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Cell Host Microbe. 2014 Mar 12;15(3):382-92. doi: 10.1016/j.chom.2014.02.005.

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

Author information

1
Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
2
Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Emory University, Atlanta, GA 30322, USA.
3
Division of Gastroenterology, Hepatology, and Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
4
Department of Computer Science, University of Colorado, Boulder, CO 80309, USA.
5
BioFrontiers Institute, University of Colorado, Boulder, CO 80309, USA.
6
Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA.
7
Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55108, USA; BioTechnology Institute, University of Minnesota, St. Paul, MN 55108, USA.
8
Division of Gastroenterology, Hepatology, and Nutrition, Hospital for Sick Children, University of Toronto, Toronto, ON M5G 1X8, Canada.
9
Children's Hospital of Buffalo, Buffalo, NY 14222, USA.
10
Goryeb Children's Hospital, Morristown, NJ 07960, USA.
11
Mayo Clinic, Rochester, MN 55902, USA.
12
University of California, San Francisco, San Francisco, CA 94143, USA.
13
North Shore Long Island Jewish Medical Center, New Hyde Park, NY 11040, USA.
14
Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
15
Hospital for Sick Children, Toronto, ON M5G 1X8, Canada.
16
Connecticut Children's Medical Center, Hartford, CT 06106, USA.
17
Children's Hospital of Eastern Ontario, Ottawa, ON K1H 8L1 Canada.
18
Nationwide Children's Hospital, Columbus, OH 43228, USA.
19
Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA.
20
BioFrontiers Institute, University of Colorado, Boulder, CO 80309, USA; Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA; Howard Hughes Medical Institute, Boulder, CO 80309, USA.
21
Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA. Electronic address: xavier@molbio.mgh.harvard.edu.

Abstract

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.

PMID:
24629344
PMCID:
PMC4059512
DOI:
10.1016/j.chom.2014.02.005
[Indexed for MEDLINE]
Free PMC Article
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