Comprehensive Metagenomic Profiling of the Cervical Microbiome in Patients with Cervical Insufficiency.

The cervicovaginal microbiome is central to pregnancy health; however, the combined influence of bacteria, viruses, and phages remains unclear. We performed shotgun metagenomic sequencing of 232 cervical samples from 116 pregnant women stratified by cerclage type, cervical insufficiency, membrane bulging, preterm birth, and anatomical site. Genome-resolved analyses revealed distinct microbial and viral signatures across clinical states. Prophages were frequently integrated in Lactobacillus crispatus, consistent with a reduced biosynthetic capacity; the enrichment of Bifidobacterium breve, Prevotella bivia, and Gardnerella vaginalis marked cervical insufficiency and membrane bulging, conditions predictive of preterm birth. Virome profiling identified the Epstein–Barr virus and high-risk human papillomaviruses, which were linked to reduced Lactobacillus, functional reprogramming, and G. vaginalis expansion. Emergent cerclage cases showed deeper dysbiosis than prophylactic cases did; preterm samples exhibited reduced lipid metabolism essential for cervical stability. These results demonstrated how phages, viruses, and bacterial dysbiosis jointly shape cervical microbial function, thus offering insights into predicting risks for adverse pregnancy outcomes.