Microbiome as an engine of sustainability: how Horizon Europe expects you to rethink food systems in HORIZON-CL6-2026-02-FARM2FORK-11

22nd December 2025 at 9:19 am

Microbiomes influence plant growth, animal health, food quality, nutrition and environmental resilience. Yet most microbiome research remains siloed, limiting its potential for food system transformation. The Horizon Europe call HORIZON-CL6-2026-02-FARM2FORK-11 supports Research and Innovation Actions (RIAs) that integrate microbiome insights across hosts, environments and ecosystems. With a deadline on 14 April 2026 and a budget of €11.00 million for two projects, the call seeks a One Health approach that supports FAIR (Findable, Accessible, Interoperable and Reusable) principles to unlock microbiomes as a foundation for resilient, competitive and sustainable food systems. It aligns with several policies of the European Union (EU), including Building the future with nature: Boosting Biotechnology and Biomanufacturing in the EU, the Strategy for European Life Sciences, the Biodiversity Strategy for 2030, the Zero Pollution Action Plan, the European Strategy on Research and Technology Infrastructures, the Research and Innovation (R&I) Food 2030 framework and the Digital Transition.

1. From individual microbiomes to interconnected food system insights

Food system microbiomes exist in a web of interactions linking plants, animals, humans, soils, water, food matrices and processing environments. The call seeks projects that adopt a holistic systems approach to understand microbiome functions across interconnected ecosystems and how these interactions influence food resilience, nutrition, biodiversity and climate outcomes.

Tips for applicants:

• Use a One Health perspective to investigate cross-ecosystem microbiome interactions.
• Connect disciplines including microbiology, ecology, agronomy, nutrition, artificial intelligence (AI) and bioinformatics.
• Show how microbiome insights support food security, durability, resilience and sustainability.
• Build conceptual frameworks that integrate microbiome function across multiple environments.

2. Integrating advanced multi-omics, modelling and AI technologies

To unlock the functional diversity of microbiomes, proposals must use existing and emerging supporting technologies, including multi-omics, high-throughput sampling, phenotyping, predictive modelling, AI, federated learning and cultivation methods. These tools will allow researchers to map interactions, identify functional pathways and explore microbiome-driven innovation opportunities.

Tips for applicants:

• Combine metagenomics, metabolomics, proteomics and transcriptomics for full functional insight.
• Integrate predictive models and AI to identify drivers of resilience, performance and risk.
• Use high-throughput systems to generate scalable datasets that support mechanistic understanding.
• Include validated in-vitro models, such as organoids or organ-on-chip systems, where relevant.

3. Translating microbiome findings into sustainable food system solutions

The purpose of this call is not only to understand microbiomes but also to identify practical, scalable solutions for competitive and sustainable food systems. These solutions may support food safety, agrifood durability, biotechnology, industrial applications, nutrition and climate resilience.

Tips for applicants:

• Demonstrate clear pathways linking microbiome data to tangible applications.
• Explore innovation opportunities in sustainable materials, functional foods, safe processing and bio-based industries.
• Highlight how microbiome-driven solutions support biodiversity conservation, climate adaptation and reduced environmental impacts.
• Engage relevant industry partners early to validate market and value-chain relevance.

4. Strengthening Europe’s microbiome data ecosystem

The European Commission (EC) expects proposals to establish further synergies between European research infrastructures, including ELIXIR, MIRRI, BBMRI-ERIC and EOSC, to enable the integration, pooling and FAIR-enabled reuse of microbiome data. Proposals should also consider the integration of other environmental, agricultural, nutritional or climate datasets to support cross-ecosystem analyses and strengthen Europe’s long-term, interoperable microbiome knowledge base.

Tips for applicants:

• Design workflows that generate “FAIR-by-design” microbiome datasets.
• Connect to biobanks, repositories and federated data networks across infrastructures.
• Use shared metadata standards for cross-domain analysis.
• Plan data governance structures that support long-term accessibility and interoperability.

5. Providing reference strains, standard protocols and quality control

To accelerate innovation and ensure comparability, proposals must provide reference strains and samples, as well as standard protocols, operating procedures and quality control measures through existing biobanks and repositories. This standardisation is essential for enabling reproducible microbiome research and supporting downstream applications.

Tips for applicants:

• Contribute reference materials (e.g., food safety strains, holobiont-associated samples).
• Develop harmonised standard operating procedures (SOPs) and quality control (QC) for sampling, processing and analysis.
• Collaborate with infrastructures to validate and distribute reference resources.
• Link protocol development to future regulatory, industrial or research applications.

6. Multi-actor collaboration for impactful microbiome innovation

This topic requires a multi-actor approach, involving researchers, SMEs, start-ups, agrifood companies, public authorities, policymakers, civil society and research infrastructures. Co-design ensures that scientific insights translate into solutions that are relevant, scalable and adopted across food systems.

Tips for applicants:

• Include all stakeholders across the microbiome–food system value chain.
• Ensure early engagement with public authorities and industry for co-development.
• Integrate disciplines from social sciences and humanities (SSH) to capture societal relevance, behavioural aspects and public perceptions.

Plan for demonstration activities that show feasibility and cross-sector applicability.

Do you need support with writing your proposal for microbiome food systems innovation?

At accelopment, we work with research consortia advancing biotechnology, food system sustainability and data-driven biological innovation. Our experience includes projects such as BioTransform, PHOTONFOOD, Train2Target and PILGRIM, which demonstrate our expertise in systems-level biology, microbiome-relevant applications, molecular and bio-based technologies, and multi-actor scientific collaboration. Together, these projects reflect our ability to support interdisciplinary research that connects biological mechanisms with practical solutions for sustainable, resilient and competitive food systems. With our expertise in proposal writing, consortium coordination and impact communication, we help teams design competitive and policy-aligned projects under Horizon Europe’s Cluster 6.

Dr. Johannes Ripperger
Research & Innovation Manager

Andreia Cruz
Research & Innovation Project Manager