Detecting Microbial Dysbiosis Associated with Pediatric Crohn Disease Despite the High Variability of the Gut Microbiota

Authors

Feng Wang, Boston University
Jess L. Kaplan, Harvard Medical School, Boston
Benjamin D. Gold, 3Children’s Healthcare of Atlanta
Manoj K. Bhasin, Beth Israel Deaconess Medical Center and Harvard Medical School
Naomi L. Ward, University of Wyoming, Laramie
Richard Kellermayer, Baylor College of MedicineFollow
Barbara S. Kirschner, University of Chicago Comer Children’s Hospital
Melvin B. Heyman, University of California, San Francisco
Scot E. Dowd, Molecular Research MR DNA, Shallowater
Stephen B. Cox, Molecular Research MR DNA, Shallowater
Haluk Dogan, University of Nebraska-LincolnFollow
Blaire Steven, University of Wyoming, Laramie
George Ferry, Baylor College of MedicineFollow
Stanley A. Cohen, Children’s Healthcare of Atlanta
Robert N. Baldassano, The Children’s Hospital of Philadelphia
Christopher J. Moran, Harvard Medical School
Elizabeth A. Garnett, University of California, San Francisco
Lauren Drake, Harvard Medical School, Boston
Hasan H. Otu, University of Nebraska-LincolnFollow
Leonid A. Mirny, Massachusetts Institute of Technology, Cambridge
Towia A. Libermann, Harvard Medical School, Boston
Harland S. Winter, Harvard Medical School, BostonFollow
Kirill S. Korolev, Boston UniversityFollow

Document Type

Article

Date of this Version

2016

Citation

Wang et al., 2016, Cell Reports 14, 945–955 February 2, 2016

Copyright 2016 The Authors

Comments

Cell Reports 14, 945–955, February 2, 2016 ª2016 The Authors

Abstract

The relationship between the host and its microbiota is challenging to understand because both microbial communities and their environments are highly variable. We have developed a set of techniques based on population dynamics and information theory to address this challenge. These methods identify additional bacterial taxa associated with pediatric Crohn disease and can detect significant changes in microbial communities with fewer samples than previous statistical approaches required. We have also substantially improved the accuracy of the diagnosis based on the microbiota from stool samples, and we found that the ecological niche of a microbe predicts its role in Crohn disease. Bacteria typically residing in the lumen of healthy individuals decrease in disease, whereas bacteria typically residing on the mucosa of healthy individuals increase in disease. Our results also show that the associations with Crohn disease are evolutionarily conserved and provide a mutual information-based method to depict dysbiosis.