Shanghai pet dog gut microbiome

Using long-read metagenomics, we characterized the gut microbiome of Shanghai pet dogs (n=50) to recover high-quality metagenome assembled genomes (MAGs). For each sample, we obtained a minimum of: 20Gb of long-read metagenomics data (Oxford Nanopore Technologies) to assemble the metagenomes; and 20Gb of short-read metagenomics data (Illumina) to polish the assemblies. We assembled 2,676 MAGs --most of them as high-quality-- representing 320 distinct bacterial species. The most recovered MAGs belonged to the Bacillota A phylum, with Blautia hansenii, Faecalimonas umbilicata, and Ruminococcus B gnavus present in nearly all dogs in the cohort. We mapped external pet dog datasets from diverse geographies (USA, Germany, South Africa) to our MAG collection, achieving mapping rates of >90%, which suggests that our MAG collection is broadly representative of the pet dog gut microbial diversity.