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Updated: Jul 3, 2026

Efficient Nucleic Acid Extraction and 16S rRNA Gene Sequencing for Bacterial Community Characterization
Published on: April 14, 2016
Complete rpoB gene sequencing as a suitable supplement to DNA-DNA hybridization for bacterial species and genus
Toïdi Adékambi1, Thomas M Shinnick, Didier Raoult
1Unité des Rickettsies, CNRS UMR 6020 IFR 48, Faculté de Médecine, Université de la Méditerranée, Marseille, France.
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 rpoB gene sequences retrieved from GenBank for strains of 230 bacterial species representative of 45 genera. Intraspecific rpoB sequence similarity was 98.2-100 %. We observed that an rpoB gene sequence similarity
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