Sex shapes the human genitourinary microbiome, including many species recognized as uropathogens: urine profiles from a population-level shotgun metagenomics study

BackgroundUntil recently, the urine and urinary tract were considered sterile. Over the past decade, the discovery of a urinary microbiome has prompted growing interest in its potential role in urinary symptoms and disease. However, the composition and diversity of the urinary microbiome in the population remain poorly defined and prior studies have been limited by small sample sizes, selected patient populations, and low-resolution sequencing. Here, we characterize urine samples and their microbial content in a large population-based Swedish cohort using shotgun metagenomics. MethodsWe performed shotgun metagenomic sequencing of non-invasively collected (voided) urine samples from 2,062 participants of the population-based Swedish CArdioPulmonary bioImage Study (SCAPIS; 55% women, age range 50-65 years). These samples are considered genitourinary as they can contain microbiota of the urinary tract but also from the surrounding skin and genital tract. ResultsOf the 3,668 identified species, 90% were assigned at the species level taxonomy. Only 26 species were present in more than half of samples. Males had higher Shannon and inverse Simpson indices although no significant differences in species richness were observed by sex. Age showed only modest associations with alpha diversity. Beta diversity was significantly associated with sex, with females exhibiting greater within-group dispersion than males, and age had only a minimal effect in microbial composition. Microbial communities differed substantially between sexes, with several lactobacilli and bifidobacteria enriched in females, while Cutibacterium acnes, Enterococcus and Propionimicrobium lymphophilum were in males. Well-known urinary tract pathogens as Enterococcus faecalis or Escherichia coli were common even though all participants were asymptomatic and reported no urinary tract symptoms at the time of sampling. ConclusionsIn this large population-based study, we provide the most detailed characterization of voided urine profiles and their genitourinary microbiota to date, revealing substantial sex-specific differences and frequent occurrence of recognized uropathogens. These findings broaden the concept of a normal genitourinary microbiome and highlight the need to account for sex when studying the microbial content of urine samples. This sex-specificity may be key to define the functional role of the urinary or genitourinary microbiomes in health and disease.