gcMeta 2025: a global repository of metagenome-assembled genomes enabling cross-ecosystem microbial discovery and function research
Yan Sun, Qi Chen, Guomei Fan, Qinglan Sun, Qing Zhou, Jiaqing Zhang, Jingyi Nie, Juncai Ma, Linhuan Wu
Abstract
The rapid growth of metagenomic sequencing has generated an unprecedented wealth of metagenome-assembled genomes (MAGs), transforming opportunities for microbial discovery and functional characterization. Yet, full utilization of these resources has been constrained by heterogeneous data generation practices and inconsistent analytical pipelines. The gcMeta database addresses this gap by compiling MAGs through both public acquisition and de novo assembly. This release integrates over 2.7 million MAGs from 104 266 samples spanning various biomes, covering human, animal, plant, marine, freshwater, and extreme environments. It establishes 50 biome-specific MAG catalogues comprising 109 586 species-level clusters, of which 63% (69 248) represents previously uncharacterized taxa, and annotates >74.9 million novel genes. By linking functional traits with microbial co-occurrence networks, gcMeta identifies keystone taxa central to biogeochemical cycling and environmental adaptation. The platform further supports cross-ecosystem functional comparisons, revealing niche-specific metabolic pathways and stress-response genes. Moreover, gcMeta provides standardized, AI-ready datasets encompassing microbial enzymes, anti-phage defense systems, and other functional modules, enabling advanced machine learning applications. By bridging microbial "sequence discovery" with "functional utilization," gcMeta establishes a foundation for ecological research, industrial biotechnology, and novel gene mining. The platform is freely accessible at https://gcmeta.wdcm.org/.