google Scholar]
  27. Sakata, S., Ryu, C. S., Kitahara, M., Sakamoto, M., Hayashi, H., Fukuyama, M. & Benno, Y. ( 2006; ). Characterization of the genus Bifidobacterium by automated ribotyping and 16S rRNA gene sequences. Microbiol Immunol 50, 1–10.[CrossRef]
    [Google Scholar]
  28. Satokari, R. M., Vaughan, E. E., Akkermans, A. D., Saarela, M. & de Vos, W. M. ( 2001; ). Bifidobacterial diversity in human feces detected by genus-specific PCR and denaturing gradient gel electrophoresis. Appl Environ Microbiol 67, 504–513.[CrossRef]
    [Google Scholar]
  29. Schell, M. A., Karmirantzou, M., Snel, B., Vilanova, D., Berger, B., Pessi, G., Zwahlen, M. C., Desiere, F., Bork, P. & other authors ( 2002; ). The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract. Proc Natl Acad Sci U S A 99, 14422–14427.[CrossRef]
    [Google Scholar]
  30. Sela, D. A., Chapman, J., Adeuya, A., Kim, J. H., Chen, F., Whitehead, T. R., Lapidus, A., Rokhsar, D. S., Lebrilla, C. B. & other authors ( 2008; ). The genome sequence of Bifidobacterium longum subsp infantis reveals adaptations for milk utilization within the infant microbiome. Proc Natl Acad Sci U S A 105, 18964–18969.[CrossRef]
    [Google Scholar]
  31. Severinov, K., Mustaev, A., Kukarin, A., Muzzin, O., Bass, I., Darst, S. A. & Goldfarb, A. ( 1996; ). Structural modules of the large subunits of RNA polymerase. Introducing archaebacterial and chloroplast split sites in the beta and beta′ subunits of Escherichia coli RNA polymerase. J Biol Chem 271, 27969–27974.[CrossRef]
    [Google Scholar]
  32. Shimodaira, H. & Hasegawa, M. ( 1999; ). Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol Biol Evol 16, 1114–1116.[CrossRef]
    [Google Scholar]
  33. Stackebrandt, E., Frederiksen, W., Garrity, G. M., Grimont, P. A., Kämpfer, P., Maiden, M. C., 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]
  34. Swofford, D. ( 2003; ). paup*. Phylogenetic analysis using parsimony (*and other methods), version 4. Sunderland, MA: Sinauer Associates.
  35. 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]
  36. Ventura, M. & Zink, R. ( 2003; ). Comparative sequence analysis of the tuf and recA genes and restriction fragment length polymorphism of the internal transcribed spacer region sequences supply additional tools for discriminating Bifidobacterium lactis from Bifidobacterium animalis. Appl Environ Microbiol 69, 7517–7522.[CrossRef]
    [Google Scholar]
  37. Ventura, M., Meylan, V. & Zink, R. ( 2003; ). Identification and tracing of Bifidobacterium species by use of enterobacterial repetitive intergenic consensus sequences. Appl Environ Microbiol 69, 4296–4301.[CrossRef]
    [Google Scholar]
  38. Ventura, M., Canchaya, C., van Sinderen, D., Fitzgerald, G. F. & Zink, R. ( 2004a; ). Bifidobacterium lactis DSM 10140: Identification of the atp (atpBEFHAGDC) operon and analysis of its genetic structure, characteristics, and phylogeny. Appl Environ Microbiol 70, 3110–3121.[CrossRef]
    [Google Scholar]
  39. Ventura, M., van Sinderen, D., Fitzgerald, G. F. & Zink, R. ( 2004b; ). Insights into the taxonomy, genetics and physiology of bifidobacteria. Antonie van Leeuwenhoek 86, 205–223.[CrossRef]
    [Google Scholar]
  40. Ventura, M., Lee, J. H., Canchaya, C., Zink, R., Leahy, S., Moreno-Munoz, J. A., O'Connell-Motherway, M., Higgins, D., Fitzgerald, G. F. & other authors ( 2005; ). Prophage-like elements in bifidobacteria: insights from genomics, transcription, integration, distribution, and phylogenetic analysis. Appl Environ Microbiol 71, 8692–8705.[CrossRef]
    [Google Scholar]
  41. Ventura, M., Canchaya, C., Del Casale, A., Dellaglio, F., Neviani, E., Fitzgerald, G. F. & van Sinderen, D. ( 2006; ). Analysis of bifidobacterial evolution using a multilocus approach. Int J Syst Evol Microbiol 56, 2783–2792.[CrossRef]
    [Google Scholar]
  42. Ventura, M., Canchaya, C., Zhang, Z., Fitzgerald, G. F. & van Sinderen, D. ( 2007; ). Molecular characterization of hsp20, encoding a small heat shock protein of Bifidobacterium breve UCC2003. Appl Environ Microbiol 73, 4695–4703.[CrossRef]
    [Google Scholar]
  43. Ventura, M., Turroni, F., Ribbera, A., Foroni, E. & van Sinderen, D. ( 2008; ). Basic biology: Biology of effector organisms for probiotic and replacement therapy. 4. Bifidobacteria: the model human gut commensal. In Therapeutic Microbiology: probiotics and related strategies, pp. 35–50. Edited by Versalovic, J. & Wilson, M.. Washington, DC. : American Society for Microbiology.
    [Google Scholar]
  44. Vincent, D., Roy, D., Mondou, F. & Dery, C. ( 1998; ). Characterization of bifidobacteria by random DNA amplification. Int J Food Microbiol 43, 185–193.[CrossRef]
    [Google Scholar]
  45. Vitali, B., Turroni, S., Serina, S., Sosio, M., Vannini, L., Candela, M., Guerzoni, M. E. & Brigidi, P. ( 2008; ). Molecular and phenotypic traits of in-vitro-selected mutants of Bifidobacterium resistant to rifaximin. Int J Antimicrob Agents 31, 555–560.[CrossRef]
    [Google Scholar]
  46. Yun, Y. J., Lee, K. H., Haihua, L., Ryu, Y. J., Kim, B. J., Lee, Y. H., Baek, G. H., Kim, H. J., Chung, M. S. & other authors ( 2005; ). Detection and identification of Mycobacterium tuberculosis in joint biopsy specimens by rpoB PCR cloning and sequencing. J Clin Microbiol 43, 174–178.[CrossRef]
    [Google Scholar]
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