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Controlling mIcRobiomes CircuLations for bEtter food Systems

Periodic Reporting for period 2 - CIRCLES (Controlling mIcRobiomes CircuLations for bEtter food Systems)

Reporting period: 2020-05-01 to 2021-10-31

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 general, the project is in a good state of advancement, the observation phase is nearing its end for all the labs-in-the-field, and we are now analyzing the sequencing results for producing the required food system microbiomes knowledge to design innovative intervention strategies on the food system microbiomes (intervention phase). For the observation phase, in each labs-in-the-fields (poultry, swine, spinach, tomatoes, sea bream and salmon), samples collection throughout the whole productive cycles has been carried out, as well as the DNA extraction, even if the Covid-19 emergency posed some problems for the conclusion of some of the sampling campaigns. In total more than 3000 samples have been collected - and biobanked - from these food chains. Furthermore, DNA extractions and sequencing from animal, plant and environmental samples are now nearing to be terminated for almost all the food chains. Indeed, the informatics infrastructure for managing the big-data produced by CIRCLES is now widely used, hosting more than 2 Tbp of sequences from both 16S rRNA and shotgun metagenomics. Finally, sequence analysis and modelling for educating the implementation (and production) of the food specific smart microbiome modulators are now in progress for all the food chains.
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