R Code and Data for Figures for: "Treatment-Specific Composition of Gut Microbiota Is Associated with Disease Remission in a Pediatric Crohn's Disease Cohort"
Abstract/Contents
- Abstract
Background: The beneficial effects of antibiotics in Crohn's disease (CD) depends in part on the gut microbiota but are inadequately understood. We investigated the impact of metronidazole (MET) and metronidazole plus azithromycin (MET+AZ) on the microbiota in pediatric CD, and the use of microbiota features as classifiers or predictors of disease remission.
Methods: 16S rRNA-based microbiota profiling was performed on stool samples from 67 patients in a multinational, randomized, controlled, longitudinal, 12-week trial of MET vs. MET+AZ in children with mild to moderate CD. Profiles were analyzed together with disease activity and then used to construct Random Forest models to classify remission or predict treatment response.
Results: Both MET and MET+AZ significantly decreased diversity of the microbiota and caused large treatment-specific shifts in microbiota structure at week 4. Disease remission was associated with a treatment-specific microbiota configuration. Random Forest models constructed from microbiota profiles pre- and during antibiotic treatment with metronidazole accurately classified disease remission in this treatment group (AUC of 0.879, 95% CI 0.683, 0.9877; sensitivity 0.7778; specificity 1.000, P < 0.001). A Random Forest model trained on pre-antibiotic microbiota profiles predicted disease remission at week 4 with modest accuracy (AUC of 0.8, P = 0.24).
Conclusions: MET and MET+AZ antibiotic regimens in pediatric CD lead to distinct gut microbiota structures at remission. It may be possible to classify and predict remission based in part on microbiota profiles, but larger cohorts will be needed to realize this goal.
Description
Type of resource | software, multimedia |
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Date created | August 2018 - March 2019 |
Creators/Contributors
Author | Sprockett, Daniel |
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Author | Fischer, Natalie |
Contributing author | Boneh, Rotem Sigall |
Contributing author | Turner, Dan |
Contributing author | Kierkus, Jarek |
Contributing author | Sladek, Malgorzata |
Contributing author | Escher, Johanna C. |
Contributing author | Wine, Eytan |
Contributing author | Yerushalmi, Baruch |
Contributing author | Dias, Jorge Amil |
Contributing author | Shaoul, Ron |
Contributing author | Kori, Michal |
Contributing author | Snapper, Scott B. |
Contributing author | Holmes, Susan |
Contributing author | Bousvaros, Athos |
Contributing author | Levine, Arie |
Contributing author | Relman, David |
Subjects
Subject | pediatric Crohn's disease |
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Subject | microbiota |
Subject | antibiotics |
Subject | disease remission |
Subject | Random Forest model |
Genre | Dataset |
Bibliographic information
Related Publication | Levine A, Kori M, Kierkus J, et al Azithromycin and metronidazole versus metronidazole-based therapy for the induction of remission in mild to moderate paediatric Crohn’s disease : a randomised controlled trial Gut 2019;68:239-247. https://doi.org/10.1136/gutjnl-2017-315199 |
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Related item | |
Location | https://purl.stanford.edu/mp935wb0227 |
Access conditions
- Use and reproduction
- User agrees that, where applicable, content will not be used to identify or to otherwise infringe the privacy or confidentiality rights of individuals. Content distributed via the Stanford Digital Repository may be subject to additional license and use restrictions applied by the depositor.
Preferred citation
- Preferred Citation
- Sprockett D, Fischer N, Boneh RS, Turner D, Snapper S, Kierkus J, Sladek M, Escher JC, Wine E, Yerushalmi B, Dias JA, Shaoul R, Kori M, Holmes S, Bousvaros A, Levine A, and Relman DA. Treatment-Specific Composition of Gut Microbiota Is Associated with Disease Remission in a Pediatric Crohn's Disease Cohort. Stanford Digital Repository. Available at: https://purl.stanford.edu/mp935wb0227
Collection
Stanford Research Data
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- Contact
- relman@stanford.edu
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