Biodegradation of Aflatoxins by Four Novel Environmental Bacterial Isolates: A Comparative Genomic and Molecular Docking-Proof-of-Concept Study

Aflatoxin contamination remains a critical challenge for food and feed safety, necessitating effective mitigation strategies. This study addresses the challenge of aflatoxin contamination by identifying four novel bacterial candidates capable of degrading four major aflatoxin congeners (B1, B2, G1, and G2). Quantitative HPLC and qualitative LC-HRMS with MS/MS profiling revealed that the isolated bacterial strains achieved high degradation efficiencies of 86–94%, proceeding through distinct demethylation and decarboxylation pathways. Oxford Nanopore whole-genome sequencing identified these potent degraders as Escherichia coli EC_2 and Klebsiella pneumoniae (KP_4, KP_5, and KP_6). To elucidate the genomic basis of this phenotype, we performed a comparative genomic analysis against two non-degrading E. coli strains. Functional annotation revealed complete aromatic degradation modules and intact enzymatic cascades present only in the degrading strains, demonstrating that this biodegradation capability is highly strain specific. Furthermore, molecular docking of key putative enzymes unique to these active cascades demonstrated highly favorable binding affinities (up to −8.70 kcal/mol) with all four aflatoxin congeners, stabilized by robust hydrogen bonding and hydrophobic networks. These findings provide a novel genomic and structural blueprint for aflatoxin biotransformation, highlighting the specific putative candidate enzymes, paaH and mhpB, for future investigations.