Capturing global pet dog gut microbial diversity and hundreds of near-finished bacterial genomes by using long-read metagenomics in a Shanghai cohort

Pet dogs are considered part of the family, and understanding their gut microbiomes can provide insights into both animal and household health. Most comprehensive studies, however, relied on short-read sequencing, resulting in fragmented MAGs that miss mobile elements, antimicrobial-resistance genes, and ribosomal genes. Here, we applied deep long-read metagenomics (polished with short-reads) to fecal samples from 51 urban pet dogs in Shanghai, generating 2,676 MAGs —representing 320 bacterial species—, of which ~72% achieved near-finished quality, often improving on the corresponding reference public genome. Comparisons with external datasets showed that our Shanghai-based MAG catalog is representative of pet dogs worldwide (median read mapping of >90%). Moreover, we recovered circular extrachromosomal elements, including those linked to antimicrobial resistance, which were also detected in external dog gut datasets. In conclusion, we provide a high-quality reference resource and demonstrate the power of deep long-read metagenomics to resolve microbial diversity in complex host-associated microbiomes.