Cooking shapes the structure and function of the gut microbiome

Diet is a critical determinant of variation in gut microbial structure and function, outweighing even host genetics1–3. Numerous microbiome studies have compared diets with divergent ingredients1–5, but the everyday practice of cooking remains understudied. Here, we show that a plant diet served raw versus cooked reshapes the murine gut microbiome, with effects attributable to improvements in starch digestibility and degradation of plant-derived compounds. Shifts in the gut microbiota modulated host energy status, applied across multiple starch-rich plants, and were detectable in humans. Thus, diet-driven host–microbial interactions depend on the food as well as its form. Because cooking is human-specific, ubiquitous and ancient6,7, our results prompt the hypothesis that humans and our microbiomes co-evolved under unique cooking-related pressures. Cooked and raw plant diets cause different changes in gut microbiome composition and function, including mechanisms of starch digestibility and xenobiotic availability, and consequently impact host energy status.