Inflammatory bowel diseases (IBDs), including Crohn's disease (CD), are genetically
linked to host pathways that implicate an underlying role for aberrant immune responses
to intestinal microbiota. However, patterns of gut microbiome dysbiosis in IBD patients
are inconsistent among published studies. Using samples from multiple gastrointestinal
locations collected prior to treatment in new-onset cases, we studied the microbiome
in the largest pediatric CD cohort to date. An axis defined by an increased abundance
in bacteria which include Enterobacteriaceae, Pasteurellacaea, Veillonellaceae, and
Fusobacteriaceae, and decreased abundance in Erysipelotrichales, Bacteroidales, and
Clostridiales, correlates strongly with disease status. Microbiome comparison between
CD patients with and without antibiotic exposure indicates that antibiotic use amplifies
the microbial dysbiosis associated with CD. Comparing the microbial signatures between
the ileum, the rectum, and fecal samples indicates that at this early stage of disease,
assessing the rectal mucosal-associated microbiome offers unique potential for convenient
and early diagnosis of CD.
Copyright © 2014 Elsevier Inc. All rights reserved.