Microbiome for terrestrial livestock sustainability and health within a One Health approach

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.

Expected Outcome:

Project results are expected to contribute to all the following expected outcomes:

• the research community, farmers, livestock industry e.g. breeders, service providers, policymakers understand better the role of the microbiome on livestock health and production and the interaction with environment and human health within a One Health approach;
• researchers' communities and innovators in the livestock sector have access to a platform of tools for data sharing, knowledge exchange, capacity building and standardization in microbiome research and its applications through synergies with other platforms in a One Health context;
• targeted strategies and guidelines are available to farmers, service providers and livestock industry to contribute to improving livestock health, while reducing antimicrobial use and environmental impact, and securing animal welfare.

Scope:

Microbiome research offers transformative potential for livestock management within the One Health (OH) framework, which emphasises the interconnected health of animals, humans, and the environment. In livestock, microbiome innovation can address pressing issues such as antimicrobial resistance (AMR) and zoonotic disease transmission. However, gaps persist in understanding the role of variability within host-microbiome interactions, in developing sustainable farming practices, and assessing these interventions in real-world farming settings. Advancing microbiome research can enhance animal health and productivity, improve ecosystems, while reducing environmental and climate impacts. By focusing on microbiome-based solutions, the objective is to support sustainable livestock systems that align with OH principles, necessitating cross-disciplinary collaboration to ensure comprehensive health benefits.

Proposals should address all of the following activities:

• investigate the microbiome of terrestrial livestock, their influence on animal health, taking into account the holobiont/hologenome perspectives, and the interactions with the environment (soil, plant, water, air) and human health;
• develop integrated data monitoring systems that track microbiome related health indicators across livestock, plant, and human health sectors, and help in risk assessment models for zoonotic disease and/or AMR emergence and transmission;
• assess how microbiome-based solutions for animal health affect, and are affected by, soil and plant health, and the use of chemical fertilisers and pesticides;
• design holistic health models that incorporate microbiome research to enhance the robustness of animals as well as animal health and welfare, and overall productivity, taking into account soil and plant health, and to assess potential synergies and trade-offs between these objectives;
• design microbiome related intervention strategies to prevent outbreaks and cross-species transmission in animal populations and reduce the risk of zoonosis, thereby contributing to reduced antimicrobial usage while enhancing resilience, animal welfare, and minimizing environmental impact;
• develop, or contribute to, platforms to collaboratively assess and optimise the efficacy and implementation of microbiome-based tools, products and services in the livestock sector through synergies with other platforms within a One Health context;
• enhance collaboration among veterinarians, microbiologists, geneticists, animal and plant biologists, epidemiologists, and ecologists and other experts to work towards a One Health approach.

Projects selected under this topic should interact between themselves and build on/interact with recent or on-going EU funded projects and initiatives, including those funded under the topic HORIZON-CL6-2026-02-FARM2FORK-11: Integrating a holistic perspective in microbiome research for resilient, competitive and sustainable food systems, as well as with relevant activities of the European partnerships on animal health and welfare, on One health AMR, and on pandemic preparedness.

The projects under this topic are relevant to the EU policies related to the EU Green Deal’s goals for resilient and sustainable agri-food systems, the EU biodiversity strategy for 2030, the Life Sciences strategy, the Vision for Agriculture and Food, the EU One Health Action Plan against Antimicrobial Resistance, and the Council Recommendation on stepping up EU actions to combat antimicrobial resistance in a One Health approach.