VIRGO2 is a non-redundant catalog of genes from the human vaginal microbiome that allows for rapid taxonomic and functional analysis of metagenomic/metatranscriptomic reads. VIRGO2 is distributed as a bowtie2 index so that processed/QC'd reads can be mapped using the bowtie2 short read mapping tool. Annotation tables can be merged with mapping results to provide taxonomic and functional information.

Despite the importance of the cervicovaginal microbiome, the mechanisms that govern its composition and drive its impact on host physiology remain poorly understood. With the aim to expand our understanding of the function and ecology of the vaginal microbiome, we present VIRGO2, an enhanced non-redundant gene catalog comprising over 1.7 million well-annotated genes from body-site specific microbes and viruses. Analyses using VIRGO2 reveal insights suchas including the identification of previously uncharacterized vaginal bacteria, features of the vaginal mycobiome and phageome, and differential expression of bacterial carbohydrate catabolic genes. Constructed from over 2,500 metagenomes and 4,000 bacterial genomes, VIRGO2 broadens geographic representation and microbial diversity compared to its predecessor. This updated catalog enables more precise profiling of taxonomic and functional composition from metagenomic and metatranscriptomic datasets. VIRGO2 is a critical resource for integrative analyses of vaginalmicrobial communities and their interactions with host tissues, thereby enhancing our mechanistic understanding of vaginal health and disease.

VIRGO2: an enhanced gene catalog of the vaginal microbiome provides insights into its functional and ecology complexity. France MT, Chaudry I, Rutt L, Quain M, Shirtliff B, McComb E, Maros A, Alizadeh M, Hussain FA, Elovitz MA, Relman DA, Rahman A, Brotman RM, Price JT, Kassaro MP, Holm JB, Ma B, Ravel J. Nat Commun. 2025 Dec 6. doi: 10.1038/s41467-025-67136-2.