The Impact of Urine Collection Method on the Canine Urinary Microbiota: A Cross-Sectional Study

Urinary microbiota research poses serious technical challenges given low urine biomass and the risk of sample contamination. Urine collection technique represents a critical component of study design, though the impact of collection method on the canine urinary microbiota remains unknown. Therefore, the objective of this study was to determine whether urine collection technique alters microbial populations in canine urine samples. Urine was collected from healthy dogs by both cystocentesis and midstream voiding. Microbial DNA was isolated from each sample and submitted for amplicon sequencing of the V4 region of the bacterial 16S rRNA gene, followed by analyses to compare microbial diversity and composition between urine collection techniques. Samples collected via cystocentesis exhibited significantly lower sequence read counts (P = .036) and observed richness (P = .0024) than midstream voided urine. Bray Curtis and Unweighted UniFrac measures of beta diversity showed distinct differences in microbial composition by collection method (P = .0050 and P = .010, respectively). Seven organisms were identified as differentially abundant. Pasteurellaceae, Haemophilus, Friedmanniella, 2 variants of Streptococcus, and Fusobacterium were over-represented in voided urine, and Burkholderia-Caballeronia-Paraburkholderia was over-represented in cystocentesis samples. Microbial composition differs in canine urine samples collected via cystocentesis as compared to those collected via midstream voiding. Future researchers should select a single urine collection method based on the biological question of interest when designing canine urinary microbiota studies.