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Background  The urinary microbiota is similarly complex as the vaginal and penile microbiota, yet its role as a reservoir for pathogens and for recurrent polymicrobial biofilm diseases like bacterial vaginosis (BV) is not clear.    Results  Here, we analysed the urinary microbiota of healthy men and women and compared it with that of women during BV and after antibiotic treatment using next-generation sequencing of the 16S rRNA gene V1-V2 regions. Eight different community types, so called urotypes (UT), were identified in healthy humans, all of which were shared between men and women, except UT 7, dominated in relative abundance by  Lactobacillus crispatus , which was found in healthy women only. Orally applied metronidazole significantly reduced Shannon diversity and the mean relative abundance of  Gardnerella vaginalis ,  Atopobium vaginae , and  Sneathia amnii , while  L. iners  increased to levels twofold higher than those found in healthy women. Although individual urine microbial profiles strongly responded to the antibiotic, the healthy community could not be restored. The correlation between urinary and vaginal fluid microbiota was generally weak and depending on UT and BV status. It was highest in UT 1 in acute BV (59% of samples), but after metronidazole treatment, only 3 out of 35 women showed a significant correlation between their urinary and vaginal microbiota composition.    Conclusions  Urethra and bladder thus harbor microbial communities distinct from the vagina. The high abundance of BV related species in the urine of both men and women suggests that urine may act as a reservoir of pathogens and contribute to recurrence.    Trial registration  ClinicalTrials.gov,  NCT02687789Electronic supplementary material  The online version of this article (doi:10.1186/s40168-017-0305-3) contains supplementary material, which is available to authorized users.

The urinary microbiota of men and women and its changes in women during bacterial vaginosis and antibiotic treatment