Diet dominates host genotype in shaping the murine gut microbiota

Rachel N Carmody; Georg K Gerber; Jesus M Luevano Jr; Daniel M Gatti; Lisa Somes; Karen L Svenson; Peter J Turnbaugh

doi:10.1016/j.chom.2014.11.010

Diet dominates host genotype in shaping the murine gut microbiota

Cell Host Microbe. 2015 Jan 14;17(1):72-84. doi: 10.1016/j.chom.2014.11.010. Epub 2014 Dec 18.

Authors

Rachel N Carmody¹, Georg K Gerber², Jesus M Luevano Jr³, Daniel M Gatti⁴, Lisa Somes⁴, Karen L Svenson⁴, Peter J Turnbaugh⁵

Affiliations

¹ FAS Center for Systems Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA; Department of Microbiology and Immunology, Hooper Foundation, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA.
² Center for Clinical and Translational Metagenomics, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, 221 Longwood Avenue, Boston, MA 02115, USA.
³ FAS Center for Systems Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA.
⁴ The Jackson Laboratory, 610 Main Street, Bar Harbor, ME 04609, USA.
⁵ FAS Center for Systems Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA; Department of Microbiology and Immunology, Hooper Foundation, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA. Electronic address: peter.turnbaugh@ucsf.edu.

Abstract

Mammals exhibit marked interindividual variations in their gut microbiota, but it remains unclear if this is primarily driven by host genetics or by extrinsic factors like dietary intake. To address this, we examined the effect of dietary perturbations on the gut microbiota of five inbred mouse strains, mice deficient for genes relevant to host-microbial interactions (MyD88(-/-), NOD2(-/-), ob/ob, and Rag1(-/-)), and >200 outbred mice. In each experiment, consumption of a high-fat, high-sugar diet reproducibly altered the gut microbiota despite differences in host genotype. The gut microbiota exhibited a linear dose response to dietary perturbations, taking an average of 3.5 days for each diet-responsive bacterial group to reach a new steady state. Repeated dietary shifts demonstrated that most changes to the gut microbiota are reversible, while also uncovering bacteria whose abundance depends on prior consumption. These results emphasize the dominant role that diet plays in shaping interindividual variations in host-associated microbial communities.

Publication types

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

MeSH terms

Animals
Diet*
Feeding Behavior*
Gastrointestinal Tract / microbiology*
Mice
Microbiota*

Abstract

Publication types

MeSH terms

Grants and funding