The human vagina harbours diverse microorganisms—bacteria, viruses and fungi—with profound implications for women’s health. Genome-level analysis of the vaginal microbiome across multiple kingdoms remains limited. Here we utilize metagenomic sequencing data and fungal cultivation to establish the Vaginal Microbial Genome Collection (VMGC), comprising 33,804 microbial genomes spanning 786 prokaryotic species, 11 fungal species and 4,263 viral operational taxonomic units. Notably, over 25% of prokaryotic species and 85% of viral operational taxonomic units remain uncultured. This collection significantly enriches genomic diversity, especially for prevalent vaginal pathogens such as BVAB1 (an uncultured bacterial vaginosis-associated bacterium) and Amygdalobacter spp. (BVAB2 and related species). Leveraging VMGC, we characterize functional traits of prokaryotes, notably Saccharofermentanales (an underexplored yet prevalent order), along with prokaryotic and eukaryotic viruses, offering insights into their niche adaptation and potential roles in the vagina. VMGC serves as a valuable resource for studying vaginal microbiota and its impact on vaginal health.

人类阴道蕴藏着多种微生物——细菌、病毒和真菌——对女性健康有着深远的影响。对多个领域的阴道微生物组的基因组水平分析仍然有限。在这里，我们利用宏基因组测序数据和真菌培养建立了阴道微生物基因组保藏库 (VMGC)，其中包括 33,804 个微生物基因组，涵盖 786 个原核物种、11 个真菌物种和 4,263 个病毒操作分类单位。值得注意的是，超过 25% 的原核物种和 85% 的病毒操作分类单位仍未培养。该集合显着丰富了基因组多样性，特别是对于常见的阴道病原体，例如 BVAB1（一种未培养的细菌性阴道病相关细菌）和杏仁杆菌属。 （BVAB2 和相关物种）。利用 VMGC，我们表征了原核生物的功能特征，特别是糖发酵目（一种尚未充分探索但普遍存在的目）以及原核和真核病毒，从而深入了解它们的生态位适应和在阴道中的潜在作用。 VMGC 是研究阴道微生物群及其对阴道健康影响的宝贵资源。