Impact Of Specimen Type On Findings For Bacterial Composition Within The Intestinal Tract Of Dogs And Cats With And Without Chronic Enteropathy

OBJECTIVETo compare bacterial diversity and community composition among fecal, rectal swab, and colonic mucosal biopsy specimens from dogs and cats with and without chronic enteropathy (CE).ANIMALS9 healthy dogs, 8 dogs with CE, 8 healthy cats, and 9 cats with CE.PROCEDURESIn a cross-sectional study design, fecal, rectal swab, and colonic mucosal biopsy specimens were obtained by colonoscopy from healthy dogs and dogs and cats with CE. Fecal and rectal swab specimens were collected from healthy cats. Genomic DNA was extracted, the 16S rRNA V4 gene region was amplified, and sequencing was performed by use of primers 515F to 806R on a paired-end platform.RESULTSFor healthy dogs and dogs and cats with CE, bacterial diversity based on the Chaol estimate of total species richness was higher for colonic mucosal biopsy specimens than for fecal specimens. Analysis of similarities by use of the Bray-Curtis dissimilarity index revealed that the bacterial communities captured in rectal swab specimens were similar to those captured in fecal specimens for healthy dogs and dogs with CE and similar to those captured in colonic mucosal biopsy specimens for both dog groups and cats with CE.CONCLUSIONS AND CLINICAL RELEVANCERectal swab and colonic biopsy specimens were successfully used to characterize the bacteriome of the intestinal tract in dogs and cats by 16S rRNA gene sequencing. Although the specimen types evaluated in this study were not interchangeable in results, rectal swab specimens were practical to collect from dogs and cats to study bacterial composition within the intestinal tract and may provide an alternative to colonic mucosal biopsy and fecal specimens.