MGnify is an EMBL-EBI microbiome data resource for submitting, analysing, discovering, and comparing microbiome datasets. It contains microbiome-associated sequence data and derived analysis outputs that support text-based discovery, protein sequence searches, and browsing across public microbiome studies. The resource is intended to help researchers explore complex biological information, compare microbial community data, and identify functional or taxonomic patterns relevant to environmental, host-associated, and other microbiome research applications.