The Kitty Microbiome Project: Defining the Healthy Fecal “Core Microbiome” in Pet Domestic Cats

SIMPLE SUMMARY: We surveyed the fecal microbial communities (termed ‘microbiome’) of North American pet domestic cats to further our understanding of the range of variation found in a population of apparently healthy cats. We also investigated whether differences in fecal microbial communities were significantly associated with the age, diet, and living environment of the individual. Results showed that thirty different bacteria were found in the fecal microbiomes of most cats. The composition of the fecal microbiome depended on the diet of the cat, their age, and whether the cat lived in a private home or a shelter. This study helped establish the expected ranges for the structure of these communities within a healthy population of cats and provides valuable insights for veterinarians, pet owners, and pet-related industries. ABSTRACT: 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.