Food production now is too expensive, it is responsible for the 70% of H2O consumption and of the 30% of energy usage, while delivering the 25% of greenhouse gasses. The current food systems exert a strong pressure on the natural sources, exceeds the planetary boundaries and compromise the capacity of earth to produce safe and secure foods for the future. Thus, the sustainable food production is now a European – as well as planetary – priority. We need to change the paradigm of food production, reducing footprint on natural resources, while keeping production of secure and safe food for the future. Natural microbiomes and their circulation - with their centrality for environmental, plant and animal health - can be exploited as an untapped resource of probiotic functions for the main actors of the food systems, and thus represents an emerging opportunity to reduce the food system footprint on natural resources, while keeping the production of safe and secure food for the future. Being aware of this “microbiomes power” CIRCLES aims to discover, translate and communicate innovative microbiome-based applications to improve EU food systems in term of quality, productivity, safety and sustainability. CIRCLES will provide Smart Microbiome Food Systems (SMFSs) for 7 food chains relevant for the EU market - spinach and tomatoes, poultry and pigs meat food, Atlantic salmon and seabream aquaculture, and wild marine organisms (e.g. wild fishes, corals, shellfish, crustaceous) – as new food systems paradigm, where the microbiomes circulation and dynamics are optimized for better performances in term of productivity, quality, safety and sustainability. The SMFS will be obtained by means of a microbiome biotechnology approach involving the design of microbiome tailored circular actions based on the integrative usage of Smart Microbiome Modulators (SMMs) for optimizing the food system microbiomes. The insights gained through CIRCLES will provide decision-makers, academia, businesses and consumers with a common vision on the impact microbiomes have on food systems, from farm to fork. Ultimately, they will enable Europe to contribute to the needs of the rising world population, implementing resource-efficient circular economy principles in food production and helping to reduce Europe’s environmental footprint.