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

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Abstract 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. Highlights: Comprehensive genomic resource comparing with high-quality long-read whole genomes and reference Gardnerella vaginalis and Lactobacillus iners strains. Integrated multi-omics and functional analysis on the most common vaginal microbiome species using 16S rRNA gene sequencing, proteomics, metabolomics, and in vitro assays. Key phenotypes quantified, including biofilm formation and polymicrobial interactions. Conserved Type II Secretion/Tad Pilus System identified across all Gardnerella vaginalis strains, with AI-predicted structural modeling. Evaluation of growth inhibition using metabolites against a panel of relevant microbes, including vaginal microbes and opportunistic pathogens.

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