Cooking shapes the structure and function of the gut microbiome

Nat Microbiol. 2019 Dec;4(12):2052-2063. doi: 10.1038/s41564-019-0569-4. Epub 2019 Sep 30.


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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adult
  • Animals
  • Bacteria / classification*
  • Cooking*
  • Diet*
  • Feces / microbiology
  • Female
  • Food*
  • Gastrointestinal Microbiome*
  • Genetic Variation
  • Germ-Free Life
  • Hot Temperature
  • Humans
  • Male
  • Metabolomics
  • Mice
  • Mice, Inbred BALB C
  • Mice, Inbred C57BL
  • RNA, Ribosomal, 16S / genetics
  • Raw Foods / analysis*
  • Transcriptome
  • Young Adult


  • RNA, Ribosomal, 16S