Macronutrients, micronutrients and non-nutritive compounds are major drivers of the composition and metabolic functions of gut microbial communities. However, nutrient composition alone cannot explain the way people’s gut microbiomes are so different to each other.

One feature that distinguishes humans from other species is our ability to heat-treat our meals. This process alters nutrients and makes foods more digestible, while also developing flavors and tastes not present in raw versions.

But can cooking affect the gut microbiome and should it therefore be considered as a new covariable in microbiome studies?

This seems to be the case, according to a new study from Dr. Rachel Carmody at Harvard University (USA), Dr. Peter Turnbaugh at University of California San Francisco (USA) and colleagues, which shows that raw and cooked diets have a distinct effect on the structure and metabolic activities of the gut microbiome in mice and humans.

For instance, raw and cooked versions of the same foods affected the gut microbiome differently in mice. While raw and cooked lean beef had a similar impact on the gut microbiome, the mice gut microbiome responded differently when the animals were fed raw and cooked sweet potatoes. Consuming raw sweet potatoes led to lower within-subject diversity, a higher expression of genes and enzymes for metabolizing starch, sugar and xenobiotics, and altered metabolic byproducts when compared with cooked-fed mice.

By feeding the mice controlled diets with different raw and cooked low- and high-starch foods—including sweet potato, white potato, corn, peas, carrots, and beets—the authors confirmed that gut microorganisms were sensitive to starch digestibility.

Thus, starchy foods with a high amount of low-digestibility starch when raw (sweet potato and white potato) led to the most profound changes in gut microbial community structure. However, low-starch foods (carrot and beet) or foods with a high amount of high-digestibility starch when raw (corn and peas) led to almost undetectable changes in gut microbes.

Cooked foods were mainly digested and absorbed in the small intestine (thus, processed by host enzymes), whereas raw foods reached the colon, where they had detrimental effects on microbes, attributable to antimicrobial compounds.

By quantifying microbial cell damage in gut samples, Carmody and colleagues found that the mice fed raw tubers had the same extent of microbial cell damage as the mice group treated with the oral antibiotic ampicillin.

A metabolomic analysis of the six plant foods used in the experiments revealed multiple compounds that were both sensitive to cooking and showed antimicrobial activity, thus supporting the high xenobiotic gene expression found in mice that were fed raw food.

The author Rachel Carmody had previously found that poorly processed foods led to rapid weight loss in mice when compared with cooked foods. In this study, researchers wanted to explore to what extent shifts in the gut microbiota induced by cooking might affect host energy balance.

As such, germ-free mice receiving the gut microbiome of raw-fed mice rapidly lost weight. However, transplanting this altered gut microbiome into mice on a regular diet led to weight gain and increased body fat, which was associated with increased calorie intake. This shows that changes in gut microbes are not the underlying cause of the weight loss associated with a raw diet.

The relevance of raw versus cooked diets in shaping the gut microbiome was also assessed in humans. With the help of co-author and chef Vayu Main Rekdal, the researchers showed that raw and cooked menus altered the gut microbiome when fed in a random order to a small group of healthy participants for three days.

Altogether, this new research highlights that beyond nutrient intake and drugs, cooking also matters in shaping the gut microbiome. In the light of these findings, we may be able to suggest that cooking has exerted a relevant effect on changes to the composition of the microbiome during hominid evolution. Consequently, Peter Turnbaugh is planning new research to better elucidate cooking’s contribution to modulating host-microbiome interactions.



Carmody RN, Bisanz JE, Bowen BP, et al. Cooking shapes the structure and function of the gut microbiome. Nat Microbiol. 2019. doi: 10.1038/s41564-019-0569-4.