Advances in microbiome science cast light on traditional concepts on nutritional science, and are poised for clinical translation. Epidemiologic observations which linked lifestyle factors to risk of disease are being re-interpreted with mechanistic insight based on improved understanding of the microbiota. Examples include the role of dietary fibre in disease prevention, the deleterious effects of highly restricted diets, and the contribution of the microbiota to over- and undernutrition. While the microbiota transduces nutrient signals for the host, food and habitual diet shape the composition of the gut microbiota at every stage of life. The composition and diversity of food intake determines which microbes will colonise, flourish, persist, or become extinct. Disruption of the developing microbiota in infancy contributes to the risk of immune and metabolic disease in later life, whereas loss of microbes in the elderly due to monotonous diets has been linked with unhealthy ageing and frailty. This should influence modern dietary advice regarding prevention and management of chronic non-communicable inflammatory and metabolic disorders, and will inform the design of infant and future food formula. The microbiota profile is also emerging as a biomarker to predict responsiveness to dietary interventions and promises to make personalised nutrition a reality.