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 se...

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Published inNature microbiology Vol. 4; no. 12; pp. 2052 - 2063
Main Authors Carmody, Rachel N., Bisanz, Jordan E., Bowen, Benjamin P., Maurice, Corinne F., Lyalina, Svetlana, Louie, Katherine B., Treen, Daniel, Chadaideh, Katia S., Maini Rekdal, Vayu, Bess, Elizabeth N., Spanogiannopoulos, Peter, Ang, Qi Yan, Bauer, Kylynda C., Balon, Thomas W., Pollard, Katherine S., Northen, Trent R., Turnbaugh, Peter J.
Format Journal Article
LanguageEnglish
Published London Nature Publishing Group UK 01.12.2019
Nature Publishing Group
Subjects
631/326/2565/2134
631/45/320
Adult
Animals
Bacteria - classification
BASIC BIOLOGICAL SCIENCES
Biomedical and Life Sciences
Cooking
Diet
Digestibility
Energy balance
Feces - microbiology
Female
Food
Gastrointestinal Microbiome
Genetic Variation
Germ-Free Life
Hot Temperature
Humans
Infectious Diseases
Intestinal microflora
Letter
Life Sciences
Male
Medical Microbiology
Metabolomics
Mice
Mice, Inbred BALB C
Mice, Inbred C57BL
Microbiology
Microbiomes
Microbiota
Parasitology
Plants
Raw Foods - analysis
RNA, Ribosomal, 16S - genetics
Starch
Structure-function relationships
Transcriptome
Virology
Young Adult
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Summary: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. 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.
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William F. Milton Fund
Natural Sciences and Engineering Research Council of Canada (NSERC)
the Defense Advanced Research Projects Agency (DARPA)
AC02-05CH11231
USDOE Office of Science (SC), Basic Energy Sciences (BES)
Leakey Foundation
National Institutes of Health (NIH)
G.W. Hooper Foundation
UCSF
Boston Nutrition Obesity Research Center
Harvard Dean’s Competitive Fund for Promising Scholarship
R.N.C. and P.J.T. designed the study. R.N.C. and K.S.C. performed the animal experiments. R.N.C., K.S.C. and V.M.R. performed the human experiments. R.N.C., J.E.B., K.S.C. and P.J.T. performed 16S rDNA sequencing and/or associated data analysis. R.N.C. and J.E.B. performed qPCR and associated data analysis. R.N.C., J.E.B., S.L., K.S.P. and P.J.T. performed microbial RNA sequencing and/or associated data analysis. Q.Y.A. performed bomb calorimetry. J.E.B., B.P.B., K.B.L., D.T., E.N.B., T.R.N. and P.J.T. performed metabolomics assays and/or associated data analysis. C.F.M. and K.C.B. performed microbial physiology assays and associated data analysis. P.S. performed in vitro growth experiments and associated data analysis. T.W.B. validated and performed measurements of body composition in mice. R.N.C., J.E.B. and P.J.T. wrote the manuscript with input from all co-authors.
Author contributions
ISSN:2058-5276
2058-5276
DOI:10.1038/s41564-019-0569-4