Predicting a Human Gut Microbiota’s Response to Diet in Gnotobiotic Mice
Abstract
The interrelationships between our diets and the structure and operations of our gut microbial communities are poorly understood. A model community of 10 sequenced human gut bacteria was introduced into gnotobiotic mice, and changes in species abundance and microbial gene expression were measured in response to randomized perturbations of four defined ingredients in the host diet. From the responses, we developed a statistical model that predicted over 60% of the variation in species abundance evoked by diet perturbations, and we were able to identify which factors in the diet best explained changes seen for each community member. The approach is generally applicable, as shown by a follow-up study involving diets containing various mixtures of pureed human baby foods.
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Published In
Science
Volume 333 | Issue 6038
1 July 2011
1 July 2011
Copyright
Copyright © 2011, American Association for the Advancement of Science.
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Submission history
Received: 24 March 2011
Accepted: 28 April 2011
Published in print: 1 July 2011
Acknowledgments
Acknowledgments: We are indebted to D. O’Donnell, M. Karlsson, and S. Wagoner for their help with various aspects of gnotobiotic mouse husbandry and to B. Mickelson, I. Mogno, A. Goodman, N. Griffin, H. Seedorf, G. Simon, J. Chase, and B. Cohen for their many helpful suggestions during the course of this work. This work was supported by grants from NIH (DK30292 and DK70977) and the Crohn’s and Colitis Foundation of America. COPRO-seq and microbial RNA-seq data are available in the Gene Expression Omnibus (accession GSE26687). Processed data can be obtained at http://gordonlab.wustl.edu/modeling_microbiota/.
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