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 genetics 1 – 3 . Numerous microbiome studies have compared diets with divergent ingredients 1 – 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 ancient 6 , 7 , our results prompt the hypothesis that humans and our microbiomes co-evolved under unique cooking-related pressures.