Human health and disease have increasingly been shown to be impacted by the gut microbiota, and mouse models are essential for investigating these effects. However, the compositions of human and mouse gut microbiotas are distinct, limiting translation of microbiota research between these hosts. To address this, we constructed the Mouse Gastrointestinal Bacteria Catalogue (MGBC), a repository of 26,640 high-quality mouse microbiota-derived bacterial genomes. This catalog enables species-level analyses for mapping functions of interest and identifying functionally equivalent taxa between the microbiotas of humans and mice. We have complemented this with a publicly deposited collection of 223 bacterial isolates, including 62 previously uncultured species, to facilitate experimental investigation of individual commensal bacteria functions in vitro and in vivo. Together, these resources provide the ability to identify and test functionally equivalent members of the host-specific gut microbiotas of humans and mice and support the informed use of mouse models in human microbiota research. Display omitted •MGBC allows functional translation between human and mouse microbiotas•Previously uncultured isolates expand culture collection of mouse gut microbes•Bioinformatic toolkit maps taxonomic locations of microbial functions of interest Beresford-Jones et al. find that while less than 3% of bacterial species are shared between human and mouse gut microbiotas, they can identify the closest functionally related species between these host-specific microbiotas using the bacterial genome catalog they developed. This will facilitate translation of microbiota-related research between humans and mice.