Cats with GI disease have shown increases in Clostridium spp and decreases in Bifidobacterium spp, Lactobacillus spp, and Bacteroides spp. This may be influenced by dietary changes—including those in fermentable fiber. Fifteen adult cats with chronic diarrhea were divided into 2 groups, each fed 1 of 2 different therapeutic diets as the sole diet for 1 month. The groups were then switched and fed the alternate therapeutic diet for 1 month, with 3 weeks to adapt to the new diet. Fecal microbiome was assessed using 454-pyrosequencing before and after dietary changes. Significant improvements in fecal score (FS) and significant changes in GI microbiota were noted with both diets. In addition, significant associations were found between the microbiome and FS. Bacteria with the strongest correlation to FS included Coriobacteriaceae Slackia spp, Campylobacter upsaliensis, Enterobacteriaceae Raoultella spp, Coriobacteriaceae Collinsella spp, and bacteria of unidentified genera in the families of Clostridiales Lachnospiraceae and Aeromonadales Succinivibrionacease, suggesting increases in these bacteria may be important to gut health. More studies are needed to determine whether improvement resulted from altered microbiome or the altered microbiome resulted from improvement in the diarrhea. Study supported by Nestlé Purina PetCare.