Background: Female reproductive tract microbiota may impact human reproduction. This study evaluated if a more detailed characterization of the vaginal microbiota could improve prediction of IVF patients at risk of a poor reproductive outcome.

Methods: Vaginal samples from 120 IVF patients were sequenced using the V4 region of the 16S rRNA gene with clustering of G. vaginalis genomic clades. Abnormal vaginal microbiota was defined by microscopy and qPCR for Gardnerella vaginalis and/or Atopobium vaginae above a threshold. The study was registered on clinicaltrials.gov (NCT02042352).

Results: Three major Community State Types with abundance of L. crispatus, L. iners and a diverse community type were identified, including two sub-types, characterized by a high abundance of L. crispatus and L. iners, respectively, but in combination with common diversity type Operational Taxonomic units. No significant association between Community state type and the reproductive outcome could be demonstrated, however, abnormal vaginal microbiota by qPCR and a grouping based on high Shannon Diversity Index predicted the reproductive outcome equally well.

Conclusions: The predictive value of 16S rRNA gene sequencing was not superior to the simpler and less expensive qPCR diagnostic approach in the prediction of IVF patients at risk of a poor reproductive outcome.