Risk assessment of genome-edited bacteria for innovative food applications

New genetic techniques, such as genome editing and synthetic biology, are a powerful tool to develop new microbial strains for food production. Genome editing (GE) targets the insertions, deletion of mutation to site-specific locations. Synthetic biology (SynBio) is the application of science, technology and engineering to facilitate and accelerate the design, manufacture and/or modification of genetic materials in living organisms.
Globally in the last decade GE and SynBio microorganisms have been widely used for the production of food improvement agents (e.g. enzymes, vitamins, novel food components) and, more recently, used as viable cells released in the or in the food system. The EU has recently requested EFSA to appraise if the existing RA methodologies for microorganisms are applicable to those modified by GE and SynBio. The EFSA’s outcomes highlighted the lack of knowledge, in particular for intentional release of these modified organisms in the food chain.

UniCatt will perform experiments to assess the risk of GE and SynBio bacteria, based on:

• the WGS-based risk assessment, implementing and optimizing the tools developed in TASK 3.1.1. to genetically modified bacteria; 
• the study and modelling of the fate of GE/SynBioM bacteria and their genes in microcosm models representing the food chain (food, fermentation, gut of model animals, environment), including the ability to colonize ecological nique, to compete with existing microbiota and the HGT of GE and SynBio genetic loci;
• a pool of strains will be used: minimal genome bacteria, GE strain in a single gene, SynBio designed to boost a technical property (overproduction of bacteriocin) or harboring reporter genes. The bacterial groups most frequently used in food or to produce food improvement agents will considered: B. subtilis, E. coli, Lactic Acid Bacteria. The non-modified counterpart, the comparators, will be included in the experiments.

The modelling of quantitative data from the WGS based RA an on the fate of GE/SynBioM bacteria will provide relevant information to fill the gap on the safety of bacteria deriving from NGT approaches. The following results are expected: 

• data on the effect of genome minimisation (e.g. 30% reduction) on the ability to persist in the environments and on the ability to acquire exogenous genes by HGT from food bacterial communities in comparison with its parental strain;
• data on the colonisation, competitiveness and persistence of strains obtained by intragenesis/self-cloning in comparison with the non-modified counterpart
  information on the rate of transfer in the food microbiome of the genetic loci modified by GE and SynBio approaches of strain obtained by intragenesis/self-cloning;
• data for a risk benefit analysis of the GE strains obtained by self-cloning (e.g. overexpression of bacteriocins against foodborne pathogens)