Microbiome Responses to Fecal Microbiota Transplantation in Cats with Chronic Digestive Issues

SIMPLE SUMMARY: The effectiveness and potential impacts of fecal microbiota transplants (FMT) on the intestinal microbial communities of domestic cats have been severely understudied. To date, only two case studies have examined FMT treatment in resolving diarrhea and chronic colitis in two adult cats. Here we provide an analysis of the fecal microbiome responses to an oral capsule FMT course in a group of 46 cats experiencing chronic vomiting, diarrhea, and/or constipation. Changes in the composition of the fecal microbiome were observed for all cats. Fecal microbiome responses were correlated with clinical signs and dry kibble consumption. Furthermore, we compared the fecal microbiomes of FMT recipients to those from their stool donors (N = 10) and from cats in a healthy reference set (N = 113) and discussed findings regarding donor bacterial engraftment in FMT recipients. We also report increases in the fecal microbiome similarity between FMT recipients and healthy cats. Our study attempts to address a large gap in the literature and provides a comprehensive analysis of fecal microbiome changes in a cohort of cats receiving oral FMTs. ABSTRACT: There is growing interest in the application of fecal microbiota transplants (FMTs) in small animal medicine, but there are few published studies that have tested their effects in the domestic cat (Felis catus). Here we use 16S rRNA gene sequencing to examine fecal microbiome changes in 46 domestic cats with chronic digestive issues that received FMTs using lyophilized stool that was delivered in oral capsules. Fecal samples were collected from FMT recipients before and two weeks after the end of the full course of 50 capsules, as well as from their stool donors (N = 10), and other healthy cats (N = 113). The fecal microbiomes of FMT recipients varied with host clinical signs and dry kibble consumption, and shifts in the relative abundances of Clostridium, Collinsella, Megamonas, Desulfovibrio and Escherichia were observed after FMT. Overall, donors shared 13% of their bacterial amplicon sequence variants (ASVs) with FMT recipients and the most commonly shared ASVs were classified as Prevotella 9, Peptoclostridium, Bacteroides, and Collinsella. Lastly, the fecal microbiomes of cats with diarrhea became more similar to the microbiomes of age-matched and diet-matched healthy cats compared to cats with constipation. Overall, our results suggest that microbiome responses to FMT may be modulated by the FMT recipient’s initial presenting clinical signs, diet, and their donor’s microbiome.