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Background  This study was undertaken to discover whether the vaginal microbe of women at childbearing age is different among groups defined by urogenital tract infections, childbearing history and menstrual cycle, respectively.    Results  This was a multiple case-control study of women at childbearing age who were assigned to case or control groups according to their states of urogenital tract infections. The participants were also grouped by childbearing history and menstrual cycle. Vaginal swabs were collected and stored at − 70 °C until assayed. The V3-V4 region of 16S rRNA gene was amplified using PCR and sequenced on the Illumina MiSeq platform. We tested the hypothesis of whether the relative abundance of microbial species in vaginal microbiota was varied with urogenital tract infections, childbearing history and menstrual cycle. The vaginal microbial richness (Alpha diversity measured by PD_whole tree) was decreased in normal women (without reproductive tract infections) than in those with bacterial vaginosis (BV), and decreased in pregnant women than in other groups of non-pregnancy. Similarly, women from groups of normal and in pregnancy had lower beta diversity on measure of unweighted_unifrac distance in comparison to those of infected and non-pregnant. The top 10 genus relative abundance, especially  Lactobacillus , which was the most dominant genus with the relative abundance of 71.55% among all samples, did not differ significantly between groups of childbearing history and menstrual cycle analyzed by ANOVA and nonparametric kruskal_wallis.  Lactobacillus iners  and  Lactobacillus helveticus  have the most abundance, totally account for 97.92% relative abundance of genus  Lactobacillus . We also found that a higher  L.helveticus / L.iners  ratio is more likely to present in normal women than in the infected and in pregnant than in non-pregnant, although these comparisons lack statistical significance.    Conclusions  The relative abundance of dominant bacterial taxa in vaginal microbial communities of women at childbearing age were not different among groups of childbearing history and menstrual cycle. Women from groups of in pregnancy and without reproductive tract infections had lower alpha and beta diversity. The composition of the main  lactobacillus  species may shift upon phases of a menstrual cycle and the status of reproductive tract infections.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12866-021-02300-4.

Reproductive tract microbiota of women in childbearing age shifts upon gynecological infections and menstrual cycle