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

Abstract

Summary16SpeB (16S rRNA-based Species Boundary) 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.\n\nResultsThe 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.\n\nAvailability16SpeB and user manual are freely available for download from: https://github.com/pnpnpn/16SpeB. A video tutorial is available at: https://youtu.be/Vd6YmMhyBiA\n\nContactcw442@cornell.edu\n\nSupplementary informationSupplementary data are available at Bioinformatics online.