HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS		QUICK SEARCH:   [advanced] Author: Keyword(s): Year:  Vol:  Page:

This Article Full Text Full Text (PDF) Alert me when this article is cited Alert me if a correction is posted Citation Map Services Email this article to a friend Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via HighWire Citing Articles via CrossRef Citing Articles via Google Scholar Google Scholar Articles by Goris, J. Articles by Tiedje, J. M. Search for Related Content PubMed PubMed Citation Articles by Goris, J. Articles by Tiedje, J. M. Agricola Articles by Goris, J. Articles by Tiedje, J. M.

DNA–DNA hybridization values and their relationship to whole-genome sequence similarities

Johan Goris^1,, Konstantinos T. Konstantinidis^1,, Joel A. Klappenbach¹, Tom Coenye², Peter Vandamme² and James M. Tiedje¹

¹ Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, USA
² Laboratory for Microbiology, Gent University, K. L. Ledeganckstraat 35, B-9000 Gent, Belgium

Correspondence
Johan Goris
johan_goris{at}applied-maths.com

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.

Present address: Applied Maths NV, Keistraat 120, B-9830 Sint-Martens-Latem, Belgium.

Present address: 15 Vassar Street, Room 48-336, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

This article has been cited by other articles:

				T. Adekambi, T. M. Shinnick, D. Raoult, and M. Drancourt Complete rpoB gene sequencing as a suitable supplement to DNA-DNA hybridization for bacterial species and genus delineation Int J Syst Evol Microbiol, August 1, 2008; 58(8): 1807 - 1814. [Abstract] [Full Text] [PDF]

				M. Martens, P. Dawyndt, R. Coopman, M. Gillis, P. De Vos, and A. Willems Advantages of multilocus sequence analysis for taxonomic studies: a case study using 10 housekeeping genes in the genus Ensifer (including former Sinorhizobium) Int J Syst Evol Microbiol, January 1, 2008; 58(1): 200 - 214. [Abstract] [Full Text] [PDF]