Assessment of bacterial and fungal populations in urine from clinically healthy dogs using next‐generation sequencing

Abstract

Background: Urine from clinically healthy dogs is not sterile. Characterizing microbial diversity and abundance within this population of dogs is important to define normal reference ranges for healthy urine.Objectives: To establish composition and relative representation of bacterial and fungal microbiomes in urine of clinically healthy dogs. Animals: Fifty clinically healthy dogs.Methods: Analytic study. Urine sampling via cystocentesis. Comprehensive evaluation of urine including standard urinalysis, culture and sensitivity, next-generation sequencing (NGS), and bioinformatics to define bacterial and fungal microbiome.Results: Culture did not yield positive results in any samples. Next-generation sequencing of urine established low presence of bacteria, fungi, or both in all samples. Diversity and abundance of bacterial and fungal communities varied between urine samples from different dogs. Struvite crystals were associated with bacterial community structure (P = .07) and there was a positive correlation between struvite crystals and pH.Conclusions and Clinical Importance: The microbiome in urine of clinically healthy dogs has diverse bacterial and fungal species These findings highlight limitations of conventional culture testing and the need for culture-independent molecular diagnostics to detect microorganisms in urine.

Urine and Fecal Microbiota in a Canine Model of Bladder Cancer

“…In this study, the four most abundant phyla in urine were Firmicutes, Actinobacteria, Bacteroides, and Proteobacteria. These phyla also dominate the urine microbiota in humans [17,36,38,40,44,45] and have been reported in previous studies on healthy dog urine [80,81]. In humans, taxa associated with UC vary widely across studies, but Acinetobacter and Actinomyces have been found at increased abundances in patients with UC across at least three studies [35,42,44].…”

Evaluating extraction methods to study canine urine microbiota

“…There are only two studies, to our knowledge, on the healthy canine urine microbiota. Both employed cystocentesis for sampling, and microbial diversity did not differ by sex [ 56 , 57 ]. Hormones have also been linked to changes in the fecal microbiome of women and could feasibly be altering the urine microbiota [ 84 ].…”

“…In addition, dogs are a valuable translational model for many human diseases, including urogenital diseases like bladder cancer [55]. However, there have only been two studies, to our knowledge, characterizing canine urine microbiota [56,57] and none evaluating canine urine DNA extraction methods. Multiple methods of urine microbial DNA isolation have been reported in human studies [12,51,[58][59][60][61], and there are a few studies that have compared microbial DNA extraction methods.…”

Dysbiosis of the Urinary Bladder Microbiome in Cats with Chronic Kidney Disease

“…In the only two studies of the canine bladder microbiome, genera belonging to the family Xanthomonadaceae were commonly detected in the urine of healthy dogs. Melgarejo et al ( 16 ) detected Xanthomonas , along with Stenotrophomonas and Bradyrhizobium . Burton et al ( 15 ) also detected Xanthomonadaceae , but when we reanalyzed their sequence data using the bioinformatics protocols used in this study, most of them were assigned to Bradyrhizobium and Stenotrophomonas , and none were assigned to Xanthomonas .…”

“…Given the proven existence of the urinary microbiome in humans and dogs ( 15 , 16 ), it seems reasonable to hypothesize that a feline urinary microbiome also exists and may interact differently with the host depending on the health of the urinary system. Certainly, subclinical bacteriuria is not uncommon in cats ( 17 ), and urinary tract diseases, notably CKD and feline idiopathic cystitis (FIC), are common causes of morbidity and mortality in cats.…”