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Cell Host Microbe DOI:10.1016/j.chom.2014.02.005

The treatment-naive microbiome in new-onset Crohn's disease.

Publication TypeJournal Article
Year of Publication2014
AuthorsGevers, D, Kugathasan, S, Denson, LA, Vázquez-Baeza, Y, Van Treuren, W, Ren, B, Schwager, E, Knights, D, Song, SJin, Yassour, M, Morgan, XC, Kostic, AD, Luo, C, Gonzalez, A, McDonald, D, Haberman, Y, Walters, T, Baker, S, Rosh, J, Stephens, M, Heyman, M, Markowitz, J, Baldassano, R, Griffiths, A, Sylvester, F, Mack, D, Kim, S, Crandall, W, Hyams, J, Huttenhower, C, Knight, R, Xavier, RJ
JournalCell Host Microbe
Date Published2014 Mar 12
KeywordsAdolescent, Bacteria, Child, Child, Preschool, Cohort Studies, Crohn Disease, Dysbiosis, Gastrointestinal Tract, Humans, Metagenome, Microbiota

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.


Alternate JournalCell Host Microbe
PubMed ID24629344
PubMed Central IDPMC4059512
Grant ListU54 DK102557 / DK / NIDDK NIH HHS / United States
P30 DK043351 / DK / NIDDK NIH HHS / United States
R01 DK092405 / DK / NIDDK NIH HHS / United States
R01DK092405 / DK / NIDDK NIH HHS / United States
T32 GM074897 / GM / NIGMS NIH HHS / United States
U54 DE023798 / DE / NIDCR NIH HHS / United States
R01 HG005969 / HG / NHGRI NIH HHS / United States