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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 58, Issue 8

Complete gene sequencing as a suitable supplement to DNA–DNA hybridization for bacterial species and genus delineation Free

Abstract

DNA–DNA hybridization (DDH), the gold standard for bacterial species delineation, is a laborious method and the alternative, average nucleotide identity (ANI), a genomic sequence-derived parameter, is not applicable to non-sequenced species. A universal cut-off value to delineate bacterial species does not exist, yet a DDH value <70 % and ANI <95±0.5 % have proved useful in selected examples. We herein compare published values for DDH and ANI with sequence similarity of gene sequences retrieved from GenBank for strains of 230 bacterial species representative of 45 genera. Intraspecific sequence similarity was 98.2–100 %. We observed that an gene sequence similarity ≤97.7 % significantly correlated with a DDH value <70 % and an ANI value <94.3 %. An gene sequence similarity <85.5 % correlated with membership of different genera. When applied to fastidious and as-yet-uncultivated organisms lacking experimental DDH values, these cut-off values suggested that ‘ Blochmannia pennsylvanicus’ and ‘ Blochmannia floridarius’ may belong to different genera, that the different endosymbiotic organisms may belong to different genera and that, while the tsetse fly enteric symbiont may belong to the , the endocellular obligate symbiont from the same host may belong to the group of as-yet-uncultivated gammaproteobacteria. gene sequence similarity provides an efficient supplement to DDH and ANI measurements to delineate bacterial species and genera, including delineation of as-yet-uncultivated, non-sequenced organisms.

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Keyword(s): ANI, average nucleotide identity and DDH, DNA–DNA hybridization
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2008-08-01
2024-04-24
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Complete rpoB gene sequencing as a suitable supplement to DNA–DNA hybridization for bacterial species and genus delineation
Int J Syst Evol Microbiol 58, 1807 (2008); https://doi.org/10.1099/ijs.0.65440-0
/content/journal/ijsem/10.1099/ijs.0.65440-0
/content/journal/ijsem/10.1099/ijs.0.65440-0
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