Computational Microbiology  Unit

Environmental pollution from a wide range of organic and inorganic compounds poses serious ecological and health risks. While bioremediation offers a promising solution, its application is limited by fragmented genomic resources and insufficient understanding of microbial biodegradation pathways.

To address this, we developed the Microbial BioRemediation database, a comprehensive and manually curated repository comprising over 620,000 bacterial protein sequences associated with the degradation of 564 pollutant compounds across 25 chemical classes. Optimized for both genomic and metagenomic analyses, the Microbial BioRemediation database enables high-resolution functional and taxonomic profiling of microbial communities and individual bacterial strains. Validation using public genome and metagenome datasets from contaminated environments confirmed the database’s ability to detect both conserved and environment-specific biodegradation functions. Its application to host-associated microbiomes further revealed how environmental exposures likely shape microbial catabolic potential across ecological contexts.

The Microbial BioRemediation database thus serves as a strategic tool for the early-stage identification and prioritization of microbial candidates for bioremediation. By enabling the in silico selection of key taxa and enzymatic functions, it supports a rational pipeline that progresses toward targeted in vitro validation and experimental characterization. This integrative approach facilitates development of next-generation, tailored strategies for the remediation of complex polluted ecosystems.