WP 3.1Spoke 03

Assessment of new and re-emerging risks in the food system

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Research projects
The main objective of WP 3.1 is to compile an updated assessment of new, emerging, and potential food safety risks, using various techniques to identify chemical and biological risks and understand their impacts on the environment, macrobiotic evolution, and food production. 

Meta-omic approaches will be applied to investigate the effects of food on human health and the microbial composition of the gut through the study of proteins and metabolites produced by microorganisms in the gastrointestinal tract. Other methodologies will also be applied, such as genomic sequencing, computational techniques, and ISO protocols.

Furthermore, food risk prevention cannot be separated from research on packaging materials, whose microbiological contamination is now one of the main causes of the deterioration of fresh food products. Therefore, WP 3.1 research activities, in collaboration with the teams of Spoke 02, focus on the study and implementation of innovative technologies to prevent microbiological contamination and improve food safety while reducing the use of chemicals.

The results of WP 3.1 activities will then be translated into guidelines for the food industry on the risks and benefits associated with new and emerging technologies, the safety assessment of bacteria derived from genome editing, and the study of their fate in the food system. The results of these studies will be used to promote an independent view of the risks and benefits of these new technologies.

Task and deliverables

Task 3.1.1.

Standard protocols (ISO), whole genome sequencing (WGS), computational methodologies, and MetaOmic approaches (metagenomics, metatrascriptomics, metabolomics, lipidomics, culturomics and phenomics) will be applied for the identification and characterization of the new and (re)-emerging chemical and biological hazards in traditional products, related to climate changes, microbial evolution, and modifications in the manufacturing processes. Omics techniques will also be applied to study factors affecting the survival and the stress resistance mechanisms of pathogens and antimicrobial resistant (AMR) bacteria during food processing and shelf life. In addition, a CAD-based automatic feature recognition procedure will be developed for hygienic design of food machinery, as a prerequisite for GMP in food production.

Task 3.1.2.

MetaOmics and MultiOmics approaches will be used for the identification and quantification of toxic compounds in novel sources or ingredients, also to anticipate risks related to novel foods and new sustainable food processes. The culture collection from task 3.1.1 will be used for challenge experiments in pilot plants mimicking industrial manufacturing. Food toxicants in new ingredients and food processing technologies will be evaluated (in connection with Spoke 2). Allergenicity (also with computational approaches) and toxicity will be considered by in vitro and in vivo tests. Exposure assessment and risk- benefit assessment (RBA) of novel foods will be performed.

Task 3.1.3.

New/existing materials will be characterised in terms of migration studies of both intentionally and non-intentionally added substances, small-/micro/nano- plastics, metal nanoparticles, food packaging suitability and growth of mycotoxigenic moulds, even after being subjected to innovative/emerging processing technologies (e.g., cold gas plasma, HPP). Potential antimicrobial properties will also be assessed, particularly for developed functional packaging systems. The safety of new materials used as FCM, from recyclable sources, bioplastics or derived from by-products, will be assessed in collaboration with Spoke 2

Task 3.1.4

A guideline of actual risks and benefits for the food chain will be realised to promote an independent point of view. Safety of bacteria derived from genome editing (GE) by using intragenesis and synthetic biology will be assessed using model organisms. The RA will be conducted considering deliberate release for food production or for fermentations in confined environments. WGS approaches for RA of GE-strains will be applied. Lab-scale models to study the fate of GE- bacteria and their DNA will be developed following recent EFSA indications.



Culture collection (M12)


Identification of new and re-emerging risks (M18)


Ontology for the classification of the features pertaining to hygienic design and the implementation into a CAD software (M18)


List of hazards in novel food sources, ingredients and/or processes (M18)


List of materials and identification of migration conditions (M18)


Procedures for RA of GE microorganisms in confined environments (M24)


Procedures for risk assessment of GE microorganisms for deliberate release in food (M24)