1887

Abstract

Analysis of 16S rRNA gene sequences is one of the most common methods for investigating the phylogeny and taxonomy of bacteria. However, several studies have indicated that the 16S rRNA gene does not distinguish between certain species. We therefore selected for phylogenetic analysis an alternative marker, , encoding gyrase subunit B. The aim of this investigation was to examine the applicability of gene fragments (∼1100 bp) for the phylogenetic study of 16 species and a total of 33 strains included in this study. Based on the sequenced fragments, a phylogenetic tree was obtained that contained two distinct clusters, with gastric species forming one cluster and enterohepatic species the other. The only exception was the gastric species , which clustered with the enterohepatic species. The calculated similarity matrix revealed the highest interspecies similarity between and (89 %) and the lowest similarity between and (60 %). The DNA G+C content of the sequenced fragments was ⩽40 mol% in enterohepatic species and >46 mol% in gastric species, excluding and , with G+C contents of 34 and 42 mol%, respectively. In summary, the gene fragments provided superior resolution and reliability to the 16S rRNA gene for differentiating between closely related species. A further outcome of this study was achieved by designing gene-based species-specific PCR primers for the identification of .

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2007-03-01
2019-10-16
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References

  1. Alm, R. A., Ling, L. S., Moir, D. T., King, B. L., Brown, E. D., Doig, P. C., Smith, D. R., Noonan, B., Guild, B. C. & other authors ( 1999; ). Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori. Nature 397, 176–180.[CrossRef]
    [Google Scholar]
  2. Chenna, R., Sugawara, H., Koike, T., Lopez, R., Gibson, T. J., Higgins, D. G. & Thompson, J. D. ( 2003; ). Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res 31, 3497–3500.[CrossRef]
    [Google Scholar]
  3. Dewhirst, F. E., Fox, J. G. & On, S. L. ( 2000; ). Recommended minimal standards for describing new species of the genus Helicobacter. Int J Syst Evol Microbiol 50, 2231–2237.[CrossRef]
    [Google Scholar]
  4. Dewhirst, F. E., Shen, Z., Scimeca, M. S., Stokes, L. N., Boumenna, T., Chen, T., Paster, B. J. & Fox, J. G. ( 2005; ). Discordant 16S and 23S rRNA gene phylogenies for the genus Helicobacter: implications for phylogenetic inference and systematics. J Bacteriol 187, 6106–6118.[CrossRef]
    [Google Scholar]
  5. Euzéby, J. P. ( 1997; ). List of Bacterial Names with Standing in Nomenclature: a folder available on the Internet. Int J Syst Bacteriol 47, 590–592. Last full update 4 April 2006. http://www.bacterio.cict.fr [CrossRef]
    [Google Scholar]
  6. 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]
  7. Gueneau, P. & Loiseaux-De Goër, S. ( 2002; ). Helicobacter: molecular phylogeny and the origin of gastric colonization in the genus. Infect Genet Evol 1, 215–223.[CrossRef]
    [Google Scholar]
  8. Hänninen, M. L., Happonen, I., Saari, S. & Jalava, K. ( 1996; ). Culture and characteristics of Helicobacter bizzozeronii, a new canine gastric Helicobacter sp. Int J Syst Bacteriol 46, 160–166.[CrossRef]
    [Google Scholar]
  9. Hänninen, M. L., Utriainen, M., Happonen, I. & Dewhirst, F. E. ( 2003; ). Helicobacter sp. flexispira 16S rDNA taxa 1, 4 and 5 and Finnish porcine Helicobacter isolates are members of the species Helicobacter trogontum (taxon 6). Int J Syst Evol Microbiol 53, 425–433.[CrossRef]
    [Google Scholar]
  10. Hänninen, M. L., Kärenlampi, R. I., Koort, J. M., Mikkonen, T. & Björkroth, K. J. ( 2005; ). Extension of the species Helicobacter bilis to include the reference strains of Helicobacter sp. flexispira taxa 2, 3 and 8 and Finnish canine and feline flexispira strains. Int J Syst Evol Microbiol 55, 891–898.[CrossRef]
