Fecal Microbiota of Cats with Naturally Occurring Chronic Diarrhea Assessed Using 16S rRNA Gene 454‐Pyrosequencing before and after Dietary Treatment

BACKGROUND: The gastrointestinal (GI) microbiota has a strong impact on the health of cats and these populations can be altered in GI disease. Little research has been done to associate improvement in diarrhea with changes in GI microbiota. OBJECTIVE: To evaluate GI microbiota changes associated with diet change and related improvement in diarrhea in cats with chronic naturally occurring diarrhea. ANIMALS: Fifteen adult Domestic Shorthair cats with naturally occurring chronic diarrhea. METHODS: Controlled crossover dietary trial for management of diarrhea. Fecal microbiome was assessed using 454‐pyrosequencing. Relationships among fecal score (FS), diet, and microbiome were explored using partial least square method, partial least square method – discriminant analysis, and orthogonal partial least square method with discriminant analysis (OPLS‐DA). RESULTS: Dominant bacterial phyla included the Firmicutes and Bacteroidetes, followed by Fusobacteria, Proteobacteria, Tenericutes, and Actinobacteria. Orthogonal partial least squares (OPLS‐DA) clustering showed significant microbial differences within cats when fed Diet X versus Diet Y, and with Diet Y versus baseline. Significant correlations were found between the microbiome and FSs. Those bacteria with the strongest correlation with FS included Coriobacteriaceae Slackia spp., Campylobacter upsaliensis, Enterobacteriaceae Raoultella spp., Coriobacteriaceae Collinsella spp., and bacteria of unidentified genera within the families of Clostridiales Lachnospiracea and Aeromonadales Succinivibrionacease, suggesting that increased numbers of these organisms may be important to gut health. CONCLUSIONS AND CLINICAL IMPORTANCE: Alterations in intestinal microbiota were associated with improvement in diarrhea, but, from our data we cannot conclude if changes in the microbiome caused the improvement in diarrhea, or vice versa.