We propose to investigate the hypothesis that consistent changes in the human gut microbiome are associated with Crohn's disease, a form of inflammatory bowel disease, and that altered microbiota contributes to pathogenesis. Analysis of this problem is greatly complicated by the fact that multiple factors influence the composition of the gut microbiota, including diet, host genotype, and disease state. For example, data from others and us document a drastic impact of diet on the composition of the gut microbiome. No amount of sequencing will yield a useful picture of the role of the microbiota in disease if samples are confounded with uncontrolled variables. Our proposed project will take advantage of our experience with deep sequencing to characterize the composition of the gut microbiome, but also control diet, host genotype, and disease state. Diet will be controlled by analyzing children treated for Crohn's disease by placing them on a standardized elemental diet, and by testing effects of different diets on the gut microbiome composition in adult volunteers. Genotype will be analyzed by large scale SNP genotyping, which is already underway and separately funded team member Hokan Hakonarson is currently genotyping 50 children a week at ~half a million loci each and investigating connections with inflammatory bowel disease. Clinical status will be ascertained in the very large IBD practice in the UPenn/CHOP hospital system. Effects of diet, host genotype, and disease state on the gut microbiome will be summarized in a multivariate model, allowing connections between microbiome and disease to be assessed free of confounding factors.

Public Health Relevance

The bacteria present in the intestinal tract, known as the gut microbiome, probably play a role in the pathogenesis of Crohn's disease, but the mechanism remains unclear. In this study, we propose to determine the composition of the gut microbiome associated with Crohn's disease while controlling for confounding factors known to alter the gut microbiome, such as host genetics and diet. These studies will provide a clearer vision of the types of bacteria associated with Crohn's disease and provide new insights into pathogenic mechanisms and potential therapy.

National Institute of Health (NIH)
National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)
Exploratory/Developmental Cooperative Agreement Phase II (UH3)
Project #
Application #
Study Section
Special Emphasis Panel (ZRG1-IDM-A (52))
Program Officer
Karp, Robert W
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
University of Pennsylvania
Internal Medicine/Medicine
Schools of Medicine
United States
Zip Code
Koeth, Robert A; Wang, Zeneng; Levison, Bruce S et al. (2013) Intestinal microbiota metabolism of L-carnitine, a nutrient in red meat, promotes atherosclerosis. Nat Med 19:576-85
Chen, Jun; Bushman, Frederic D; Lewis, James D et al. (2013) Structure-constrained sparse canonical correlation analysis with an application to microbiome data analysis. Biostatistics 14:244-58
Mei, Junjie; Liu, Yuhong; Dai, Ning et al. (2012) Cxcr2 and Cxcl5 regulate the IL-17/G-CSF axis and neutrophil homeostasis in mice. J Clin Invest 122:974-86