gcPathogen 2.0: an expanded multi-omics database advancing global pathogen surveillance and One Health research.

Abstract

Launched in 2024, gcPathogen established a critical foundation for the genomic surveillance of human pathogens. Here, we present gcPathogen 2.0, a major multi-omics update designed to address key analytical bottlenecks, including the integration of genomic and transcriptional profiles, systematic tracking of cross-habitat distribution, and large-scale discovery of antimicrobial peptides (AMPs). This release expands coverage from 1134 to 1506 pathogenic species, spanning 557 bacteria, 508 fungi, 258 viruses, and 183 parasites, and increases total genomic records past 2.3 million. By incorporating 12 597 transcriptomes across 148 species, gcPathogen 2.0 bridges the gap between gene carriage and functional expression for risk assessment. Furthermore, the platform integrates 285 925 pathogen metagenome-assembled genomes (MAGs) spanning human, animal, and environmental niches. Mapped across 68 Environment Ontology (ENVO) habitat categories, these MAGs enable comprehensive tracking of cross-habitat distribution of pathogens, antibiotic resistance genes (ARGs), virulence factors (VFs), and mobile genetic elements (MGEs). Leveraging a nonredundant reference set curated from seven public databases, we identified over 77 million AMPs belonging to >55 000 families across 438 bacterial pathogens. Finally, pan-genome analyses of 440 bacterial species map intraspecies functional distributions across core, accessory, and unique gene repertoires. gcPathogen 2.0 is publicly accessible at https://nmdc.cn/gcpathogen/.