MGnify Genomes: A Resource for Biome-specific Microbial Genome Catalogues

An increasingly common output arising from the analysis of shotgun metagenomic datasets is the generation of metagenome-assembled genomes (MAGs), with tens of thousands of MAGs now described in the literature. However, the discovery and comparison of these MAG collections is hampered by the lack of uniformity in their generation, annotation and storage. To address this, we have developed MGnify Genomes, a growing collection of biome-specific non-redundant microbial genome catalogues generated using MAGs and publicly available isolate genomes. Genomes within a biome-specific catalogue are organised into species clusters. For species that contain multiple conspecific genomes, the highest quality genome is selected as the representative, always prioritising an isolate genome over a MAG. The species representative sequences and annotations can be visualised on the MGnify website and the full catalogue and associated analysis outputs can be downloaded from MGnify servers. A suite of online search tools is provided allowing users to compare their own sequences, ranging from a gene to sets of genomes, against the catalogues. Seven biomes are available currently, comprising over 300,000 genomes that represent 11,048 non-redundant species, and include 36 taxonomic classes not currently represented by cultured genomes. MGnify Genomes is available at https://www.ebi.ac.uk/metagenomics/browse/genomes/.& COPY; 2023 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).

Automated summary

An increasing number of shotgun metagenomic datasets now yield metagenome-assembled genomes (MAGs), but the lack of standardization in their generation, annotation, and storage hinders the discovery and comparison of MAG collections. To address this, MGnify Genomes offers a growing collection of biome-specific non-redundant microbial genome catalogues generated using MAGs and publicly available isolate genomes. Users can access visualized species representative sequences and annotations on the MGnify website and download the full catalogue and associated analysis outputs from MGnify servers. Currently, there are seven available biomes with over 300,000 genomes representing 11,048 non-redundant species and including 36 taxonomic classes not represented by cultured genomes. MGnify Genomes is accessible at https://www.ebi.ac.uk/metagenomics/browse/genomes/.