Here, we present a taxonomically defined fecal microbiome dataset for healthy domestic cats (Felis catus) fed a range of commercial diets. We used this healthy reference dataset to explore how age, diet, and living environment correlate with fecal microbiome composition. Thirty core bacterial genera were identified. Prevotella, Bacteroides, Collinsella, Blautia, and Megasphaera were the most abundant, and Bacteroides, Blautia, Lachnoclostridium, Sutterella, and Ruminococcus gnavus were the most prevalent. While community composition remained relatively stable across different age classes, the number of core taxa present decreased significantly with age. Fecal microbiome composition varied with host diet type. Cats fed kibble had a slightly, but significantly greater number of core taxa compared to cats not fed any kibble. The core microbiomes of cats fed some raw food contained taxa not as highly prevalent or abundant as cats fed diets that included kibble. Living environment also had a large effect on fecal microbiome composition. Cats living in homes differed significantly from those in shelters and had a greater portion of their microbiomes represented by core taxa. Collectively our work reinforces the findings that age, diet, and living environment are important factors to consider when defining a core microbiome in a population.

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 effectiveness in the domestic cat (Felis catus). Here we use 16S rRNA gene sequencing to examine fecal microbiome changes in 68 domestic cats with chronic digestive issues that underwent FMT treatment using lyophilized stool that was delivered in oral capsules. Fecal samples were collected from FMT recipients before and two weeks after treatment, as well as from their stool donors, and healthy animals. We found that according to their owners, 77% of cats were reported to show improvement in their clinical signs (termed ‘Responders’), and 23% were reported to exhibit no change or a worsening of their clinical signs (termed ‘Non-Responders’). Variation in the fecal microbiomes of FMT recipients most strongly correlated with host clinical signs, diet, and IBD diagnosis. The relative abundances of Collinsella, Negativibacillus, Parabacteroides, and Peptoclostridium changed differentially in FMT recipients. Overall, on average 13% of the bacterial amplicon sequence variants (ASVs) were shared between stool donors and FMT recipients (excluding ASVs already present in FMT recipients prior to treatment). The most commonly shared ASVs were classified as Prevotella 9, Peptoclostridium, Bacteroides, Collinsella and unclassified Lachnospiraceae. Lastly, FMT recipients that had recently taken antibiotics exhibited increases in microbiome similarity to an age-matched healthy reference set compared to other cats. Cats that had diarrhea or diarrhea with vomiting became more similar to healthy cats than did cats exhibiting other clinical signs. Overall, our results suggest that oral capsule FMT treatment was effective in this group of cats and microbiome responses may be modulated by the FMT recipient’s initial presenting clinical signs, prior IBD diagnosis, recent antibiotic use, and their diet.