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The vagina contains at least a billion microbial cells, which are dominated by Lactobacilli. Here we perform metagenomic shotgun sequencing on cervical samples from 1148 women. Factors such as pregnancy, delivery histories and breast-feeding were all more important than menstrual cycle in shaping the microbiome. Bifidobacterium breve was seen with older age at sexual debut; Lactobacillus crispatus negatively correlated with pregnancy history; potential markers for lack of menstrual regularity, heavy flow, dysmenorrhea, contraceptives were also identified. Other features such as mood fluctuations and facial speckles could potentially be deduced from the vagino-cervical microbiome. Gut and oral microbiome, plasma vitamins, metals, amino acids and hormones showed associations with the vagino-cervical microbiome. Our results offer an unprecedented glimpse into the microbiota of the female reproductive tract and call for international collaborations to better understand its long-term health impact. Highlights Shotgun sequencing of 1148 vagino-cervical samples reveal subtypes; Other omics such as moods and skin features could be predicted by the vagino-cervical bacteria; Factors such as delivery mode and breast-feeding associate with the vagino-cervical microbiome; With dwindled Lactobacilli, postmenopausal samples are relatively enriched for viruses.

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