Nationwide profiling of vaginal microbiota in Chinese women reveals age‐dependent shifts and predictive biomarkers for reproductive health

The vaginal microbiome is central to reproductive health, yet large-scale studies in East Asian populations remain scarce. Here, we characterized the vaginal microbiota of 6423 Chinese women of reproductive age across 18 provinces and assessed associations with 33 host factors. We observed a striking compositional transition around age 40, marked by declining <i>Lactobacillus crispatus</i> and enrichment of dysbiosis-associated taxa including <i>Gardnerella vaginalis</i>, independent of lifestyle or sociodemographic influences. Sexual behavior, contraceptive use, and educational attainment emerged as key determinants of community structure, differentially shaping <i>Lactobacillus crispatus</i> and <i>Lactobacillus</i> iners. Despite these associations, host factors explained less than 2% of overall variation, highlighting the resilience and individuality of the vaginal microbiome. To quantify vaginal health, we derived a microbiome balance score, validated it in external cohorts, and demonstrated its predictive power for incident bacterial vaginosis and sexually transmitted infections. Our findings establish a national-scale reference for the vaginal microbiome in Chinese women, reveal a midlife inflection point in microbial composition, and introduce a clinically actionable metric for risk stratification. These insights advance mechanistic understanding of host-microbiome interactions and inform strategies for precision interventions to preserve vaginal health.