Bioinformatics Application Tool

16SpeB (16S rRNA Species Boundary)

16SpeB is a bioinformatics application tool that can be used to investigate total 16S rRNA gene sequence variation within specific bacterial species through publicly-available sequences. It determines the minimum % sequence identity of the (near)-full or individual variable (V) regions of the 16S rRNA gene that defines a species of interest. We developed this tool in collaboration with Patrick Ng (Computer Science, Cornell).

Users can submit 16S rRNA gene sequences of a bacterial species collated from public databases (Greengene, RDP, and Silva). The 16SpeB pipeline filters sequences from duplicated strains and of low quality, extracts a V region (e.g. V2 or V6) of interest using general primer sequences; and evaluates % sequence identity through all possible pairwise sequence alignments (Needleman-Wunsch algorithm).

16SpeB has been used to study species boundaries in various bacteria, including the genera Acetobacter andLactobacillus (Wong CN, Ng P and Douglas AE, 2011. Low diversity bacterial community in the gut of the fruitfly Drosophila melanogaster. Environmental Microbiology 13: 1889-1900).

The manual and scripts to download and use 16SpeB are available as Downloads (see sidebar on left), together with the pdf of Wong et al. (2011) in which 16SpeB has been used.

A video with step-by-step instructions is available below (full screen view is recommended for optimal viewing)