Microbiomes at the heart of sustainable agri-food systems and global health

Key points • Healthy food requires healthy microbiomes: From soils to the human gut, microbial communities shape nutrient quality, food safety, and resilience. • Food systems and health are inseparable: Managing microbiomes supports both sustainable agriculture and disease prevention, aligning with the One Health framework. • Microbes offer natural solutions: Biocontrol, probiotics, and fermentation can reduce waste, replace antimicrobials, and enrich diets. • Future priorities: Research must shift from taxonomy to function, regulatory issues must be considered, and equitable global access to microbiome innovations is essential. The accelerating convergence of climate change, biodiversity loss, and food insecurity represents one of the defining challenges of this century. Agrifood systems are under increasing pressure to deliver safe, nutritious, and sufficient food while limiting environmental harm, prompting the search for new scientific approaches to guide innovation. Among these, microbiome research has emerged as both transformative and integrative. In their lead article in Frontiers in Science, Harnessing agrifood system microbiomes for sustainability and human health, Fernández-Gómez et al. (2025) highlight the pivotal role of microbial networks across soils, aquatic environments, crops, livestock, food processing, and human health. Their review provides a timely anchor for this special editorial project, positioning microbiomes at the intersection of sustainability, resilience, and the One Health framework. From meta-omics to modulation Rapid advances in meta-omic tools—including metagenomics, metatranscriptomics, metaproteomics, and metabolomics—have paved the way for microbiome research over the past decade (Ferrocino et al., 2023). These approaches allow researchers to move beyond cataloguing microbial communities to uncovering functional roles and ecological interactions. Applications range from outbreak detection and food safety monitoring (Pightling et al., 2018), to mapping microbial transmission between mothers and infants (Feehily et al., 2023), and exploring phage–host interactions that underpin ecosystem resilience (Chevallereau et al., 2022). Yet the true promise lies in the ability to intervene. Strategies such as probiotics, prebiotics, biocontrol agents, and synthetic consortia open possibilities for designing more resilient agrifood systems (Gibson et al., 2017; Schmitz et al., 2022). The main challenge remains scaling these laboratory successes to real-world contexts, where ecological complexity, socioeconomic factors, and regulatory uncertainty complicate translation. Microbiomes in the One Health concept: a connective infrastructure Advances in methodology have made it increasingly clear that microbiomes should not be viewed as isolated units but as dynamic, interconnected systems that span soil, water, plants, animals, and humans. They regulate nutrient cycling, contribute to disease resistance, shape food quality, and ultimately influence health outcomes (Berg et al., 2020). This ecological continuity makes it useful to think of microbiomes as infrastructure: the largely invisible scaffolding that supports agrifood systems. Fernández-Gómez et al. describe how microbial communities intersect in multiple ways—from rhizosphere interactions that drive crop productivity to rumen microbes influencing greenhouse gas emissions, and from spoilage organisms in distribution chains to fermentation processes that enrich dietary diversity. By embedding microbiomes within a One Health perspective, this work broadens the concept of food system sustainability beyond efficiency metrics to encompass planetary and public health (Law et al., 2024). Sustainability, in this framing, becomes a matter of microbial stewardship. From soil to sea: microbiomes as driver for sustainability Nowhere is the potential of microbiome science more apparent than in primary production. Microorganisms in soil and on plants influence nutrient cycling, protect crops from stress, and shape food quality. By improving nitrogen fixation, mobilizing phosphorus, or producing metabolites that enhance plant resilience, soil microbes contribute directly to crop nutrition (Banerjee & van der Heijden, 2023). For example, microbial inoculants can boost mineral uptake and improve yields under drought or salinity stress (Schmitz et al., 2022). These microbiomes also affect food safety: the phyllosphere can carry beneficial or harmful microbes that are transferred to edible products (Santoyo, 2022). Understanding and managing these communities is critical for delivering fruits and vegetables that are not only abundant but safe for consumption. Animal-associated microbiomes shape feed conversion, growth, and resistance to disease. In ruminants, the rumen microbiome influences productivity and methane emissions; targeted dietary interventions can both enhance feed efficiency and reduce greenhouse gas outputs. In aquatic systems, microbial communities sustain oxygen production and nutrient cycles while underpinning aquaculture productivity (Peixoto et al., 2022). Healthy animal microbiomes therefore contribute to both high-quality food production and