Methods and Results: Fecal samples from household dogs (n=10) were subjected to bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP) and a spotted DNA microarray to identify antimicrobial resistance genes. Twelve distinct phyla were identified and Firmicutes represented the most dominant phylum, followed by Fusobacterium. Two phyla, Lentisphaerae (<1%) and Fibrobacteres (<1%) are reported for the first time from healthy dogs. A total of twelve different genera were identified across all the fecal samples tested. Notable genera detected in all the fecal samples were Lactobacillus, Ruminococcus, Turicibacter, Clostridium, and Fusobacterium (each represented >2% of the sequences). We observed dog to dog variation in the microbial community composition with respect to relative abundance and diversity in bacterial taxa. The microarray data showed that overall prevalence of antibiotic and metal resistance in the fecal microbiota of healthy dogs was low. Several antibiotic (tetracycline, erythromycin and aminoglycoside) and metal resistance genes (four copper resistance genes) were detected. However, one dog with a history of antibiotic treatment for chronic skin disease had multiple AMR genes.

Conclusions: Our findings indicate that dog to dog variation occurs in the microbial community composition with respect to relative abundance, diversity in bacterial taxa and antibiotic and metal resistance genes harbored by these microbes. There is low prevalence of resistance genes in the healthy dogs. Significance and Impact of study: This is the first study to perform a microarray-based analysis of antibiotic and metal resistance genes in the feces of healthy dogs with insights into the diversity of resistance genes in the gut microbiota of healthy household dogs.