Characterization of the Oral Microbiome and Anticipated Functional Profiles of Companion Animals in Private and Cohabiting Environments: A Pilot Study

The intricate interaction of a host’s microbiome, the microbiomes of other hosts, and environmental microbial populations significantly impacts host health, given the essential physiological functions the microbiome performs within the organism. The oral microbiome of domesticated animals is also influenced by a variety of host and environmental factors. This study investigated the characteristics of the oral microbiome of dogs and cats under comparable and disparate living conditions, emphasizing the description of diversity patterns, taxonomic composition, and predicted functional profiles. Oral buccal swabs were collected from four groups of companion animals (n = 5 per group): dogs housed alone in single-pet households (Group A), dogs cohabiting with cats in multi-pet households (Group B), cats cohabiting with dogs from the same households (Group C), and cats housed alone in single-pet households (Group D). The cohabiting groups were derived from five multi-pet households, with one dog and one cat sampled from each household. Amplicon sequence variations (ASVs) were used for downstream analysis after 16S rRNA gene sequencing. Rarefaction curve behavior indicated proper sequencing depth. Alpha diversity varied by group (Shannon index, p = 0.045), with Groups C and D having larger diversity. A Beta diversity study revealed community composition differences (Bray–Curtis dissimilarity, R2 = 0.257, p = 0.001), with some overlap between groupings. In all samples, Proteobacteria, Firmicutes, Bacteroidota, and Fusobacteriota dominated the microbiome. The relative abundance of Fusobacterium, Porphyromonas, and Pasteurella varied across groups. Core microbiome analysis identified limited overlap of core ASVs between groups, with most taxa being group-specific. Functional prediction using PICRUSt2 suggested differences in predicted metabolic and cellular pathways. Overall, these exploratory findings suggest that the oral microbiome of companion animals may be influenced by host species and cohabitation conditions. Although limited by the small sample size, the study provides preliminary insights into microbial diversity, community structure, and predicted functional profiles that may inform future One Health-oriented investigations.