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.