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Food contamination by ochratoxin A (OTA) constitutes a significant threat to public health and global food safety and security, a challenge increasingly intensified by climate change. Due to the high thermal and chemical stability of OTA, traditional physical and chemical decontamination methods often prove insufficient or detrimental to food quality. Consequently, microbial detoxification has emerged as a sustainable alternative. This review delves into the two primary biological mechanisms for OTA detoxification: physical adsorption—predominantly mediated by yeast and bacterial cell walls—and enzymatic biotransformation. Among the documented metabolic pathways, the hydrolysis of the amide bond by carboxypeptidases and amidohydrolases is recognised as the most reliable detoxification pathway. Conversely, alternative pathways, such as lactone ring opening, are hindered by their potential toxicity and chemical reversibility under acidic conditions. While various lactic acid bacteria, yeast, and filamentous mould species demonstrate high efficacy in OTA decontamination, their industrial implementation is currently limited by the complexity of food matrices and the lack of in vivo validation. The integration of multi-omics (proteomics and metabolomics), alongside CRISPR/Cas9 genome editing, is essential for identifying novel biocontrol agents. These precision biotechnological tools are fundamental for translating laboratory findings into industrial-scale OTA detoxification strategies. Full article

(1) Background: ochratoxins are mycotoxins produced by filamentous fungi with important implications in the food manufacturing industry due to their toxicity. Decontamination by specific ochratoxin-degrading enzymes has become an interesting alternative for the treatment of contaminated food commodities. (2) Methods: using a structure-based approach based on homology modeling, blind molecular docking of substrates and characterization of low-frequency protein motions, we performed a proteome mining in filamentous fungi to characterize new enzymes with potential ochratoxinase activity. (3) Results: the proteome mining results demonstrated the ubiquitous presence of fungal binuclear zinc-dependent amido-hydrolases with a high degree of structural homology to the already characterized ochratoxinase from Aspergillus niger. Ochratoxinase-like enzymes from ochratoxin-producing fungi showed more favorable substrate-binding pockets to accommodate ochratoxins A and B. (4) Conclusions: filamentous fungi are an interesting and rich source of hydrolases potentially capable of degrading ochratoxins, and could be used for the detoxification of diverse food commodities. Full article