Periodic Reporting for period 4 - CIRCLES (Controlling mIcRobiomes CircuLations for bEtter food Systems)
Période du rapport: 2023-05-01 au 2024-10-31
Food production has proven to be too expensive, responsible for 70% of H2O consumption and 30% of energy usage, while delivering 25% of greenhouse gas emissions. The food systems in place have exerted excessive pressure on natural resources, exceeding planetary boundaries and compromising the Earth’s ability to produce safe and secure food for the future. Thus, sustainable food production has become a European and global priority. A paradigm shift in food production was necessary to reduce the environmental footprint while ensuring the continuous supply of safe and secure food.
Recognizing the central role of natural microbiomes in environmental, plant, and animal health, CIRCLES has successfully explored their potential as an untapped resource of probiotic functions within food systems. This approach has presented a significant opportunity to reduce the ecological impact of food production while maintaining its safety and efficiency. With this awareness, CIRCLES has worked to discover, translate, and communicate innovative microbiome-based applications to enhance the EU food systems in terms of quality, productivity, safety, and sustainability.
CIRCLES has provided Smart Microbiome Food Systems (SMFSs) for eight key food chains relevant to the EU market: spinach, tomatoes and grapes (wine), poultry and pig meat, Atlantic salmon and seabream aquaculture, and wild marine organisms (e.g. wild fish, corals, shellfish, and crustaceans). These new food system paradigms have been structured to optimize microbiome circulation and dynamics, improving productivity, quality, safety, and sustainability. The SMFSs were achieved through a microbiome biotechnology approach, involving microbiome-tailored circular actions supported by Smart Microbiome Modulators (SMMs) to optimize food system microbiomes.
The insights gained through CIRCLES have provided decision-makers, academia, businesses, and consumers with a comprehensive vision of microbiomes’ impact on food systems, from farm to fork. Ultimately, this has enabled Europe to address the needs of a growing global population by implementing resource-efficient circular economy principles in food production and significantly reducing Europe’s environmental footprint.
Recognizing the central role of natural microbiomes in environmental, plant, and animal health, CIRCLES has successfully explored their potential as an untapped resource of probiotic functions within food systems. This approach has presented a significant opportunity to reduce the ecological impact of food production while maintaining its safety and efficiency. With this awareness, CIRCLES has worked to discover, translate, and communicate innovative microbiome-based applications to enhance the EU food systems in terms of quality, productivity, safety, and sustainability.
CIRCLES has provided Smart Microbiome Food Systems (SMFSs) for eight key food chains relevant to the EU market: spinach, tomatoes and grapes (wine), poultry and pig meat, Atlantic salmon and seabream aquaculture, and wild marine organisms (e.g. wild fish, corals, shellfish, and crustaceans). These new food system paradigms have been structured to optimize microbiome circulation and dynamics, improving productivity, quality, safety, and sustainability. The SMFSs were achieved through a microbiome biotechnology approach, involving microbiome-tailored circular actions supported by Smart Microbiome Modulators (SMMs) to optimize food system microbiomes.
The insights gained through CIRCLES have provided decision-makers, academia, businesses, and consumers with a comprehensive vision of microbiomes’ impact on food systems, from farm to fork. Ultimately, this has enabled Europe to address the needs of a growing global population by implementing resource-efficient circular economy principles in food production and significantly reducing Europe’s environmental footprint.
Since its launch in November 2018, CIRCLES successfully established 20 labs-in-the-field within real-world EU production sites across the eight identified food systems. The project has advanced well, with the observation phase reaching completion in all labs-in-the-field. The sequencing results have been analyzed, providing crucial knowledge on food system microbiomes to design innovative intervention strategies.
During the observation and intervention phases, extensive sample collections were carried out across all food chains, covering the entire production cycles. Despite challenges posed by the COVID-19 emergency, which affected some sampling campaigns, over 6,000 samples were collected and analyzed. DNA extraction and sequencing from animal, plant, and environmental samples were completed for all food chains.
The bioinformatics infrastructure developed for managing the large volumes of data produced by CIRCLES has been widely used, storing over 10 Tbp of sequencing data from both 16S rRNA and shotgun metagenomics. Sequence analysis and modeling have been actively pursued to support the implementation and production of food-specific Smart Microbiome Modulators.
During the observation and intervention phases, extensive sample collections were carried out across all food chains, covering the entire production cycles. Despite challenges posed by the COVID-19 emergency, which affected some sampling campaigns, over 6,000 samples were collected and analyzed. DNA extraction and sequencing from animal, plant, and environmental samples were completed for all food chains.
The bioinformatics infrastructure developed for managing the large volumes of data produced by CIRCLES has been widely used, storing over 10 Tbp of sequencing data from both 16S rRNA and shotgun metagenomics. Sequence analysis and modeling have been actively pursued to support the implementation and production of food-specific Smart Microbiome Modulators.
Beyond expanding basic knowledge on the significance of natural microbiomes in food systems, CIRCLES has successfully developed microbiome-based applications—circular actions—to enhance probiotic functionalities across the entire food chain. These advancements have improved overall food system performance and sustainability.
CIRCLES has demonstrated its strength by combining extensive academic expertise with private sector resources and know-how. This collaboration has facilitated the translation of research advancements into concrete applications across various fields, including agriculture, animal production, food processing, waste management, and environmental protection.
The microbiome-based applications developed by CIRCLES have introduced a new paradigm in food production, integrating microbiome monitoring and modulation to achieve enhanced sustainability, safety, quality, and productivity. Through this work, CIRCLES has delivered knowledge, products, strategies, protocols, and guidelines, all of which contribute to a more sustainable future by reducing the impact of food chains on natural resources.
CIRCLES has demonstrated its strength by combining extensive academic expertise with private sector resources and know-how. This collaboration has facilitated the translation of research advancements into concrete applications across various fields, including agriculture, animal production, food processing, waste management, and environmental protection.
The microbiome-based applications developed by CIRCLES have introduced a new paradigm in food production, integrating microbiome monitoring and modulation to achieve enhanced sustainability, safety, quality, and productivity. Through this work, CIRCLES has delivered knowledge, products, strategies, protocols, and guidelines, all of which contribute to a more sustainable future by reducing the impact of food chains on natural resources.