Multi-omics uncovers interaction in the vaginal microbiome and a type II secretion/Tad pilus system in Gardnerella vaginalis

The vaginal microbiome is a critical determinant of women’s health. We investigated the genetic basis of common vaginal microbiome species and their biofilm formation. Genomic analysis of Gardnerella vaginalis ( Gv ) revealed a fundamental phylogenetic split correlating with high- versus low-biofilm phenotypes, driven by clade-specific genomic islands and allelic variants. In a dual-species coculture model of five key vaginal bacteria, Gv achieved numerical dominance, triggering extensive, asymmetric proteomic reprogramming in partner species while showing limited shifts itself. Proteins from biofilm-associated modules showed functional divergence, supported by AI-predicted structural variations in a type II secretion/Tad pilus system, which is first discovered from Gv strains. Integrated metabolomics identified a methyl- β -carboline compound that is elevated in cocultures containing Prevotella bivia ( Pb ). This compound acts as a potent and selective inhibitor of Gv and Pb biofilms, sparing Lactobacillus crispatus . This work establishes a direct genomic basis for Gv virulence and demonstrates how interspecies interactions govern community dynamics and antimicrobial metabolite production.