The urinary pathobiont Actinobaculum massiliense can generate androgens via the dirAB pathway

While overlooked during the Human Microbiome Project, characterizing the urinary microbiota in health and disease is a new frontier in microbiome science. Recent studies have associated differential abundance of bacterial taxa including Propionimicrobium lymphophilum and Actinobaculum/Actinotignum spp. with prostate cancer. In this study, we collected urine from subjects before prostate biopsy and applied a Human Sterolbiome Discovery High-throughput (HSDH) assay to identify culturable urinary bacteria with the ability to generate androgens. Application of the HSDH Assay to urine samples led to the isolation of eight P. lymphophilum strains positive for cortisol side-chain cleavage (steroid-17,20-desmolase), 17β-HSDH activity, or both. In addition, we isolated three strains of Actinobaculum massiliense that carry the DHEA isomerase reductase (dir) genes. The dirA gene encodes a multifunctional 3β/17β-hydroxysteroid dehydrogenase/Δ^4,5-isomerase and the dirB gene encodes a 17β-hydroxysteroid dehydrogenase isoform. Structural prediction and molecular dynamics reveal probable catalytic mechanisms based on the shared catalytic triad but distinct binding-pocket geometries of DirA and DirB, which enabled predictions of their respective reactions. Phylogenetic analysis of DirA and DirB revealed homologs in urinary tract commensals and in bacteria associated with steroid degradation in aquatic and terrestrial environments. Taken together, the development of the HSDH Assay and the identification of the dir pathway genes provide the methodological foundation and provide the molecular basis for advancing our understanding of the role of urinary tract bacteria in host endocrine physiology.