Improving the quality, safety and sustainability of fermented vegetable food and fruit beverage using a knowledge-driven synthetic ecology and modelling approach – MetaSimFOOD

The increasing consumption of fermented foods and beverages is among one of the more notable diet transitions observed in our societies. However, the strong demand for clean label food (rejection of chemical preservatives) and for sustainable agricultural practices (e.g. change towards organic production with low input of fertilizers and pesticides) leads to unforeseen modifications in the quality and safety of these food, especially those made from plant products (vegetables and fruits). Some raw materials are also undergoing biochemical modifications (e.g. in sugar content) due to climate change and increased water stress. These changes in raw materials lead to unexpected modifications in microbial ecology that can be detrimental to the fermentation processes and to the quality of fermented foods and beverages. In this context, the development of generic scientific approaches to help in understanding and anticipating the effects of multiple and complex changes in these productions is a real and urgent need.
In addition, solutions to tackle these changes must be sustainable, like the exploitation of taxonomic and functional biodiversity of microorganisms. We will apply an approach of multi-omics-analysis and modelling of the food transformation ecosystems to two typical fermented foods: wine (liquid) and vegetables (solid), for which different challenges exist. These include low-alcohol wine production in a context of climate change, together with organic production and sulphite reduction, and, for various fermented vegetables, addressing health, safety and quality issues in a context of changing production scale (household versus semi-industrial), organic production and salt reduction.
The goal of the project is to develop a knowledge-driven approach using synthetic ecology that aims, through the reconstitution of model foods, to predict the behaviour of microbial communities under different constraints. The objective of this strategy is to demonstrate that the production of meta-omics data (gene expressions at the ecosystem scale; global analyses of metabolite production) organized in microbial ecological networks by computational approaches is relevant to anticipate the impacts described above. Furthermore, the project will take advantage of the biodiversity of microbial strains available in partner’s collections for the construction of tailor-made microbial consortia based on the functional properties required to adapt to the expected ecological network changes. Finally, our hypothesis and the solutions obtained on model and simplified foods will be tested at the pilot scale of fermentations of real food to evaluate their validity and the organoleptic and/or nutritional relevance.
In a context where fermented foods are at the heart of a societal (food production and healthy nutrition) and environmental (sustainability of production and processes) transition, the results of the METASIMFOOD project will have three major impacts. We will demonstrate the relevance and efficiency of the scientific discipline of synthetic ecology to predict, anticipate and control the behaviour of microbial communities involved in food fermentation processes. Our project will serve as a lever for the deployment of this strategy to other examples of food. It will provide the necessary knowledge base for the development of downstream research programs with industrial partners in the field of fermented foods. Finally, we will ensure a very strong communication towards the general public with an educational and popularization objective.