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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.

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