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Nutrition and diet influence human health and development through their effects on the gut microbiome and host immune homeostasis. These mechanisms are involved in a wide range of conditions and diseases, such as metabolic syndrome and immune-mediated diseases. This Collection contains Reviews from Nature Reviews Microbiology, Nature Reviews Gastroenterology & Hepatology and Nature Reviews Immunology that explore the relationship between diet, the microbiome and immunity, and the potential for novel diagnostic, preventive and therapeutic interventions.