VIRGO2: an enhanced gene catalog of the vaginal microbiome provides insights into its functional and ecology complexity
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 such as 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 2500 metagenomes and 4000 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 vaginal microbial communities and their interactions with host tissues, thereby enhancing our mechanistic understanding of vaginal health and disease.
Authors
- Joan T. Price (ORCID: https://orcid.org/0000-0003-4178-0405)
- Rebecca M. Brotman (ORCID: https://orcid.org/0000-0001-8762-6214)
- Alexandra Maros (ORCID: https://orcid.org/0009-0006-4884-1476)
- Elias McComb (ORCID: https://orcid.org/0000-0001-6324-2718)
- Issac Chaudry (ORCID: https://orcid.org/0000-0002-3497-3105)
- Madeline Alizadeh (ORCID: https://orcid.org/0000-0001-5650-3393)
- Bing Ma (ORCID: https://orcid.org/0000-0002-3488-2393)
- Michal A. Elovitz (ORCID: https://orcid.org/0000-0001-7554-7180)
- Johanna B. Holm (ORCID: https://orcid.org/0000-0002-7646-4085)
- Marian Dorcas Quain (ORCID: https://orcid.org/0000-0001-6109-8628)
- Jacques Ravel (ORCID: https://orcid.org/0000-0002-0851-2233)
- David A. Relman (ORCID: https://orcid.org/0000-0001-8331-1354)
- Fatima A. Hussain (ORCID: https://orcid.org/0000-0002-3669-795X)
- Lindsay Rutt
- Michael France (ORCID: https://orcid.org/0000-0002-6029-0201)
- Anisur Rahman (ORCID: https://orcid.org/0000-0001-8279-9810)
- Margaret P. Kassaro
- Breanna Shirtliff
Institutions
- University of North Carolina at Chapel Hill (US)
- Tufts University (US)
- University of Maryland, Baltimore (US)
- VA Palo Alto Health Care System (US)
- International Centre for Diarrhoeal Disease Research (BD)
- Institute for Learning Innovation (US)
- Biomedical Research Institute (US)
- National HIV/AIDS/STI/TB Council (ZM)
- World Health Organization - Zambia (ZM)
- Stanford University (US)
- Icahn School of Medicine at Mount Sinai (US)
Publication Details
- Journal
- Nature Communications
- Published
- 2025-12-06
- DOI
- https://doi.org/10.1038/s41467-025-67136-2
- Citations
- 2
- Primary Topic
- Reproductive tract infections research
- Type
- article
- Field-Weighted Citation Impact
- 2.37