Deciphering microbial ecology requires linking community composition to genome-resolved functional potential across diverse environmental contexts. Yet, limited availability of genomes from underexplored environments and high cost of environmental genome recovery often impede researchers from contextualising taxonomic profiles with the functional potential of detected taxa.

To bridge ecological distribution and genomic context, we have previously introduced the mOTUs database: a large-scale genome collection comprising 124,295 species, represented by 3.7 million genomes, 75% of which are systematically reconstructed metagenome-assembled genomes (MAGs) from over 50 habitats.

Here we present mOTUs 4.1, which adds 150,815 MAGs from underexplored environments including subsurface systems, wetlands, and hot springs. The updated web interface supports interactive sample and taxon abundance exploration on a map and introduces a new hierarchical environmental ontology, enabling customizable sample grouping and meta-analysis. Furthermore, each genome is now enriched with functional annotations from KEGG, Pfam, and eggNOG. The accompanying mOTUs command-line tool enables shotgun metagenome profiling, classification of user genomes into species-level units, and selective retrieval of genomes based on identifiers, taxonomic labels, and functional annotations, enabling their integration into custom pipelines.

Taken together, mOTUs 4.1 provides a comprehensive foundation for advancing microbial ecology by enabling the systematic integration of taxonomic composition, functional potential, and environmental distribution within a unified analytical framework.

Co-authors: Marija Dmitrijeva, Kang Li, Taylor Priest, Samuel Miravet-Verde, Luca Kristina Schnepp-Pesch, Janko Tackmann, Christian von Mering, Daniel Mende, Georg Zeller, Shinichi Sunagawa