Building a microbiome-informed approach to agri-food systems and childhood nutrition policies
Julie Barrett O’Brien: CEO, OpenBiome Foundation
Majdi Osman: Chief Medical Adviser, OpenBiome Foundation
Paul Miller: Chief Scientific Adviser, OpenBiome Foundation
A holistic, microbiome-informed approach to agrifood systems and childhood nutrition policies—rooted in global collaboration, evidence-building, and equitable innovation—can drive sustainable solutions to undernutrition and improve children’s health worldwide.
Published on July 31th, 2025
Introduction
The entire continuum of food production, from soil preparation to processing and consumption, relies on the co-evolved interaction of microbes with plants, animals, humans, and the environment. To date, microbiome science across these domains has largely taken a reductionist view, studying each ecosystem and elucidating the interactions of microbes with other microbes, nutritional/biochemical inputs, and the host. In translating microbiome science to improve human health, efforts have largely focused on identifying certain microbial communities to be restored (e.g., via probiotics or live biotherapeutics) or on identifying foods or chemical compounds that can restore microbial function and composition.
Taking microbiome science “upstream”
How can we begin to build a foundation for integrating microbiome science at all levels across sectors to inform the agri-food system for human health? Perhaps there's no more pressing need than in the case of child undernutrition, a microbiome-mediated disease and a quintessential food systems/public health problem that, if optimally addressed, could significantly reduce child mortality globally. Addressing the persistent global challenge of childhood undernutrition, which affects 150 million children and perpetuates long-term health deficits and economic burden, demands innovative solutions that move beyond conventional approaches.
To this end, the OpenBiome Foundation hosted an expert panel at the 2024 UN Science Summit titled Why the gut microbiome is critical to children’s health: harnessing microbiome science to end malnutrition (1). The panel underscored the pivotal role of the gut microbiome in childhood health and nutrition, highlighting that restoring and supporting this internal ecosystem is essential to modern nutrition and public health. Food, in this context, is more than just calories. Food is medicine—a source of bioactive compounds that interact with the gut microbiome, influencing nutrient absorption, immune function, and developmental health, effectively acting as medicine through microbial interactions (2, 3). Consequently, solving malnutrition requires not only nutrient delivery but also addressing the microbial capacity to process and absorb these nutrients (4). However, as highlighted by Fernández-Gómez et al. in their Frontiers in Science lead article (5), there is a pressing need to consider these ecosystems as interconnected through the food chain in their contribution to human, animal, and planetary health. Accumulating evidence shows that differences in microbiome composition between rural and urban populations, as well as between high-income and low- and middle-income countries (LMICs), suggest that “upstream” factors, including the food systems, must be considered. This presents a gap in knowledge and an opportunity to address health through microbiome- informed policy and interventions that embrace an integrated view of microbial life (6).
Moving beyond isolated discoveries, a holistic understanding of how microbial ecosystems interact within the broader agri-food system is crucial. This goes beyond identifying specific microbial culprits or beneficial strains; it's about recognizing the profound influence of diverse environments, agricultural practices, and dietary patterns on microbial communities and, by extension, on human health outcomes. Embracing this interconnectedness allows us to design more effective and sustainable interventions.
Policy priorities: cultivating a microbiome-informed agri-food system for child health
Building on insights from the UN Science Summit panel, the following policy priorities are crucial for integrating microbiome science across the agri-food system to effectively address childhood undernutrition. These points emphasize a holistic, interconnected approach, moving beyond isolated discoveries to foster systemic change.
Bolster local, multisectoral collaboration
There is a need for in-country data to identify the etiology of malnutrition-related diseases in specific populations. Partnerships among governments, the private sector, and NGOs are essential to supporting international clinical trials that bring products from discovery to implementation. Current microbiome-directed therapeutics available in high-income countries are often prohibitively costly. New technologies, product development techniques, and collaboration with regulators and finance/health departments are necessary for affordability and impact. The most innovative partnerships involve in-country experts and funding science to meet patient needs and iterate innovations on the ground. Evidence of efficacy is likely to drive demand and reduce prices. Additionally, government and private sector funding is required to boost capacity for costly genomic research. Success measures would include the establishment of baseline microbiome datasets across a geographically diverse range of communities to define and distinguish healthy and unhealthy microbial community structures, the cost of which would vary by country. These data could further inform the design of clinical studies testing the effectiveness of microbiome repair strategies on healthy child growth trajectories.
Build an open-source body of globally representative evidence
The World Health Organization (WHO) plays a role in developing guidance for interventions and driving the research agenda. To make recommendations, evidence of efficacy from randomized clinical trials and mechanistic studies that demonstrate an intervention reverses the trajectory of malnutrition or improves immune status is required. While many studies show an association between microbiome composition and health, proof of efficacy for interventions is currently lacking. However, with high-quality evidence from diverse settings, the WHO could issue recommendations globally. Trials from diverse communities showing evidence of immune recovery, linear growth, and other developmental or functional outcomes, even if they don't follow participants long enough to show major changes in wasting or weight, can still be valuable. Unfortunately, microbiome science today captures a fraction of global diversity (7) with few samples and microbiomes from Africa, Asia, and South America represented in publicly available datasets. Unless intentional steps are taken to diversify our data, geographical bias may limit the impact of innovations and recommendations. Accordingly, a significant financial commitment from both governmental and non-governmental organizations is required to support both baseline microbiome data acquisition and subsequent clinical trials.
Technical capacity building
Manufacturing and distributing nutritional interventions require significant technical capacity building. For a feasible and affordable scale-up, the manufacturing process should rely on locally available quality ingredients, including crops whose production requires their own microbiome optimizations. Supply chain studies should accompany clinical trials, and scientists should engage early with local manufacturers on ingredients to ensure rapid implementation once interventions are approved. More efficient animal husbandry will also benefit from a better understanding of microbial interactions with food and diets, similar to understanding how a child’s microbiome influences healthy growth (8).
Invest in innovation equitably
Accelerating novel interventions is crucial, given the lack of effective cures for severe acute malnutrition, which is linked to approximately half of childhood deaths under five years old (9). Yet, as public and private sector investment flows to research and development of microbiome interventions in high-income countries, there is a widening gap in representation and participation from scientists and communities in LMICs. This growing disparity risks delivering a more inequitable world, where the many potential benefits of microbiome science accrue only to the wealthy few. We encourage continued investment in microbiome science as a core global scientific competency, ensuring that local scientists are equipped to tackle the unique challenges of their communities.
Conclusion
By integrating microbiome science across the entire agri-food system, from healthy soils to human digestion, and fostering strategic, integrated policy interventions and partnerships, we can achieve comprehensive and sustainable improvements in global health outcomes, particularly for our most vulnerable populations. This perspective, recognizing the profound interplay between our food systems and the microbial world, offers a more inclusive, holistic pathway toward a healthier future. While globalizing microbiome science to address child malnutrition will be costly, the return on investment will be incalculable.
Copyright statement
Copyright: © 2025 [author(s)]. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in Frontiers Policy Labs is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
Generative AI statement
The author declares that no generative AI was used in the creation of this article.
References
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