public health, exemplifying the One Health perspective. Microbiomes also provide a natural barrier for disease. Probiotic and prebiotic strategies in dairy, poultry, and aquaculture systems can lower pathogen loads, reducing the need for antimicrobials and supporting global efforts to combat antimicrobial resistance (Chevallereau et al., 2022). As Fernández-Gómez et al. note, poor management, such as fertilizer runoff or heavy antimicrobial use, destabilizes these microbial networks, spreading antimicrobial resistance and driving ecosystem decline. Conversely, practices such as biofertilizers and integrated multi-trophic aquaculture exemplify how microbiome-informed approaches can balance productivity with ecological integrity. Microbiome science also offers concrete pathways to mitigate agriculture's contribution to climate change, particularly through reducing nitrous oxide and methane emissions (Richardson et al., 2023). Microbiomes in the food chain: from spoilage to fermentation Food loss and waste remain major inefficiencies, with nearly half of fresh products spoiled post-harvest (UNEP, 2024). Microbiome insights provide opportunities to extend shelf life and improve safety while also enhancing functionality. Examples include lactic acid bacteria that protect shrimp against pathogens (Saraoui et al., 2017) and yeast-based treatments that limit spoilage in strawberries (Zhimo et al., 2021). At the same time, fermentation illustrates the long history of beneficial microbiome use in food systems. Fermented foods not only reduce waste but also deliver live microbes and bioactive compounds that contribute to gut health, counteracting the microbiome-depleting effects of ultra-processed foods (EFSA, 2018). Future innovations will need to carefully balance safety considerations with efforts to restore microbial diversity in the human diet. The human dimension: diet, gut microbiota, and health The impact of food system microbiomes ultimately converges in the human gut. Dietary patterns, from fiber-rich plant-based diets to high-fat Western diets, profoundly influence microbial diversity and shape risks for non-communicable diseases. Loss of microbial diversity is increasingly associated with obesity, cancer, and gut–brain disorders (Valdes et al., 2018). Interventions such as fermented foods, probiotics, and prebiotics offer avenues for restoring microbial functions (Hill et al., 2014; Gibson et al., 2017). These strategies extend beyond individual nutrition, representing public health interventions with the potential to alter population-level disease burdens. Incorporating microbiome science into dietary policy could therefore benefit both healthcare and sustainability agendas. Direct microbial transmission from food to the gut can enrich diversity. For instance, studies have documented how maternal microbes, including Bifidobacterium, are transferred through diet-related pathways to infants, shaping immune development (Feehily et al., 2023). This highlights the promise of microbiome-aware dietary strategies — probiotics, prebiotics, and functional foods — as medical nutrition tools for preventing gastrointestinal and metabolic disorders (Gibson et al., 2017). Governance and education: the path forward Scientific progress has outpaced governance frameworks. As Fernandez-Gomez et al. observe, there is no standardized approach for evaluating the safety, efficacy, and environmental implications of microbiome-based products (Olmo et al., 2023). Regulators face the dual task of enabling innovation while protecting public interests. Education is equally critical. Farmers, industry actors, consumers, and policymakers all need a clearer understanding of microbial stewardship to support adoption and prevent misuse. Embedding microbiome literacy into curricula and consulting services will be key to fostering cultural change. Addressing inequities in microbiome science is also essential: innovations should not remain the privilege of high-income regions but must be made accessible to communities most vulnerable to food insecurity and biodiversity loss. Conclusion: microbial stewardship for a resilient future The WHO's call for healthier diets cannot be met without transforming how we view and manage microbiomes. Microbes shape the safety, quality, and health-promoting properties of food at every step — from soil fertility to human digestion. They are not invisible passengers but active partners in food production and public health. The review from Fernández-Gómez et al. underscores a central point: microbiomes are not peripheral but fundamental to food system resilience, sustainability, and health. As this special issue demonstrates, microbiome research offers a unifying framework through which agrifood challenges can be reimagined. Moving forward will require integrative and transdisciplinary thinking: coupling cutting-edge technologies with ecological principles, aligning innovation with regulation, and ensuring equitable access to solutions. Above all, it will require a commitment to microbial stewardship. If guided wisely, microbiomes may become critical allies in navigating the converging crises of climate change, food insecurity, and human health — shaping resilient futures through largely invisible means.