Recurrent urinary tract infection and estrogen shape the taxonomic ecology and functional potential of the postmenopausal urobiome

Community-acquired urinary tract infection (UTI) is among the most common bacterial infections observed in humans. Postmenopausal women are a rapidly growing and underserved demographic group who are severely affected by rUTI with a >50% recurrence rate. In this population, rUTI can persist for years, reducing quality of life and imposing a significant healthcare burden. rUTI is most often treated by long-term antibiotic therapy, but development of antibiotic resistance and allergy leave physicians with fewer treatment options. The female urobiome has been identified as a key component of the urogenital environment. However, structural and functional changes in the urobiome underlying rUTI susceptibility in postmenopausal women are not well understood. Here, we used strictly curated, controlled cross-sectional human cohorts of postmenopausal women, urobiome whole genome (shotgun) metagenomic sequencing (WGMS), advanced urine culturing techniques, extensive biobanking of >900 patient-derived urinary bacterial and fungal isolates, and mass spectrometry-based estrogen profiling to survey the urobiome in rUTI patients during infection relapse and remission as well as healthy comparators with no lifetime history of UTI. Our results suggest that a history of rUTI strongly shapes the taxonomic and functional ecology of the urobiome. We also find a putative protective commensal population, consisting of species known to convey protection against bacterial vaginosis such as Lactobacillus crispatus, within the urobiome of women who do not experience UTI. Integration of clinical metadata detected an almost exclusive enrichment of putative protective species belonging to the genus, Lactobacillus, in women taking estrogen hormone therapy (EHT). We further show that the urobiome taxonomic ecology is shaped by EHT, with strong enrichments of putatively protective lactobacilli, such as L. crispatus and L. vaginalis. Integrating quantitative metabolite profiling of urinary estrogens with WGMS, we observed robust associations between urobiome taxa, such as Bifidobacterium breve and L. crispatus, and urinary estrogen conjugate concentrations, suggesting that EHT strongly alters the taxonomic composition of the female urobiome. We have further used functional metagenomic profiling and patient-derived isolate phenotyping to identify microbial metabolic pathways, antimicrobial resistance genes (ARGs), and clinically relevant antimicrobial resistance phenotypes enriched between disease-states. Our data suggest distinct metabolic and ARG signatures of the urobiome associated with current rUTI status and history. Taken together, our data suggests that rUTI history and estrogen use strongly shape the functional and taxonomic composition of the urobiome in postmenopausal women.