Fermented food microbiome: influence on oral and gut microbiota, and human health

Abstract

The fermented food microbiome comprises live microorganisms, their genetic elements and their metabolites, and represents an established dietary approach for modulating host–microbiome interactions through the consumption of fermented foods. Fermentation enhances food preservation and nutrient bioavailability, and supplies the host with probiotics, prebiotic substrates and postbiotic metabolites. These bioactive compounds can influence the oral and gut microbiota, modulate immune function and support metabolic resilience. Fibre-rich, plant-based fermented foods retain such components within structured matrices that enhance microbial viability and mucosal interactions more consistently than do fermented dairy foods. This Review explores how the fermented food microbiome affects the oral–gut axis via both transient microbial exposure and metabolite-mediated signalling. Drawing on clinical and preclinical evidence, we examine how fermented food intake alters resident microbiota and host physiology throughout the digestive tract. Despite growing evidence, the mechanisms through which fermented food might promote health remain insufficiently defined in humans owing to strain variability, inconsistency in microbial composition across fermented foods, heterogeneous clinical outcomes and regulatory ambiguity. Taking into account these limitations, we propose a roadmap to integrate the fermented food microbiome into precision nutrition as a feasible, personalized, diet-based strategy to promote health and prevent disease. The bioactive compounds and microbial consortia contained in plant-based fermented foods support oral and gut microbiota, host immune function and metabolic resilience. This Review describes the impact of the fermented food microbiome on the oral–gut axis and identifies a strategic roadmap to integrate this edible microbiome into precision nutrition practices to promote health.