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Controlling mIcRobiomes CircuLations for bEtter food Systems

Periodic Reporting for period 1 - CIRCLES (Controlling mIcRobiomes CircuLations for bEtter food Systems)

Reporting period: 2018-11-01 to 2020-04-30

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.
From the beginning of the project, in November 2018, CIRCLES has achieved to set up 20 labs-in-the-field from real-world EU productive sites of the 7 CIRCLES food systems. In the current CIRCLES observational phase, the labs-in-the-field are instrumental for the production of basement food system microbiomes knowledge to design innovative intervention strategies for optimizing the food system microbiomes (intervention phase). In each labs-in-the-fields, samples collection throughout the whole productive cycles has been carried out and is now finishing for the poultry and swine food chains, as well as for the spinach and tomatoes food chains, even if the Covid-19 emergency posed some problems for the conclusion of some of the sampling campaigns. In total more than 1000 samples have been collected - and biobanked - from these food chains. First samples collection activity also started in the work package dedicated to the marine fishery food chains. Because of the longer productive cycle, the aquaculture food chains (salmon and seabream) were the ones more affected by the worldwide lockdown that took place in early spring 2020: for these the observational phase will re-start as soon as possible in the set up lab-in-the-field. Also during the first year of the project, all procedures for collecting, storing and analyzing samples and data were set up and standardized, to ensure comparability among all data produced by CIRCLES project. Accordingly, DNA extractions from animal, plant and environmental samples are now in progress for almost all the food chains. As a CIRCLES innovative automated platform for the real-time monitoring of the food system pressure on the surrounding environment, also in terms of dispersion of microorganisms in the atmosphere, a fully functional ground mobile robot for the automate monitoring air microbiome and environmental parameters has been developed. Further, customized tools for microbiome sampling of food system workers (and their families) were produced, such as CIRCLES-branded autosampling kits for human and household microbiomes. Such tools will also be used in the incoming CIRCLES city tours, as a crowd sampling microbiomes campaign to sensitize people about the microbiomes importance for a sustainable future. Finally, the informatics infrastructure for hosting and managing the big-data produced by CIRCLES has been set up.
Beside the increase of the basic knowledge on the importance of the natural microbiomes for the food systems, CIRCLES will also provide microbiome-based applications – as circular actions – to boost the probiotic functionalities in the food system microbiomes, across all the food system actors, allowing a better performance and sustainability. CIRCLES has the strength of combining wide academic experience with resources and knowhow of the private sector. Such combination will allow to translate progression of the knowledge into concrete applications reaching different fields and markets, such as agriculture, animal production, food production, waste management and environmental protection. These applications – based on microbiome science - will ultimately provide a new paradigm in food production, which uses microbiome monitoring and modulation as a mean to achieve a better sustainability, safety, quality and productivity of the food system. CIRCLES will provide the society and the market with knowledge, products, strategies, protocols, guidelines able to contribute to an improved future in terms of a reduced impact of food chains on natural resources.
Circles improving food systems