Safe use options of contaminated batches in the metagenomics era

Mycotoxins represent a risk to the food and feed supply chains with a consistent impact on human and animal health. A high percentage of food and feed batches has been reported to be contaminated with more than one mycotoxin. Research efforts progressively increase to develop mitigation strategies based on risk monitoring, prevention, intervention, and remediation strategies for multiple mycotoxins contamination. Since the application of pre- and post- harvest strategies, including physical or chemical removal, are not sufficiently effective, biological transformation is considered the most promising approach to reduce mycotoxins content. Biological methods consist of the use of microorganisms or enzymes which are able to metabolize toxins into stable, less toxic, up to harmless compounds. In addition, biotechnology enables to obtain massive and less expensive productions of enzymes and new engineered biological agents for detoxification in the production process. However, the decontamination of heavily contaminated batches is technologically difficult and of great economic impact. In recent years, several use options have been proposed. Among these, the valorization of contaminated batches as input for biofuel production, such as biogas, represents the most attractive and safe option. Complex consortia of microorganisms are responsible for biomass degradation and biogas production. Additionally, during the fermentation steps also mycotoxin degradation has been observed and therefore the exhaust material may be applied as fertilizer. Indeed, deciphering the microbial community and biochemical pathways involved in this process is interesting to study both the anaerobic fermentation and the decontamination process. Recent advances in sequencing technologies have given rise to deep metagenome-based analyses of complex microbiomes. In this regards, coupling "omic" approaches to the characterization of microbial community acting in a biogas fermenter fed with mycotoxin contaminated batches, will contribute to a previously unprecedented knowledge of decontamination process during biogas production and will provide new insights for the discovery of novel biological agents and enzymes for mycotoxin degradation.