    [Google Scholar]
  11. Inglis, G. D., McConville, M. & de Jong, A. ( 2006; ). Atypical Helicobacter canadensis strains associated with swine. Appl Environ Microbiol 72, 4464–4471.[CrossRef]
    [Google Scholar]
  12. Jalava, K., Kaartinen, M., Utriainen, M., Happonen, I. & Hänninen, M. L. ( 1997; ). Helicobacter salomonis sp. nov., a canine gastric Helicobacter sp. related to Helicobacter felis and Helicobacter bizzozeronii. Int J Syst Bacteriol 47, 975–982.[CrossRef]
    [Google Scholar]
  13. Jalava, K., On, S. L., Vandamme, P. A., Happonen, I., Sukura, A. & Hänninen, M. L. ( 1998; ). Isolation and identification of Helicobacter spp. from canine and feline gastric mucosa. Appl Environ Microbiol 64, 3998–4006.
    [Google Scholar]
  14. Jalava, K., On, S. L., Harrington, C. S., Andersen, L. P., Hänninen, M. L. & Vandamme, P. ( 2001; ). A cultured strain of “Helicobacter heilmannii,” a human gastric pathogen, identified as H. bizzozeronii: evidence for zoonotic potential of Helicobacter. Emerg Infect Dis 7, 1036–1038.[CrossRef]
    [Google Scholar]
  15. Kakinuma, K., Fukushima, M. & Kawaguchi, R. ( 2003; ). Detection and identification of Escherichia coli, Shigella, and Salmonella by microarrays using the gyrB gene. Biotechnol Bioeng 83, 721–728.[CrossRef]
    [Google Scholar]
  16. Kasai, H., Ezaki, T. & Harayama, S. ( 2000; ). Differentiation of phylogenetically related slowly growing mycobacteria by their gyrB sequences. J Clin Microbiol 38, 301–308.
    [Google Scholar]
  17. Mikkonen, T. P., Kärenlampi, R. I. & Hänninen, M. L. ( 2004; ). Phylogenetic analysis of gastric and enterohepatic Helicobacter species based on partial HSP60 gene sequences. Int J Syst Evol Microbiol 54, 753–758.[CrossRef]
    [Google Scholar]
  18. Paster, B. J., Lee, A., Fox, J. G., Dewhirst, F. E., Tordoff, L. A., Fraser, G. J., O'Rourke, J. L., Taylor, N. S. & Ferrero, R. ( 1991; ). Phylogeny of Helicobacter felis sp. nov., Helicobacter mustelae, and related bacteria. Int J Syst Bacteriol 41, 31–38.[CrossRef]
    [Google Scholar]
  19. Pitcher, D. G., Saunders, N. A. & Owen, R. J. ( 1989; ). Rapid extraction of bacterial genomic DNA with guanidium thiocyanate. Lett Appl Microbiol 8, 151–156.[CrossRef]
    [Google Scholar]
  20. Saitou, N. & Nei, M. ( 1987; ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425.
    [Google Scholar]
  21. Sanders, M. K. & Peura, D. A. ( 2002; ). Helicobacter pylori-associated diseases. Curr Gastroenterol Rep 4, 448–454.[CrossRef]
    [Google Scholar]
  22. Soler, L., Yanez, M. A., Chacon, M. R., Aguilera-Arreola, M. G., Catalan, V., Figueras, M. J. & Martinez-Murcia, A. J. ( 2004; ). Phylogenetic analysis of the genus Aeromonas based on two housekeeping genes. Int J Syst Evol Microbiol 54, 1511–1519.[CrossRef]
    [Google Scholar]
  23. Van den Bulck, K., Decostere, A., Baele, M., Driessen, A., Debongnie, J. C., Burette, A., Stolte, M., Ducatelle, R. & Haesebrouck, F. ( 2005; ). Identification of non-Helicobacter pylori spiral organisms in gastric samples from humans, dogs, and cats. J Clin Microbiol 43, 2256–2260.[CrossRef]
    [Google Scholar]
  24. Vandamme, P., Harrington, C. S., Jalava, K. & On, S. L. ( 2000; ). Misidentifying helicobacters: the Helicobacter cinaedi example. J Clin Microbiol 38, 2261–2266.
    [Google Scholar]
  25. Yamamoto, S. & Harayama, S. ( 1995; ). PCR amplification and direct sequencing of gyrB genes with universal primers and their application to the detection and taxonomic analysis of Pseudomonas putida strains. Appl Environ Microbiol 61, 1104–1109.
    [Google Scholar]
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