1887

Abstract

DNA–DNA hybridization (DDH) values have been used by bacterial taxonomists since the 1960s to determine relatedness between strains and are still the most important criterion in the delineation of bacterial species. Since the extent of hybridization between a pair of strains is ultimately governed by their respective genomic sequences, we examined the quantitative relationship between DDH values and genome sequence-derived parameters, such as the average nucleotide identity (ANI) of common genes and the percentage of conserved DNA. A total of 124 DDH values were determined for 28 strains for which genome sequences were available. The strains belong to six important and diverse groups of bacteria for which the intra-group 16S rRNA gene sequence identity was greater than 94 %. The results revealed a close relationship between DDH values and ANI and between DNA–DNA hybridization and the percentage of conserved DNA for each pair of strains. The recommended cut-off point of 70 % DDH for species delineation corresponded to 95 % ANI and 69 % conserved DNA. When the analysis was restricted to the protein-coding portion of the genome, 70 % DDH corresponded to 85 % conserved genes for a pair of strains. These results reveal extensive gene diversity within the current concept of ‘species’. Examination of reciprocal values indicated that the level of experimental error associated with the DDH method is too high to reveal the subtle differences in genome size among the strains sampled. It is concluded that ANI can accurately replace DDH values for strains for which genome sequences are available.

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2007-01-01
2019-08-18
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References

