Microbiome applications for sustainable food systems

The EU food system is an important part of the economy and society in Europe. Given the current context of societal, environmental and economic changes, there is need for constant improvement in terms of productivity, quality, safety, market orientation, adaptability, and international competitiveness. Knowledge of the potential of microbial systems, or microbiomes, throughout the food chains, is a promising means to this end. Microbiomes are known to regulate the productivity and health of major food sources such as plants and animals of both terrestrial and aquatic origin, therefore playing a major role in food and nutrition security. They also play a major role in food and feed processing and metabolism in different organisms throughout the evolutionary scale, ultimately influencing human health. A better understanding of the microbiomes associated with the food system would help address a number of key societal challenges including food and nutrition security, health and wellbeing, food waste management, climate change adaptation and mitigation.


Proposals shall focus on concrete microbiome applications which are of benefit to the food system. Building on knowledge already accrued from the isolation and characterization of microbiota associated to food production systems (plants, soils, animals, marine), proposals should look into ways to improve the quantity, quality and safety of the food we produce and consume in Europe. Microbiome applications in the treatment of food waste and alternative uses which promote sustainability and circularity are also included in the scope. Proposals are expected to develop holistic approaches across all stages of the food system from fork to farm including aquatic (marine and fresh water) resources. Activities shall also aim at increasing knowledge and applications derived from the marine microbiome for the development of new products, services or processes for food and health, while contributing to climate change mitigation. The inter-relations among microbiomes from different components across food chains - from soil to plants, animals, the marine and the human gut - and their impact on food and nutrition security and health shall also be considered. International co-operation, transdisciplinary research, and integration of SSH and RRI including gender aspects to ensure long-lasting implementation of the results are encouraged. Activities shall build on existing data and knowledge on the microbiomes associated to food production and processing systems, including results of EU funded projects in FP7 and Horizon 2020. Activities shall optimise the use of pre-existing databases and research infrastructures (including the distributed and virtual ones) and the opportunities granted by big data management tools, thus ensuring interoperability, standard methods and enhanced networking. The interdisciplinary and cross-sectorial nature of the project should also apply to training activities improving the professional skills and competencies and supporting the creation of new jobs in the food sector and the bioeconomy.

The Commission considers that proposals requesting a contribution from the EU of the order of EUR 10 million would allow this specific challenge to be addressed appropriately. Nonetheless, this does not preclude submission and selection of proposals requesting other amounts.

Expected Impact

In the framework of SDG no 2, 3, 9, 12, 13 and 15, the EU's Bioeconomy Strategy 2012, and the FOOD 2030 SWD, and the Blue Economy communication, proposals should explain how activities included are expected to:

  • Raise awareness of the potential behind microbiomes from terrestrial and aquatic environments in transforming and future-proofing our food system;
  • Bring to market new and cost-effective commercial applications to assist different stages and processes throughout the food chains, by 2025;
  • Improve overall knowledge of microbiomes from land and seas towards the market needs in areas where applicability and readiness is not visible;
  • Improve overall sustainability, including climate change mitigation, and innovation capacity of the food system through the use of microbiome applications and knowledge;
  • Move available solutions from TRL 5/6 to TRL 7.

Cross-cutting Priorities

  • Socio-economic science and humanities
  • International cooperation
  • RRI
Application date
Social sciences : Economy, Environmental Sciences, Law, Political science, Psychology & Cognitive Sciences