Canine Urinary Microbiome Analysis Challenges Long-Held Assumptions


A team of researchers has determined that the urinary bladder of healthy dogs contains a diverse bacterial population that differs from the genital and rectal microbiomes.

In a study recently published in PLoS ONE, researchers identified a diverse urinary microbiome (UM) in dogs free of urinary disease, challenging the dogmatic assumption of a sterile urinary bladder in healthy dogs. According to the authors, this was the first study to use culture-independent techniques to characterize the canine UM composition.

Human and veterinary medicine studies have increasingly reported the importance of the microbiome, particularly the gastrointestinal microbiome, on an individual’s health.

Although the UM of healthy women has been analyzed, revealing a rich and diverse bacterial population, this analysis has not yet been performed in healthy dogs. The advent of 16S rRNA sequencing has enabled highly sensitive microbiome analysis beyond the detection capabilities of routine urine culture.

Nearly 15% of dogs will experience a urinary tract infection (UTI) during its lifetime. Although routine urine culture remains the gold standard for diagnosing canine UTIs, the current study’s researchers noted that UTI treatment is often more complex than simply eliminating bacteria detected using routine urine culture.

Study Design

The study included 20 dogs (10 male, 10 female) free of clinical urinary signs and with a negative urine culture. Samples were collected from 3 sites: (1) bladder, via cystocentesis; (2) genitalia (vaginal vault or preputial sheath); and (3) rectum. From each sample, DNA was extracted and the bacterial 16S rRNA gene was sequenced. Gene sequences were then grouped into operational taxonomic units (OTUs) according to nucleotide sequence similarity.

Researchers performed the following analyses:

  • UM composition
  • Diversity and richness of each microbiome
  • Taxonomic comparison of the microbiomes


UM Composition

UM composition was similar between the sexes. Of all OTUs detected in the urine samples, only 5 had mean relative abundances above 1%; these OTUs, all within the Proteobacteria phylum, included the gram-negative bacteria Pseudomonas sp (~81% abundance) and Acinetobacter johnsonii (~4% abundance).

Diversity and Richness

Researchers evaluated α-diversity, which measures a combination of taxa richness (overall number of different taxa) and evenness of taxa distribution. This diversity measure has 2 indices that preferentially weight either richness (Chao 1) or evenness (Shannon).

Overall, to the researchers’ surprise, urine samples had significantly greater OTU richness than the rectal or genital samples.

Sex did not significantly affect taxa richness or diversity, suggesting UM conservation between the sexes. Sample site had a significant influence, indicated, for example, by significantly greater taxa richness in rectal samples than in genital samples.

Taxonomic Comparisons

Similar to the urinary microbiome, the genital microbiome predominantly contained Pseudomonas sp and Acinetobacter sp. Overall, the urinary and genital microbiomes were more similar to each other relative to the rectal microbiome.

Researchers used principal component analysis (PCA) as another way to observe taxonomic relatedness between the microbiomes. Graphic representation of the PCA revealed overlapping clusters of the urinary and genital microbiomes, with the rectal microbiome distinctly separated from the other groups. Despite this overlap, statistical analysis indicated significant differences between the urinary and genital microbiome compositions.


According to the researchers, study results suggested several important points:

  • Microbiome characterization is limited with routine urine culture.
  • The rectal microbiome plays a minor role in the UM of healthy dogs.
  • A relationship may exist between the female urinary and genital microbiomes.

UM characterization in healthy dogs, the researchers noted, could open the door for non-antimicrobial treatment of canine recurrent UTIs. This type of treatment has been evaluated in women with recurrent UTIs but has not yet been extensively explored in dogs.

Dr. JoAnna Pendergrass received her Doctor of Veterinary Medicine degree from the Virginia-Maryland College of Veterinary Medicine. Following veterinary school, she completed a postdoctoral fellowship at Emory University’s Yerkes National Primate Research Center. Dr. Pendergrass is the founder and owner of JPen Communications, a medical communications company.

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