Characterizing the canine urobiome and its role in calcium oxalate urolithiasis

Abstract

The urinary microbiome, also known as the urobiome, refers to the diverse communities of microorganisms residing within the urinary tract. These commensal microbes play critical roles in urinary tract health and disease. Dogs also possess a urobiome and represent a powerful translational model for microbiome research. In both dogs and humans, additional insight is needed regarding how external variables impact urobiome composition. Therefore, the first goal of this research was to characterize how external variables, specifically urine collection technique and diet, impact urobiome composition in dogs. Results showed that urine collected via midstream voiding harbored higher abundances of several bacteria typically associated with the skin or urethro-genital tract, as compared to urine collected via cystocentesis. Measures of alpha and beta diversity also differed by collection technique, indicating that urine collection method needs to be considered in the design of urobiome research studies in dogs. When evaluating the impact of diet on urobiome composition, differences in alpha and beta diversity were not observed in relation to macronutrient content (protein, fat, and crude fiber). However, beta diversity differed between dogs fed one commercial diet brand compared to dogs consuming any other brand. Furthermore, dogs with high dietary diversity (≥ 3 unique food sources) exhibited differences in beta diversity compared to those with low dietary diversity (< 3 unique food sources). These findings support the hypothesis that dietary features can impact urobiome diversity and structure. The second goal of this research was to determine how the microbiome and metabolome impact calcium oxalate (CaOx) stone formation in dogs. CaOx urolithiasis is a devastating disease in both dogs and humans, characterized by impaired quality of life for patients, increasing disease prevalence, restricted treatment options, and high recurrence rates. First, microbial DNA was extracted from urine samples collected from Miniature Schnauzers with and without CaOx urolithiasis, followed by 16S rRNA gene amplicon sequencing. Results showed that several bacteria significantly differed in abundance between the urobiome of stone formers compared to stone-free controls. Acinetobacter was the taxa most over-represented in the urine of stone formers, and this organism has been previously associated with the urine of human stone formers. Serum lipidomics and metabolomics were also performed in Miniature Schnauzers with and without CaOx urolithiasis to better define underlying metabolic derangements in canine stone formers. No lipid species significantly differed between groups, suggesting that dyslipidemia might not be a major risk factor for stone formation in Miniature Schnauzers. However, 3 metabolites were lower in stone formers, and a distinct subset of dogs with stones were identified that exhibited unique profiles of metabolites with known biological links to CaOx stone formation. This research offers novel insight into variables shaping canine urobiome composition, highlighting the need for urobiome investigators to consider urine collection technique and dietary factors when designing and interpreting urobiome studies. This research also identified specific microbes and metabolites potentially relevant to canine CaOx stone formation. Future studies expanding upon these findings will further improve understanding of the canine urobiome and the role of the urobiome and metabolome in CaOx stone formation.