From Food Systems to Gut Microbiota: Dietary Substrates, Microbial Exposure and One Health

Food systems are usually discussed in terms of nutrition, food safety, productivity, sustainability or emissions. Less attention is given to the microbial dimension of the farm-to-fork pathway and to the way food systems shape the dietary substrates, food matrices and microbial exposures that reach the gut. Soils, plants, foods, processing environments, animals and the human gut all host microbial communities that influence nutrient cycling, plant performance, food characteristics, metabolism, immune regulation and ecological resilience. This review examines how food systems may modulate gut microbiota and microbiome resilience within a One Health framework. Evidence from soil, crop and food microbiome studies suggests that local conditions and farming practices can leave detectable microbial signatures on plants and edible tissues. However, the soil–food–gut continuum should not be understood as a simple transfer route. Microorganisms and microbial products are repeatedly filtered by plant traits, farming systems, animal-production interfaces, harvesting, processing, storage, preparation and host physiology. The review also considers how this continuity may be weakened or redirected. Agricultural intensification, pollutants, post-harvest processing, antimicrobial use, ultra-processed foods, additive mixtures, low-fibre diets, early-life microbial disruption and reduced contact with environmental biodiversity may alter microbial communities at different points of the food system. Antimicrobial resistance is also discussed as a functional microbial trait that can circulate across human, animal, food and environmental interfaces. One Health approaches to food systems should therefore combine microbial risk control with microbial stewardship: protecting useful microbial diversity and function while preserving food safety. The aim is not to maximise microbial exposure, but to understand which microbial functions matter and how food systems can support gut microbiota resilience across environments, foods and hosts.