  1. Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J. H., Zhang, Z., Miller, W. & Lipman, D. J. ( 1997; ). Gapped blast and psi-blast: a new generation of protein database search programs. Nucleic Acids Res 25, 3389–3402.[CrossRef]
    [Google Scholar]
  2. Bautz, E. K. F. & Bautz, F. A. ( 1964; ). The influence of noncomplementary bases on the stability of ordered polynucleotides. Proc Natl Acad Sci U S A 52, 1476–1481.[CrossRef]
    [Google Scholar]
  3. Brenner, D. J., Fanning, G. R., Rake, A. V. & Johnson, K. E. ( 1969; ). Batch procedure for thermal elution of DNA from hydroxyapatite. Anal Biochem 28, 447–459.[CrossRef]
    [Google Scholar]
  4. Byappanahalli, M. N., Whitman, R. L., Shively, D. A., Sadowsky, M. J. & Ishii, S. ( 2006; ). Population structure, persistence, and seasonality of autochthonous Escherichia coli in temperate, coastal forest soil from a Great Lakes watershed. Environ Microbiol 8, 504–513.[CrossRef]
    [Google Scholar]
  5. Cho, J. C. & Tiedje, J. M. ( 2001; ). Bacterial species determination from DNA-DNA hybridization by using genome fragments and DNA microarrays. Appl Environ Microbiol 67, 3677–3682.[CrossRef]
    [Google Scholar]
  6. Christensen, H., Angen, Ø., Mutters, R., Olsen, J. E. & Bisgaard, M. ( 2000; ). DNA–DNA hybridization determined in micro-wells using covalent attachment of DNA. Int J Syst Evol Microbiol 50, 1095–1102.[CrossRef]
    [Google Scholar]
  7. 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]
  8. Crosa, J. H., Brenner, D. J. & Falkow, S. ( 1973; ). Use of a single-strand specific nuclease for analysis of bacterial and plasmid deoxyribonucleic acid homo- and heteroduplexes. J Bacteriol 115, 904–911.
    [Google Scholar]
  9. De Clerck, E., Rodriguez-Diaz, M., Vanhoutte, T., Heyrman, J., Logan, N. A. & De Vos, P. ( 2004; ). Anoxybacillus contaminans sp. nov. and Bacillus gelatini sp. nov., isolated from contaminated gelatin batches. Int J Syst Evol Microbiol 54, 941–946.[CrossRef]
    [Google Scholar]
  10. De Ley, J. ( 1970; ). Re-examination of the association between melting point, buoyant density, and chemical base composition of deoxyribonucleic acid. J Bacteriol 101, 738–754.
    [Google Scholar]
  11. De Ley, J., Cattoir, H. & Reynaerts, A. ( 1970; ). The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 12, 133–142.[CrossRef]
    [Google Scholar]
  12. Ezaki, T., Hashimoto, Y. & Yabuuchi, E. ( 1989; ). Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane-filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Bacteriol 39, 224–229.[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; ). Re-evaluating prokaryotic species. Nat Rev Microbiol 3, 733–739.[CrossRef]
    [Google Scholar]
  14. Goris, J., Suzuki, K., De Vos, P., Nakase, T. & Kersters, K. ( 1998; ). Evaluation of a microplate DNA-DNA hybridization method compared with the initial renaturation method. Can J Microbiol 44, 1148–1153.[CrossRef]
    [Google Scholar]
  15. Grimont, P. A. D., Popoff, M. Y., Grimont, F., Coynault, C. & Lemelin, M. ( 1980; ). Reproducibility and correlation study of three deoxyribonucleic acid hybridization procedures. Curr Microbiol 4, 325–330.[CrossRef]
    [Google Scholar]
  16. Huß, V. A. R., Festl, H. & Schleifer, K. H. ( 1983; ). Studies on the spectrophotometric determination of DNA hybridization from renaturation rates. Syst Appl Microbiol 4, 184–192.[CrossRef]
    [Google Scholar]
  17. Huys, G., Cnockaert, M., Janda, J. M. & Swings, J. ( 2003; ). Escherichia albertii sp. nov., a diarrhoeagenic species isolated from stool specimens of Bangladeshi children. Int J Syst Evol Microbiol 53, 807–810.[CrossRef]
    [Google Scholar]
  18. Hyma, K. E., Lacher, D. W., Nelson, A. M., Bumbaugh, A. C., Janda, J. M., Strockbine, N. A., Young, V. B. & Whittam, T. S. ( 2005; ). Evolutionary genetics of a new pathogenic Escherichia species: Escherichia albertii and related Shigella boydii strains. J Bacteriol 187, 619–628.[CrossRef]
    [Google Scholar]
  19. Ishii, S., Ksoll, W. B., Hicks, R. E. & Sadowsky, M. J. ( 2006; ). Presence and growth of naturalized Escherichia coli in temperate soils from Lake Superior watersheds. Appl Environ Microbiol 72, 612–621.[CrossRef]
    [Google Scholar]
  20. Johnson, J. L. ( 1991; ). DNA reassociation experiments. In Nucleic Acid Techniques in Bacterial Systematics, pp. 21–44. Edited by E. Stackebrandt & M. Goodfellow. Chichester: Wiley.
  21. Konstantinidis, K. T. & Tiedje, J. M. ( 2005; ). Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci U S A 102, 2567–2572.[CrossRef]
    [Google Scholar]
  22. Lan, R. & Reeves, P. R. ( 2002; ). Escherichia coli in disguise: molecular origins of Shigella. Microbes Infect 4, 1125–1132.[CrossRef]
    [Google Scholar]
  23. Marmur, J. ( 1961; ). A procedure for the isolation of deoxyribonucleic acid from micro-organisms. J Mol Biol 3, 208–218.[CrossRef]
    [Google Scholar]
  24. McConaughy, B. L., Laird, C. D. & McCarthy, B. J. ( 1969; ). Nucleic acid reassociation in formamide. Biochemistry 8, 3289–3295.[CrossRef]
    [Google Scholar]
  25. Rademaker, J. L., Hoste, B., Louws, F. J., Kersters, K., Swings, J., Vauterin, L., Vauterin, P. & de Bruijn, F. J. ( 2000; ). Comparison of AFLP and rep-PCR genomic fingerprinting with DNA–DNA homology studies: Xanthomonas as a model system. Int J Syst Evol Microbiol 50, 665–677.[CrossRef]
    [Google Scholar]
  26. Rosselló-Mora, R. ( 2003; ). Opinion: the species problem, can we achieve a universal concept? Syst Appl Microbiol 26, 323–326.[CrossRef]
    [Google Scholar]
  27. Rosselló-Mora, R. ( 2006; ). DNA-DNA reassociation methods applied to microbial taxonomy and their critical evaluation. In Molecular Identification, Systematics and Population Structure of Prokaryotes, pp. 23–50. Edited by E. Stackebrandt. Berlin: Springer.
  28. Rosselló-Mora, R. & Amann, R. ( 2001; ). The species concept for prokaryotes. FEMS Microbiol Rev 25, 39–67.[CrossRef]
    [Google Scholar]
  29. Rost, B. ( 1999; ). Twilight zone of protein sequence alignments. Protein Eng 12, 85–94.[CrossRef]
    [Google Scholar]
  30. Sander, C. & Schneider, R. ( 1991; ). Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins 9, 56–68.[CrossRef]
    [Google Scholar]
  31. Stackebrandt, E. ( 2003; ). The richness of prokaryotic diversity: there must be a species somewhere. Food Technol Biotechnol 41, 17–22.
    [Google Scholar]
  32. Stackebrandt, E. & Goebel, B. M. ( 1994; ). A place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44, 846–849.[CrossRef]
    [Google Scholar]
  33. Stackebrandt, E. & Liesack, W. ( 1993; ). Nucleic acids and classification. In Handbook of New Bacterial Systematics, pp. 151–194. Edited by M. Goodfellow & A. G. O'Donnell. London: Academic Press.
  34. Stackebrandt, E., Frederiksen, W., Garrity, G. M., Grimont, P. A. D., Kämpfer, P., Maiden, M. C. J., 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]
  35. Ullmann, J. S. & McCarthy, B. J. ( 1973; ). The relationship between mismatched base pairs and the thermal stability of DNA duplexes. Biochim Biophys Acta 294, 416–424.[CrossRef]
    [Google Scholar]
  36. Vandamme, P., Pot, B., Gillis, M., De Vos, P., Kersters, K. & Swings, J. ( 1996; ). Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol Rev 60, 407–438.
    [Google Scholar]
  37. Vauterin, L., Hoste, B., Kersters, K. & Swings, J. ( 1995; ). Reclassification of Xanthomonas. Int J Syst Bacteriol 45, 472–489.[CrossRef]
    [Google Scholar]
  38. Wayne, L. G., Brenner, D. J., Colwell, R. R., Grimont, P. A. D., Kandler, O., Krichevsky, M. I., Moore, L. H., Moore, W. E. C., Murray, R. G. E. & other authors ( 1987; ). Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37, 463–464.[CrossRef]
    [Google Scholar]
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