Multi-omic approaches for microbial dynamic studies at pilot-scale food productions

There is a general trend in the food sector to industrialize traditional manufactures applying mild processing approach (e.g. fermentation) and more sustainable and less energy-consuming technologies. These, combined with the consumer attitude for minimal processed food and the request of shelf-life extension, may lead to increased microbiological risks. The limited information on the physiological properties of the foodborne pathogens new and re-emerging risks is limiting the development of mitigation strategies. The data collected in Task 3.1.1 and the culture collection will allow to perform experiments aimed to reduce this gap of knowledge.

Experiments in pilot plants will be performed by mimicking industrial manufacturing to assess the growth, survival and inactivation dynamics of pathogens in innovative food products /food processes by using a multi-omic approach (culturomics, metagenomics and metabolomics). Pilot plants used will include the manufacturing of cheese, fermented sausages, and mixed products. A selection of pathogenic strains will be tested, including mutants obtained by inactivating environmental adaptation key genes (e.g. oxidative stress response, biofilm), to identify the role of these genetic elements in the food colonization and persistence.

The quantitative data from experiments at model and pilot scale will allow to achieve information to complete the microbiological risk assessment (MRA) of innovative food processes; in particular, those aimed to minimise processing and the elimination of food additives (alternative thermal processes or nitrate/nitrate free sausages) in ready to eat (RTE) products. The MRA activities will be targeted to provide information on the inactivation of most relevant food borne pathogens (STEC and Salmonella), also by using derivative strains harbouring mutations in specific genes coding for key features (e.g. pathogenicity, environmental adaptation).