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The past decade has provided ample evidence that humans host an enormous web of interacting microbial communities of great diversity and complexity. Sensitive microbial profiling approaches have documented a diverse microbial community in urine: the “urobiome.” While the role of this microflora in urinary tract health is unclear, patients with a range of urinary conditions exhibit clinical and biochemical features that implicate a microbial etiology to these diseases; quantitative shifts in the urobiome have been implicated in multiple urologic diseases from incontinence to malignancies. Yet despite a decade of studies detailing correlative urobiome differences between controls and patients with urologic diseases, these studies have yet to provide mechanistic insight into these conditions or meaningful guidance on how these differences inform clinical care. We hypothesize that this lack of progress results from significant knowledge gaps regarding optimal approaches to isolate and analyze urinary microbial populations. Most microbial profiling approaches in humans have been developed and tested in other organs, primarily the gut, but the principles developed for this biological niche may not apply to the urinary tract and have not been rigorously evaluated there. We do not know if the technologies commonly used to examine the urobiome are sufficient to examine the breadth of bladder-resident microbes. Preliminary data suggest non-bacterial microbes may be critical in urinary symptomatology (e.g., bladder pain), but these species are not captured in most urobiome analyses. As most urinary nucleic acids in urine are human in origin, methods to deplete human-derived materials may be needed to provide an adequate picture of urinary microbial content. In the gut, sampling location dramatically impacts the results of microbial analyses, yet significant debate still surrounds the question about whether non-invasive urine sampling reliably reproduces bladder-resident microbiota or predominantly reflects skin and vaginal contamination. This study seeks to advance our progress in urinary microbiome research by: 1) determining the optimal method for sampling the bladder-resident microbiota and 2) examining the utility and feasibility of different microbial profiling approaches in examining bladder-resident microbial communities. To make advances in understanding urinary host-microbe interactions, this proposal seeks to make evidence-based decisions to ensure our analytic approaches truly reflect the pathologic processes occurring in the bladder.
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