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

TLDR

DDH has long been the primary criterion for bacterial species delineation, measuring strain relatedness. The study aimed to quantify how DDH values correlate with genome‑derived metrics such as average nucleotide identity (ANI) and conserved DNA percentage. The authors measured 124 DDH values across 28 strains from six diverse bacterial groups, all sharing >94 % 16S rRNA identity. DDH values closely matched ANI and conserved DNA percentages, with a 70 % DDH cut‑off corresponding to 95 % ANI, 69 % conserved DNA, and 85 % conserved genes in coding regions, revealing extensive gene diversity and indicating that ANI can replace DDH for sequenced strains.

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.