Version 1: Exploring Bacterial Strain Diversity in the Asymptomatic Urinary Microbiome

Taxa of the asymptomatic (“healthy”) urinary tract microbiota (urobiome) have been identified through high-throughput, short-read sequencing of the 16S rRNA and culture-based studies. These methods have identified numerous genera and species, respectively, that persist within this low biomass environment. Studies employing shotgun metagenomic sequencing of urine samples has only recently been done, and they have primarily focused on identifying non-prokaryotic constituents and/or assessing the functional capacity of the community. Species diversity within the urobiome has yet to be explored. Here we conducted a proof-of-concept study using the software tool STRONG to identify taxa and strain diversity within the asymptomatic urobiome. Two mock communities of urinary strains were produced and sequenced to provide a benchmark for such analyses. Sixty-one urobiome data sets were examined. Species were identified in 29 (47.54%) of the samples examined, including 9 samples containing more than one species, and 8 samples containing more than one strain of a given species. This suggests that the asymptomatic urobiome can include strain diversity, despite being a low biomass community. Further investigation into strain diversity within the urobiome will provide insight into dynamics of this community, in particular with respect to lower urinary tract symptoms.