Integrating A Holistic Perspective In Microbiome Research For Resilient, Competitive And Sustainable Food Systems
HORIZON Research and Innovation Actions
Basic Information
- Identifier
- HORIZON-CL6-2026-02-FARM2FORK-11
- Programme
- Call 02 - single stage (2026)
- Programme Period
- 2021 - 2027
- Status
- Open (31094502)
- Opening Date
- January 14, 2026
- Deadline
- April 14, 2026
- Deadline Model
- single-stage
- Budget
- €11,800,000
- Min Grant Amount
- €5,000,000
- Max Grant Amount
- €6,000,000
- Expected Number of Grants
- 2
- Keywords
- HORIZON-CL6-2026-02-FARM2FORK-11HORIZON-CL6-2026-02Agricultural biotechnologyEnvironmental biotechnologyIndustrial biotechnologyMicroalgaeMicrobiology
Description
Project results are expected to contribute to all the following expected outcomes:
- a better systems-level understanding through a One Health approach of the complex interactions and functional impacts of microbiomes across different hosts (plants, humans, animals...), environments (water, food matrices...), and interconnected ecosystems;
- solutions are identified for resilient, competitive, and sustainable food systems that cover e.g. food security, agrifood systems durability and resilience, industrial applications, nutrition, health, and relevant aspects of biodiversity, climate change and the environment;
- synergies are identified between existing European research infrastructures for sample biobanking and data-gathering/gathering/sharing to facilitate the exchange, pooling and integrated analysis of integrated microbiome (meta)-data, promoting inter and trans-disciplinary collaboration among different stakeholders under the FAIR (Findable, Accessible, Interoperable and Re-usable) principles.
Microbiomes hold immense potential for food systems applications, but microbiomes are often studied in siloes or one ecosystem at a time. Unlocking the functional diversity of food microbiomes to help develop innovative applications requires a systems approach[1]. The topic is relevant to the EU policies related to the Commission communication on: Building the future with nature: Boosting Biotechnology and Biomanufacturing in the EU[2], the Life Science Strategy, the EU Biodiversity Strategy for 2030, the Zero Pollution Action Plan, the EU strategy on research and technology infrastructure, the R&I Food 2030 Framework and the policies related to the digital transition (e.g. AI Act, etc) and contributes to climate action and biodiversity goals.
Proposals should address all the following activities:
- establish a holistic system approach to study the microbiome, and its interaction with its host and/or environment, its function and contribution to ecosystem(s) functions, connecting inter and trans-disciplinary fields of science (e.g. microbiology, ecology, AI and bioinformatics, biotechnology, synthetic/molecular biology, agronomy, plant sciences, etc.);
- investigate existing and new supporting technologies such as multi-omics technologies, high-throughput sampling/phenotyping systems, predictive models, AI, federated learning, cultivation methods and/or in-vitro validated models (e.g. organoids, organ-on-a-chip, genetic and metabolic engineering) for application in integrated microbiome studies;
- establish further synergies between existing infrastructures (for instance, ELIXIR, MIRRI, BBMRI-ERIC, EOSC, etc.) to enhance their capacity to integrate and valorise integrated microbiome data (integrating samples and associated (meta)-data from diverse sources) as well as considering the integration of other environmental, agricultural, nutritional or climate datasets;
- provide references strains and/or samples (e.g. for food safety or holobiont selection), standard protocols, operating procedures and quality control measures through the existing biobanks and data-repositories to support and facilitate further microbiome studies.
Proposals must follow a multi-actor approach, engaging researchers, businesses (including SMEs and startups), public authorities and policy makers, research infrastructures and civil society to co-develop solutions.
[1] Meisner, A., Wepner, B., Kostic, T., van Overbeek, L.S., Bunthof, C. J., de Souza, R. S. C., Olivares, M., Sanz, Y., Lange, L., Fischer, D., Sessitsch, A., Smidt, H. (2022). Calling for a systems approach in microbiome research and innovation. Current Opinion in Biotechnology, 73, 171–178. https://doi. org/10.1016/j.copbio.2021.08.003
Destination & Scope
This destination will support the EU Commission priority ‘Sustaining our quality of life: food security, water and nature’.
R&I will provide new knowledge and innovation in support of the EU Vision for Agriculture and Food, built on the recommendations of the Strategic Dialogue on Agriculture, to ensure the long-term competitiveness and sustainability of our farming, fisheries, aquaculture and food sector within the boundaries of our planet. The implementation of the Green Deal actions will continue to guide R&I in this destination to foster sustainable food systems, addressing potential trade-offs between economic competitiveness and environmental sustainability.
The R&I activities under this Destination will contribute to the ambitious objectives of the current CAP concerning the competitiveness and sustainability of feed, food and non-food production as well as additional future CAP policy priorities. More specifically, actions will contribute to the specific objectives of the CAP; EU action plan for the development of organic production; food safety regulations; sustainable use of pesticides requirements under the plant protection products framework; action plan against antimicrobial resistance; animal health and welfare legislations; legislative and non-legislative initiatives to enhance cooperation of primary producers and improve their competitiveness and position in the food chain; protein strategy; contingency plan for ensuring food supply and food security and communications on food security and fertilizers, the Nature Restoration Regulation, the Zero Pollution Action Plan.
R&I will also support the announced Vision for the Fisheries Sector with a 2040 perspective and the European Ocean Pact, a framework of coherence across all policies linked to the ocean. R&I will also be relevant to the outcomes of the evaluation of the common fisheries policy (CFP) and will support its placement under this Pact, as fisheries and aquaculture are affected by other ocean related policies.
