Fecal microbiome associations with age, body condition score, and stool consistency in domestic cats (Felis catus) living in an animal shelter

Abstract Background: Few studies delve into the gut microbiome of domestic cats, and many feline-specific studies are hampered by small sample population sizes. We investigated the fecal microbiome as a proxy for gut microbiome within a large shelter cat population (n=288) in Raleigh, NC, USA from February to July 2021. Single stool samples were collected from cats of various age groups that lived in one of four rooms (adoption, n=117; feral, n=113; quarantine, n=37; isolation, n=20; no room, n=1) at the shelter during the sampling period. The fecal microbiome was characterized by shotgun sequencing. Statistical differences in α- and β-diversity were assessed based on assigned shelter room as well as cat age group, body condition score (BCS; scale 1-9), and stool consistency (Bristol fecal scale). Enrichment of composition (as characterized by microbial taxa) and functional potential (as characterized by Kyoto Encyclopedia of Genes and Genomes (KEGG) orthology (KO) terms) based on subject characteristics were evaluated. Results: Analyses consistently indicated significant (p<0.05) differences in β-diversity based on assigned shelter room, age, body condition score, and stool consistency. The β-diversity within samples from cats housed within the adoption room was different from that of the other rooms. In KO terms, samples from the isolation room were also different from the adoption and feral room but not the quarantine room. Regarding age, kittens differed significantly in β-diversity from mature adults in post-hoc comparisons, and mature adults were abundant in much fewer microbiome species and KO terms when compared to kittens and young adults. Underweight and normal weight cats had different microbial profiles, and underweight cats were deficient in a KO term related to microbial lysine biosynthesis. Microbial taxa enriched in felines with overly dense stool or diarrhea were reported, with felines producing dense stools abundant in members of the genera Desulfovibrio and Alistipes and deficient in probiotic Lactobacillus spp. and diarrhetic cats abundant in members of the families Lachnospiraceae and Streptococcaceae . There were no significant differences among α-diversity metrics. Conclusions: To our knowledge, this research utilizes the largest feline microbiome dataset to date and validates previously reported differences in gut microbiome diversity due to age, BCS, and stool consistency while illuminating novel differences associated with the shelter setting. Gaining insight into the diverse microbial populations within the feline gut microbiome is essential for future research into enhancing host health and quality of life.