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

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. [Display omitted] •Mutual information distinguishes Crohn disease and controls by using the microbiome•Stool and ileal microbiomes contain the same information about Crohn disease•Microbes more abundant in ileum than in stool positively correlate with Crohn disease•Statistical power to detect association varies greatly among commonly used methods Wang et al. develop computational methods to detect and depict associations between microbes and disease. These methods improve diagnosis of Crohn disease based on the microbiome, especially from fecal samples.