Culturomics-generated vaginal and endometrial microbiome profiles in subfertile patients

Abstract Study question In subfertile patients, do the endometrial and vaginal microbiome correspond to one another when applying high-throughput culturing techniques? Summary answer High interpatient variation was observed in the number of different isolated species. Furthermore, there was a diverse patient-specific concordance between vaginal and endometrial microbiota profiles. What is known already The microbiome of the female reproductive tract is potentially implicated in fertility and in vitro fertilization success rates. Of particular interest is Lactobacillus iners, an ineffective lactic acid producer, that is related with vaginal dysbiosis and adverse reproductive health outcomes. Previous metagenomics-based studies have highlighted that the endometrial and vaginal microbiome can be quite distinct in the same patient. Here, we investigated the applicability of a novel methodology, i.e. culturomics, in studying the vaginal-uterine microbiome. In contrast to metagenomics, a culturomics-generated microbiome profile is not influenced by depth bias or DNA contamination from extraction kits and reagents. Study design, size, duration In this pilot study, paired samples of vaginal swabs and endometrial biopsies were obtained from six subfertile women undergoing a diagnostic hysteroscopy. Vaginal swabs were taken prior to the hysteroscopy, while biopsies were harvested afterwards, with a pipelle technique. Participants/materials, setting, methods A plethora of enrichment broths and (non)selective agars were processed in an aerobic and anaerobic manner to ensure exhaustive culturomics results. Agars were incubated until 30 days post-inoculation and processed applying the Copan WASPLab® system. Bacterial colonies were identified using the Brüker MALDITOF MS Biotyper® system. Main results and the role of chance A total of 3218 colonies were detected using the MALDI Biotyper® system, enabling the identification of 79 different species. High inter-patient variability was observed in the number of detected isolated species (11–49). Also, the concordance between vaginal and endometrial microbiota differed from 4 to 48 %. Interestingly, the percentage of vagino-endometrial similarity and microbial diversity seemed to be associated with the presence of certain Lactobacillus species. We observed that the less diverse microbiome profiles (11-27 species) were dominated by eubiosis-related strains such as L. crispatus, L. jensenii, L. gasseri, L. salivarius and L. vaginalis, while the more diverse microbiome profile (49 species) was colonized by de dysbiosis-associated L. iners. Limitations, reasons for caution Only a small number of patients was included as this was a proof-of-principle study investigating the applicability of culturomics on vaginal swabs/endometrial biopsies. Wider implications of the findings Culturomics-acquired microbiome profiles could have a place in personalized fertility medicine with potential implications in therapy. The true value of our findings and their relationship with endometrial pathologies and IVF success rates needs to be confirmed in larger series. Trial registration number 143201420916