Identification and Characterization of Novel Antimicrobial Compounds Encoded by Biosynthetic Gene Clusters from Human Vaginal Lactobacillus Species

Abstract

The lactic acid-producing genus Lactobacillus dominates in vaginal bacterial communities in healthy women and is thought to play a role in protecting against pathogens. Consistent with this idea, bacterial vaginosis, which involves reduced proportions of vaginal Lactobacillus species, is correlated with adverse outcomes such as preterm birth and HIV transmission. Specific Lactobacillus species are associated with different outcomes, indicating a role for factors besides lactic acid. We hypothesized that certain strains of Lactobacilli secrete antimicrobial small molecules that inhibit commensals or pathogens. To investigate, we queried the genomes of 38 Lactobacillus strains for antibiotic-encoding biosynthetic gene clusters (BGCs) and identified 16 distinct BGCs. We cultured 11 Lactobacillus strains expressing BGCs and, in parallel, we cloned candidate BGCs for expression in Bacillus subtilis. For each culture, we chemically extracted the pellets and supernatants and screened extracts for BGC-encoded compounds using liquid chromatography-mass spectrometry (LC-MS). We tested endogenous extracts for activity and found that many inhibited the growth of other commensals as well as the bacterial vaginosis-associated pathogen G. vaginalis. We selected one strain of L. jensenii with a non-ribosomal peptide BGC and activity against G. vaginalis and L. iners for characterization. We are currently fractionating its supernatant extract to isolate activity. Candidate BGCs in 3 L. crispatus and 3 L. gasseri strains that inhibited G. vaginalis were also identified. Our results suggest that BGCs encoding antimicrobials in specific Lactobacillus strains could play an important role in mediating the dynamics of the vaginal bacterial community by inhibiting each other and pathogens associated with bacterial vaginosis.