16SpeB: Towards defining bacterial species boundaries by intra-species gene sequence identity

ABSTRACT Summary 16SpeB ( 16 S rRNA-based Spe cies B oundary) is a package of Perl programs that evaluates total sequence variation of a bacterial species at the levels of the whole 16S rRNA sequences or single hypervariable (V) regions, using publicly-available sequences. The 16SpeB pipelines filter sequences from duplicated strains and of low quality, extracts a V region of interest using general primer sequences, and calculates sequence percentage identity (%ID) through all possible pairwise alignments. Results The minimum %ID of 16S rRNA gene sequences for 15 clinically-important bacterial species, as determined by 16SpeB, ranged from 82.6% to 99.8%. The relationship between minimum %ID of V2/V6 regions and full-gene sequences varied among species, indicating that %ID species limits should be resolved independently for each region of the 16S rRNA gene and bacterial species. Availability 16SpeB and user manual are freely available for download from: https://github.com/pnpnpn/16SpeB . A video tutorial is available at: https://youtu.be/Vd6YmMhyBiA Contact [email protected] Supplementary information Supplementary data are available at Bioinformatics online.