An important driving force of food systems transformation should be the integration of sectors, actors (including citizens and consumers) and policies. This will involve a better understanding of the multiple interactions between the components of current food systems, to foster solutions that maximise co-benefits with respect to the priorities of Food 2030[1].
The EU Communication on Boosting Biotechnology and Biomanufacturing in the[2] EU provides an overview of the application of biotechnologies in several sectors including food and feed. R&I activities in this destination will also contribute to achieving the objectives of the Strategy for European Life Sciences, the EU Biotech Act, and the new EU bioeconomy strategy.
The Destination supports unlocking the unique assets for research and innovation of the EU outermost regions, in line with the EU strategy for outermost regions[3].
Expected impact: Proposals for topics under this destination should set out credible paths to “ensuring healthy food and nutrition security by making agriculture, fisheries, aquaculture and food systems sustainable, resilient, inclusive and within planetary boundaries”. More specifically, proposed topics should contribute to one or more of the following expected impacts:
- agriculture and food systems contribute to ensuring a secure, safe, sustainable, nutritious, and affordable supply of healthy food in Europe and beyond by fostering its long-term competitiveness, resilience, scalability and sustainability within the boundaries of our planet with the One Health approach;
- farmers are empowered to ensure the competitiveness, resilience and sustainability of the farming sector, through increasing knowledge, tools, innovative solutions, and advice that allow efficient productivity, working for and with nature, preserving and restoring biodiversity within agricultural ecosystems and helping to decarbonise the EU economy;
- sustainable fisheries and aquaculture (in marine, brackish and freshwater) contribute to fair, healthy, resilient and environment-friendly food systems in healthy aquatic ecosystems with thriving diversity of species and habitats providing ecosystem and climate services and triggering growth and jobs’ creation in coastal and rural areas;
- tools are provided so that citizens and communities are empowered to make the sustainable food choices and move towards safe, healthy, nutritious, accessible, affordable and sustainable diets. Insights and advances in life science and digital & data technologies are valorised to deploy solutions in practice across the EU;
- food businesses, including food processing industries and SMEs, are supported to increase their resilience and competitiveness, while ensuring resource efficiency and sustainability, and human, animal and ecosystem health is preserved.
[1] The four priorities of Food2030 are: 1) nutrition and health; 2) climate and environmental sustainability; 3) circularity and resource efficiency; and 4) innovation and empowering communities.
[2] https://eur-lex.europa.eu/legal-content/EN/TXT/?uri=CELEX:52024DC0137.
[3] COM(2022) Putting people first, securing sustainable and inclusive growth, unlocking the potential of the EU’s outermost regions.
Eligibility & Conditions
General conditions
1. Admissibility Conditions: Proposal page limit and layout
2. Eligible Countries
described in Annex B of the Work Programme General Annexes.
A number of non-EU/non-Associated Countries that are not automatically eligible for funding have made specific provisions for making funding available for their participants in Horizon Europe projects. See the information in the Horizon Europe Programme Guide.
3. Other Eligible Conditions
The following additional eligibility criteria apply: the proposals must apply the multi-actor approach. See definition of the multi-actor approach in this work programme part.
Subject to restrictions for the protection of European communication networks.
described in Annex B of the Work Programme General Annexes.
4. Financial and operational capacity and exclusion
described in Annex C of the Work Programme General Annexes.
5a. Evaluation and award: Award criteria, scoring and thresholds
are described in Annex D of the Work Programme General Annexes.
5b. Evaluation and award: Submission and evaluation processes
are described in Annex F of the Work Programme General Annexes and the Online Manual.
5c. Evaluation and award: Indicative timeline for evaluation and grant agreement
described in Annex F of the Work Programme General Annexes.
6. Legal and financial set-up of the grants
Eligible costs will take the form of a lump sum as defined in the Decision of 7 July 2021 authorising the use of lump sum contributions under the Horizon Europe Programme – the Framework Programme for Research and Innovation (2021-2027) – and in actions under the Research and Training Programme of the European Atomic Energy Community (2021-2025) [[This decision is available on the Funding and Tenders Portal, in the reference documents section for Horizon Europe, under ‘Simplified costs decisions’ or through this link: https://ec.europa.eu/info/funding-tenders/opportunities/docs/2021-2027/horizon/guidance/ls-decision_he_en.pdf]].
described in Annex G of the Work Programme General Annexes.
Specific conditions
described in the [specific topic of the Work Programme]
Application and evaluation forms and model grant agreement (MGA):
Application form templates — the application form specific to this call is available in the Submission System
Standard application form (HE RIA, IA)
Evaluation form templates — will be used with the necessary adaptations
Standard evaluation form (HE RIA, IA)
Guidance
Model Grant Agreements (MGA)
Call-specific instructions
Additional documents:
HE Main Work Programme 2026-2027 – 1. General Introduction
HE Main Work Programme 2026-2027 – 15. General Annexes
HE Framework Programme 2021/695
HE Specific Programme Decision 2021/764
EU Financial Regulation 2024/2509
Decision authorising the use of lump sum contributions under the Horizon Europe Programme
Rules for Legal Entity Validation, LEAR Appointment and Financial Capacity Assessment
EU Grants AGA — Annotated Model Grant Agreement
Funding & Tenders Portal Online Manual
Frequently Asked Questions About Integrating A Holistic Perspective In Microbiome Research For Resilient, Competitive And Sustainable Food Systems
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