Ocean-M: an integrated global-scale multi-omics database for marine microbial diversity, function and ecological interactions
On October 31, 2025, our research group launched Ocean-M (http://om.qnlm.ac), a comprehensive global multi-omics resource database for marine microorganisms. This research was published in the database issue of Nucleic Acids Research.
Marine microorganisms are central to marine material cycles and energy flow, underpinning the balance and health of the global ecosystem. Their remarkable adaptability to extreme environments provides vital insights into the evolution of life, while the vast array of bioactive compounds they produce holds immense potential for applications in marine resource development, environmental remediation, and biotechnology. With the rapid accumulation of multi-dimensional omics data on marine microorganisms, global marine microbiology research now faces unprecedented challenges in data integration and deep elucidation. Existing databases primarily serve as repositories and analytical tools, lacking the ability to systematically mine and interpret heterogeneous, multi-source data. Achieving comprehensive integration and in-depth analysis of “complex, high-dimensional, and massive-scale” marine microbial data and spanning from single-species studies to multi-dimensional ecological networks remains a pressing scientific challenge. To address this gap, our team developed Ocean-M, a platform that integrates global marine microbial multi-omics resources that breaks through the limitations of traditional databases, creating a unified deep-research framework that interlinks omics resources, ecological interactions, and functional mining.
The Ocean-M database consolidates global multi-habitat and multi-scale marine microbial omics datasets, making it the most comprehensive open-access resource in the field. The platform compiles over 57,000 microbial datasets from diverse marine ecosystems worldwide, encompassing metagenomic, meta-transcriptomic, meta-proteomic, and meta-metabolomic data. Samples span complete ecological gradients—from polar regions to the equator and from surface waters to the deep sea. Through unified data processing and standardized identifiers, Ocean-M integrates the world’s largest metagenome-assembled genome (MAG) dataset, comprising over 50,000 representative microbial genomes. This enables visualized exploration of microbial community structures, functional annotations, and spatial distributions on a global scale.
Ocean-M further establishes a holo-omics ecological network framework, integrating microbial community networks, host-microbiome interactions, and environmental DNA datasets. This framework allows precise characterization of microbial community composition, function, and ecological relationships, enabling comprehensive ecological interaction analyses and offering novel perspectives for ecological research. Additionally, Ocean-M features a “Genome–Gene Function–Ecological Preference” analytical framework. Through large-scale functional gene mining, it constructs a functional gene library of over one million entries, providing powerful support for microbial functional gene discovery and ecosystem function analysis. Building upon the our group’s previously developed 2bRAD-M microbial analytical method, Ocean-M includes unique 2b-RAD tag libraries for over 50,000 MAGs, capable of identifying more than 95% of marine microbial species and offering a robust tool for precise species recognition and classification in complex marine environments.
Ocean-M serves not only as a foundational data resource for marine microbiology and ecology but also as a valuable asset for marine bioresource exploration and biotechnological innovation.
Overview of the Ocean-M database architecture and functional modules.
Full paper link: https://doi.org/10.1093/nar/gkaf1098
