The impact of urine collection method on canine urinary microbiota detection: a cross-sectional study

Abstract

Background The urinary tract harbors unique microbial communities that play important roles in urogenital health and disease. Dogs naturally suffer from several of the same urological disorders as humans (e.g., urinary tract infections, neoplasia, urolithiasis) and represent a valuable translational model for studying the role of urinary microbiota in various disease states. Urine collection technique represents a critical component of urinary microbiota research study design. However, the impact of collection method on the characterization of the canine urinary microbiota remains unknown. Therefore, the objective of this study was to determine whether urine collection technique alters the microbial populations detected in canine urine samples. Urine was collected from asymptomatic 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 16 S rRNA gene, followed by analyses to compare microbial diversity and composition between urine collection techniques. Results Samples collected via midstream voiding exhibited significantly higher sequence read counts (P = .036) and observed richness (P = .0024) than cystocentesis urine. Bray Curtis and Unweighted UniFrac measures of beta diversity showed distinct differences in microbial composition by collection method (P = .0050, R2 = 0.06 and P = .010, R2 = 0.07, respectively). Seven taxa were identified as differentially abundant between groups. Pasteurellaceae, Haemophilus, Friedmanniella, two variants of Streptococcus, and Fusobacterium were over-represented in voided urine, while a greater abundance of Burkholderia-Caballeronia-Paraburkholderia characterized cystocentesis samples. Analyses were performed at five thresholds for minimum sequence depth and using three data normalization strategies to validate results; patterns of alpha and beta diversity remained consistent regardless of minimum read count requirements or normalization method. Conclusion 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. Additionally, the authors suggest caution when interpreting results across studies that did not utilize identical urine collection methods.

Gut and Urinary Microbiota in Cats with Kidney Stones

“…To our knowledge, the present study is the second that confirms the existence of a urobiome in cats. The existence of a urobiome was also demonstrated in dogs [ 73 , 74 , 75 ].…”

“…Regarding urine collection, this study goes beyond the recommendations proposed by MICROCOSM using cystocentesis, the method of choice for urine collection in cats. It avoids the risk of contamination with urethral bacteria [ 75 ]. This technique is easy, safe, as well tolerated as a subcutaneous injection, and does not require ultrasound guidance for cats with a palpable bladder.…”

Evaluation of the vaginal and urinary microbiota of healthy cycling bitches

“…Escherichia-Shigella, Enterobacteriaceae genus, Pseudomonadaceae and Rheinheimera all belong to the Pseudomonadota phylum. In women, Lactobacillus, Corynebacterium, Streptococcus, Actinomyces, Gardnerella and Bifidobacterium have been observed in urine [ 3 , 4 ]. These data suggest that the urinary microbiome could be species-specific, as reported for the intestinal microbiota [ 31 ].…”

“…In human medicine, more recent studies have used 16 S rDNA gene sequencing to show that urine is not sterile [ 2 ]. In dogs, studies established that samples collected via cystocentesis differ from those collected via midstream voiding [ 3 ]. Genome phylogenetic analysis of bacterial strains isolated from the vagina and bladder of women suggest that the female urogenital microbiota is interconnected, comprising various health-associated commensals, such as Lactobacillus, Corynebacterium, Streptococcus, Actinomyces, Gardnerella and Bifidobacterium species [ 2 – 10 ].…”