Foodborne mycotoxins and the human microbiome: a haccp based risk assessment approach

Mycotoxins, toxic secondary metabolites produced by fungi such as Aspergillus, Fusarium, and Penicillium, represent one of the most significant chemical hazards in food systems. They contaminate cereals, nuts, fruits, and processed products, posing risks not only through acute toxicity but also via chronic exposure that can disrupt the human gut microbiome. The microbiome, a complex ecosystem of bacteria, fungi, and archaea, plays a central role in digestion, immune regulation, and metabolic homeostasis. Evidence suggests that mycotoxins such as aflatoxins, ochratoxin A, fumonisins, and deoxynivalenol can alter microbial diversity, reduce beneficial taxa, and promote dysbiosis, thereby increasing susceptibility to gastrointestinal disorders, metabolic dysfunction, and immune imbalance. This review synthesizes current knowledge on the ecological interactions between foodborne mycotoxins and the human microbiome, emphasizing the need for integrated risk assessment. The Hazard Analysis and Critical Control Points (HACCP) framework provides a systematic approach to identifying and controlling hazards at critical points in food production and processing.
Applying HACCP principles to mycotoxin contamination involves monitoring agricultural practices, storage conditions, and processing steps where fungal growth and toxin production are most likely. By incorporating microbiome-focused biomarkers, such as microbial diversity indices, short-chain fatty acid levels, NF-κB activation, and metabolomic signatures, into HACCP risk assessment, food safety management can evolve beyond traditional toxicological thresholds to include microbial resilience and host health outcomes. Case studies highlight how HACCP interventions, including improved grain storage, rapid detection methods, and biocontrol strategies, reduce mycotoxin exposure. Ultimately, aligning HACCP with microbiome research offers a proactive strategy to mitigate the long-term health consequences of mycotoxin contamination. This interdisciplinary approach underscores the importance of integrating food safety, microbiology, and public health perspectives to safeguard consumer wellbeing and ensure sustainable food systems.