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Title: Cooking shapes the structure and function of the gut microbiome

Abstract

Diet is a critical determinant of variation in gut microbial structure and function, outweighing even host genetics. Numerous microbiome studies have compared diets with divergent ingredients but the everyday practice of cooking remains understudied. Here in this paper, 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, our results prompt the hypothesis that humans and our microbiomes co-evolved under unique cooking-related pressures.

Authors:
ORCiD logo [1]; ORCiD logo [2];  [3]; ORCiD logo [4];  [2];  [3]; ORCiD logo [3];  [5];  [5]; ORCiD logo [2];  [2];  [2];  [5];  [6]; ORCiD logo [7]; ORCiD logo [3]; ORCiD logo [8]
  1. Univ. of California, San Francisco, CA (United States); Harvard Univ., Cambridge, MA (United States)
  2. Univ. of California, San Francisco, CA (United States)
  3. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  4. Harvard Univ., Cambridge, MA (United States); McGill Univ., Montreal, QC (Canada). Microbiome and Disease Tolerance Centre
  5. Harvard Univ., Cambridge, MA (United States)
  6. Boston Univ., MA (United States)
  7. Univ. of California, San Francisco, CA (United States). Gladstone Inst.
  8. Univ. of California, San Francisco, CA (United States); Harvard Univ., Cambridge, MA (United States); Chan Zuckerberg Biohub, San Francisco, CA (United States)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES); National Institutes of Health (NIH); Boston Nutrition Obesity Research Center; Leakey Foundation; G.W. Hooper Foundation; Harvard Dean’s Competitive Fund for Promising Scholarship; William F. Milton Fund; the Defense Advanced Research Projects Agency (DARPA); Natural Sciences and Engineering Research Council of Canada (NSERC); UCSF
OSTI Identifier:
1615285
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Nature Microbiology
Additional Journal Information:
Journal Volume: 4; Journal Issue: 12; Journal ID: ISSN 2058-5276
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

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., and Turnbaugh, Peter J. Cooking shapes the structure and function of the gut microbiome. United States: N. p., 2019. Web. doi:10.1038/s41564-019-0569-4.
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. Cooking shapes the structure and function of the gut microbiome. United States. doi:10.1038/s41564-019-0569-4.
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., and Turnbaugh, Peter J. Mon . "Cooking shapes the structure and function of the gut microbiome". United States. doi:10.1038/s41564-019-0569-4. https://www.osti.gov/servlets/purl/1615285.
@article{osti_1615285,
title = {Cooking shapes the structure and function of the gut microbiome},
author = {Carmody, Rachel N. and Bisanz, Jordan E. and Bowen, Benjamin P. and Maurice, Corinne F. and Lyalina, Svetlana and Louie, Katherine B. and Treen, Daniel and Chadaideh, Katia S. and Maini Rekdal, Vayu and Bess, Elizabeth N. and Spanogiannopoulos, Peter and Ang, Qi Yan and Bauer, Kylynda C. and Balon, Thomas W. and Pollard, Katherine S. and Northen, Trent R. and Turnbaugh, Peter J.},
abstractNote = {Diet is a critical determinant of variation in gut microbial structure and function, outweighing even host genetics. Numerous microbiome studies have compared diets with divergent ingredients but the everyday practice of cooking remains understudied. Here in this paper, 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, our results prompt the hypothesis that humans and our microbiomes co-evolved under unique cooking-related pressures.},
doi = {10.1038/s41564-019-0569-4},
journal = {Nature Microbiology},
number = 12,
volume = 4,
place = {United States},
year = {2019},
month = {9}
}

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