Culture-Dependent and Sequencing Methods Revealed the Absence of a Bacterial Community Residing in the Urine of Healthy Cats

Abstract

A growing number of studies suggest that the lower urinary tract of humans and dogs can harbor a urinary microbiota. Nevertheless, a certain concern has developed that the microbiota reported could be due to unaccounted contamination, especially in low-biomass samples. The aim of this study was to investigate the bacterial community which populates the urine of healthy cats using two approaches: a culture-dependent approach which consisted of the expanded quantitative urine culture (EQUC) techniques capable of identifying live bacteria not growing in standard urine cultures, and a culture-independent approach which consisted of 16S ribosomal RNA next generation sequencing (16S rRNA NGS) capable of identifying bacterial DNA and exploring microbial diversity with high resolution. To avoid confounding factors of possible bacterial contamination, the urine was sampled using ultrasound-guided cystocentesis, and several sample controls and negative controls were analyzed. The urine sampled from the 10 cats included in the study showed no bacterial growth in the EQUC procedure. Although several reads were successfully originated using 16S rRNA NGS, a comparable pattern was observed between urine samples and the negative control, and no taxa were statistically accepted as non-contaminant. Taken together, the results obtained allowed stating that no viable bacteria were present in the urine of healthy cats without lower urinary tract disease and urinary tract infections, and that the bacterial DNA detected was of contaminant origin.

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

“…However, previous investigations have failed to characterize a urinary microbiome in cats. In one study, feline urine samples and a negative-extraction control had similar abundance patterns of bacterial sequence reads, indicating likely bacterial contamination of the urine samples ( 18 ). In another investigation, no feline urine samples yielded positive sequence results, likely due to methodological limitations ( 19 ).…”

Gut and Urinary Microbiota in Cats with Kidney Stones

“…This paradigm shift must now be extended to cats, previously considered to have particularly sterile urine. Two earlier studies had not detected a urobiome in cats; the first involved 10 healthy cats [ 70 ] and the second examined 38 culture-negative urine samples from cats with feline lower urinary tract disease alongside 43 culture-negative samples from healthy control cats [ 71 ]; for the second study, the authors admitted potential methodological limitation [ 71 ]. The existence of a urobiome was demonstrated in a study involving healthy cats, cats with chronic renal failure, and cats with idiopathic cystitis [ 72 ].…”

Comparative metataxonamic analyses of seeds and leaves of traditional varieties and hybrids of cucumber (Cucumis sativus L.) reveals distinct and core microbiome

“…Currently, a variety of works have been published on the incorporation of microorganisms in host plant seeds using the 16S rDNA clone library method [ 10 ], culture-dependent method [ 11 , 12 ], and the high-throughput sequencing (HTS) method [ 13 ]. The amplicon sequence variant (ASV) method has many advantages when working with difficult samples that usually make specific sequence analyses.…”