Background Atopobium vaginae is a prevalent vaginal bacterium associated with bacterial vaginosis (BV). Molecular studies targeting its 16S rRNA gene have shown A. vaginae is a useful diagnostic indicator of BV and important secondary colonizer of the vaginal biofilm. Both A. vaginae and the vagina’s primary biofilm-forming species, Gardnerella vaginalis, exhibit extreme genomic heterogeneity. This led to Gardnerella’s recent split into approximately nine genomospecies indistinguishable by their 16S genes. The objective of this work was to ascertain whether similar subdivisions should be made for A. vaginae.

Methods We performed comparative genomics on publically available A. vaginae whole genome sequences. We also genotyped 20 A. vaginae isolates from women participating in a BV treatment study and phenotypically characterized select strains to identify their biochemical properties (API/MIC tests) and virulence potential.

Results Three genomospecies were defined by cross-species nucleic acid identity <74%; each shares ≥99% 16S rRNA gene identity and belongs to the new genus Fannyhessea. Two species previously cultured and sequenced are Fannyhessea vaginae (CCUG 38953T, representing 85% of cultured isolates) and Fannyhessea massiliense (Marseille-P4126T, PB189–14T). These species differ in alkaline and acid phosphatase activity, as well as leucine arylamidase activity. Novel Fannyhessea species type 2 was distinguished by its inability to ferment sucrose or tagatose and its sensitivity to metronidazole. Colony morphology, Gram stain, and lack of detectable catalase, indole, sialidase, proteinase, and hyaluronidase activities were similar for all three species. Functional genomics revealed F. vaginae uniquely possesses sialic acid response machinery and several adhesion proteins.

Conclusions Genomic and functional differences support redefining A. vaginae as three novel Fannyhessea species. More work is needed to re-examine its role in BV in the absence of confounding by the other species, but our findings suggest F. vaginae may contribute to treatment failure and interact specifically with the Gardnerella biofilm and host epithelium.