Uncovering the class II-bacteriocin predatiome in salivarius streptococci

Abstract Facing the surge of antibiotic resistance, the medical field has a critical need for alternatives to treat bacterial infections. Among these, the use of bacteriocins is considered to be a promising route. In the human commensal Streptococcus salivarius, the production of unmodified bacteriocins is directly controlled at the transcriptional level by the quorum-sensing ComRS system. Here, we used an integrated approach combining bioinformatics and synthetic biology to discover bacteriocins from salivarius streptococci active against human pathogens. We developed a bioinformatic pipeline that combines conservation of DNA regulatory motifs and features of bacteriocin primary sequences to uncover cryptic class II bacteriocins. Notably, we identified more than 50 bacteriocin candidates clustered into 21 groups from 100 genomes of S. salivarius. Strain-based analysis of bacteriocin cocktails revealed an important diversity restricted to seven distinct loci, probably resulting from bacteriocin intra- and inter-species exchanges. Using in vitro or in vivo production and synthetic biology tools, we showed that most of them are active against a panel of Gram-positive bacteria, including clinically-relevant pathogens. Overall, this work provides a search-to-test generic pipeline for the discovery of uncharacterized bacteriocins in Gram-positive bacteria that could be used in cocktails for broad applications in the food and biomedical fields.