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Background  To date, information on healthy female urinary microbiota is available mostly at genus level and at one time point. However, profound species-level characterization of healthy urinary microbiome and its stability over time are essential for further correct interpretation of its role in healthy urogenital tract. In this study, we investigated female urogenital microbiome (FUM) at two timepoints (within 2.5-year interval) in young asymptomatic European women. We used culturomics with accurate isolates’ identification (MALDI-TOF MS and gene markers sequencing) to understand species stability within healthy FUM.    Results  Extended culturomics of voided midstream urine sample pairs revealed a mean Shannon diversity index of 1.25 and mean of 19 species/sample (range 5–39 species; total of 115 species; 1830 isolates). High overall species variability between individuals was captured by beta diversity and a variety of community structure types, with the largest cluster characterized by  Lactobacillus crispatus , often in combination with  Gardnerella vaginalis  or  Gardnerella  genomospecies 3. Significant FUM composition differences, related to  Finegoldia magna  and  Streptococcus anginosus,  according to smoking status were found.  A high species variability within individuals (Shannon index SD > 0.5 in 7 out of 10 sample pairs) with a mean of 29% of shared species (range 9.1–41.7%) was observed. Moreover, 4 out of 10 sample pairs clustered in the same community structure type. The stable FUM sample pairs presented high abundance of  Lactobacillus crispatus, Streptococcus agalactiae  or  Lactobacillus paragasseri  and  Bifidobacterium  spp.. Moreover,  Gardnerella vaginalis ,  Gardnerella  genomospecies 3 or  Gardnerella swidsinskii  were often maintained within individuals in high abundance.    Conclusions  Shift in species composition at two distant timepoints was frequently observed among urogenital microbiome of European asymptomatic women. This suggests possible interchange of particular species in healthy FUM and the existence of multiple health-associated FUM compositions in certain individuals.  Additionally, we provided additional evidence on resilience of particular bacterial communities and identified certain species more prone to persist in urogenital tract.  This study revealed important details on the FUM composition complexity relevant for studies aiming to understand microbiota role in the urogenital tract health and for identification of eubiotic and dysbiotic FUM.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12866-021-02123-3.

Long-term stability of the urogenital microbiota of asymptomatic European women