design: Metagenomic DNA was extracted from a fecal sample collected from a clinically healthy domestic dog. Shotgun metagenomic libraries were prepared using the Illumina DNA Prep Kit with unique dual indexes, quantified via Qubit and qPCR, and pooled in equimolar concentrations. Sequencing was performed on an Illumina NovaSeq X platform using paired-end reads. This dataset represents unbiased whole genome shotgun sequencing of all microbial DNA present in the sample for taxonomic and functional profiling