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Study Description

We 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 us and others 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.

We aim to characterize the composition of the gut microbiome while controlling for diet, host genotype, and disease state. Diet is 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 is analyzed by large scale SNP genotyping, which is already underway and separately funded--team member Hakon Hakonarson is currently genotyping 50 children a week at ~half a million loci each and investigating connections with inflammatory bowel disease. Clinical status is 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 are summarized in a multivariate model, allowing connections between microbiome and disease to be assessed free of confounding factors.

This project is divided into four sub-studies. In the Fecal Storage Methods (FSM) study, methods of stool storage and DNA extraction are compared to examine their impact on DNA sequence analysis results. The Controlled Feeding Experiment (CaFE) addresses the effects of controlled diets on the gut microbiome. In the Cross-sectional Study of Diet and Stool Microbiome Composition (COMBO), the effects of diet analyzed using surveys and deep sequencing of stool specimens. The fourth study, Pediatric Longitudinal Study of Elemental Diet and Stool Microbiome Composition (PLEASE), examines the effects of an elemental diet treatment on pediatric patients diagnosed with inflammatory bowel disease (IBD), particularly Crohn's disease.

  • Fecal Storage Methods (FSM): Cross-sectional study
  • Controlled Feeding Experiment (CaFE): Controlled trial
  • Cross-sectional Study of Diet and Stool Microbiome Composition (COMBO): Cross-sectional study
  • Pediatric Longitudinal Study of Elemental Diet and Stool Microbiome Composition (PLEASE): Longitudinal cohort study

  • Study Types: Cross-Sectional, Controlled Trial, Longitudinal Cohort
  • Number of study subjects that have individual level data available through Authorized Access: 128

Authorized Access
Publicly Available Data (Public ftp)

Connect to the public download site. The site contains release notes and manifests. If available, the site also contains data dictionaries, variable summaries, documents, and truncated analyses.

Study Inclusion/Exclusion Criteria

Fecal Storage Methods (FSM):
Participants must be 18 years of age or older.
Exclusion criteria:

  • Diagnosis or history of inflammatory bowel disease, including ulcerative colitis or Crohn's disease, celiac sprue, irritable bowel syndrome, or other inflammatory disorders of the intestine
  • Diarrhea within 1 week prior to sampling
  • Antibiotic use within 4 weeks prior to sampling

Controlled Feeding Experiment (CaFE):
Participants must be between the ages of 18 and 40.
Exclusion criteria:

  • Diagnosis or history of ulcerative colitis, Crohn's disease, celiac sprue, irritable bowel syndrome, any other chronic intestinal disorders, diabetes mellitus (DM), coronary artery disease, congestive heart failure, myocardial infarction, dyslipidemia, hypercholesterolemia, HIV, AIDS, or any other condition resulting in immunosuppression
  • On average, bowel movements less than every two days or more than 3 bowel movements per day
  • 7 or more cigarettes or cigars per week over the month prior to admission
  • Consumption of alcohol 72 hours prior to admission
  • BMI less than 18.5 or greater than 35
  • WBC less than 3,500
  • Neutrophil count of less than 1,000
  • Platelet count of less than 100,000 or an INR greater than 1.2
  • Fasting glucose >125 mg/dl
  • Antibiotic use within 6 months prior to admission
  • Use of antacids, NSAIDs, dietary supplements in 2 weeks prior to admission
  • Use of proton pump inhibitors (PPI), histamine receptor antagonists, narcotics, tricyclic antidepressants, anticholinergics (e.g., hyoscamine), metoclopramide, anti-diarrhea medications, laxatives in 4 weeks prior to admission
  • Any allergy or intolerance to the components of the study diet
  • Diarrhea within 2 weeks of admission
  • Pregnancy

Cross-sectional Study of Diet and Stool Microbiome Composition (COMBO):
Participants must be between the ages of 2 and 50.
Exclusion criteria:

  • Inflammatory bowel disease (including ulcerative colitis and Crohn's disease), celiac sprue, irritable bowel syndrome, or other inflammatory disorders of the intestine
  • On average, bowel movements less than every two days or more than 3 bowel movements per day
  • Previous bowel resection surgery
  • Antibiotic use within 6 months prior to sampling
  • Use of antacids, NSAIDS, or dietary supplements in 2 weeks prior to sampling
  • Use of proton pump inhibitors (PPI), histamine receptor antagonists, narcotics, tricyclic antidepressants, anticholinergics (e.g., hyoscamine), metoclopramide, anti-diarrhea medications, laxatives, or non-steroidal anti-inflammatory agents in 4 weeks prior to admission
  • Pregnancy
  • Diagnosis with HIV, AIDS or other known conditions resulting in immunosuppression
  • Consumption of breast milk or infant formula in 1 month prior to sampling
  • Diarrhea within 2 weeks prior to sampling
  • Consumption of prebiotics or probiotics in 4 weeks prior to sampling
  • Participation of immediate household member or roommate in study

Pediatric Longitudinal Study of Elemental Diet and Stool Microbiome Composition (PLEASE):
Inclusion criteria:

  • Participant is treated at CHOP for Crohn's disease with plans to initiate an elemental or semi-elemental diet. Patients with suspected Crohn's disease undergoing evaluation and for whom elemental or semi-elemental diet therapy is planned may be enrolled. However, these patients will not continue in the study after the initial sample collection if the clinical evaluation determines that they do not have Crohn's disease.
  • Age less than 22 years at the time of initiation of elemental or semi-elemental diet.

Exclusion criteria:

  • Presence of an ostomy.
  • Antibiotic use within 2 weeks prior to providing the first stool specimen.
  • Anticipation of needing treatment with antibiotics in the 8 weeks after initiating elemental diet therapy.
  • Treatment with probiotic therapy in the 2 weeks prior to initiation of elemental or semi-elemental diet therapy. (Probiotics include products marketed specifically to change the gut microbiome by providing live bacteria. Standard composition yogurt is not considered a probiotic.)

Molecular Data
TypeSourcePlatformNumber of Oligos/SNPsSNP Batch IdComment
16S rRNA Roche 454 GS FLX Titanium N/A N/A
Metagenomic Sequencing Roche 454 GS FLX Titanium N/A N/A
Selected publications
Diseases/Traits Related to Study (MESH terms)
Links to Other NCBI Resources
Authorized Data Access Requests
Study Attribution
  • Co-Principal Investigators
    • Gary D. Wu, MD. University of Pennsylvania School of Medicine, Philadelphia, PA, USA
    • James D. Lewis, MD, MSCE. University of Pennsylvania School of Medicine, Philadelphia, PA, USA
    • Frederic D. Bushman, PhD. University of Pennsylvania School of Medicine, Philadelphia, PA, USA
  • Funding Source
    • UH2DK083981. National Institutes of Health, Bethesda, MD, USA