Microbiomes in One Health
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Microbiomes, the complex and dynamic communities of microorganisms present in humans, animals, plants, soils, water, air, food and built environments, are increasingly recognized as foundational to health, ecosystem functioning and the sustainability of agrifood systems. This FAO position paper examines the integration of microbiome science into the One Health framework, and outlines key policy implications for global agrifood, health and environmental governance.While the One Health approach has traditionally emphasized zoonotic pathogens and antimicrobial resistance, it has not yet fully incorporated the broader microbial ecosystems in which these processes occur. Growing scientific evidence demonstrates that microbiomes play essential roles in nutrient cycling, soil fertility, plant productivity, animal health, human nutrition, immune development and climate regulation. Conversely, disruption of microbiomes, driven by intensive agricultural practices, antimicrobial overuse, pollution, urbanization and climate change, contributes to increased risks of infectious and non-communicable diseases, antimicrobial resistance emergence and dissemination, reduced agricultural productivity, biodiversity loss, and ecosystem degradation.Recognizing microbiomes as interconnected across human, animal, plant and environmental systems provides a unified lens for addressing complex One Health challenges. Advances in genomics, data science, and biotechnology now enable large-scale microbiome monitoring and the development of microbiome-based innovations, including diagnostics, probiotics, biostimulants, biopesticides and precision management tools. These approaches offer opportunities to enhance resilience, reduce reliance on chemical inputs, and improve sustainability across agrifood systems.The paper recommends explicit integration of microbiomes into One Health definitions and implementation frameworks, the establishment of harmonized monitoring and data standards, strengthened interdisciplinary research and capacity development, and the promotion of microbial stewardship. It further highlights the need for coherent regulatory frameworks and international collaboration, particularly through coordinated action among Quadripartite partners. Integrating microbiomes into One Health represents a strategic opportunity to advance sustainable agrifood systems transformation, improve global health outcomes, and support achievement of the Sustainable Development Goals.