Petroleum-Associated Genome Database - PaGeD: An Interactive Web Platform of genes and genomes related to the oil supply chain

Abstract Background Microbial communities play key roles across the oil supply chain, mediating both detrimental processes, such as microbial influenced corrosion and souring, and beneficial applications like bioremediation. However, genomic and functional data of these microorganisms remain fragmented across repositories, hindering integrative analyses and biotechnological use. Results Here, we present the Petroleum-associated Genome Database (PaGeD), an open-source interactive platform designed to organize, explore, and analyze genomic and functional information from oil-associated microbiomes. PaGeD compiles 3,334 curated prokaryotic genomes retrieved from oil reservoirs, produced waters, hydrocarbon-polluted sites, and related environments worldwide. These genomes were clustered into 2,522 species-level units, more than half representing previously undescribed taxa, underscoring the hidden microbial diversity in petroleum systems. Functional profiling based on 144 KEGG ortholog groups related to hydrocarbon degradation revealed a modular organization in which central catabolic pathways are broadly conserved across habitats and phylogenetic groups, whereas peripheral, substrate-specific pathways are restricted to a limited number of taxa. A bipartite gene-genome network analysis highlighted this architecture, revealing a gradient of functional richness across genomes: taxa encoding broad repertoires of degradation genes occupy central positions, whereas genomes encoding few such functions are located at the periphery. Despite geographic and ecological heterogeneity, hydrocarbon degradation profiles were largely conserved, indicating convergent functional adaptation to petroleum-associated conditions. Conclusions PaGeD provides a scalable framework for genome-resolved exploration of oil-associated microbiomes, enabling the identification of candidate keystone taxa and functional markers and supporting future studies on the ecological and biotechnological potential of microorganisms in petroleum environments.