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Gigascience. 2017 Jul 1;6(7):1-11. doi: 10.1093/gigascience/gix050.

Two distinct metacommunities characterize the gut microbiota in Crohn's disease patients.

He Q1,2,3, Gao Y4,5, Jie Z4,5, Yu X4,5, Laursen JM6, Xiao L4,5, Li Y1, Li L2, Zhang F7, Feng Q4,8, Li X4,5, Yu J4,5, Liu C4,5, Lan P1,3, Yan T2, Liu X4,5, Xu X4,5, Yang H4,9, Wang J4,9, Madsen L4,10,11, Brix S6, Wang J1,3, Kristiansen K4,10, Jia H4,5,12.

Author information

Department of Gastroenterology, The Sixth Affiliated Hospital of The Sun Yat-sen University, Guangzhou 510610, China.
Department of Nutrition, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou 510610, China.
Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, the Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510610, China.
BGI-Shenzhen, Shenzhen 518083, China.
China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China.
Department of Biotechnology and Biomedicine, Technical University of Denmark (DTU), Kongens Lyngby, Denmark.
Digestive Endoscopy and Medical Center for Digestive Diseases, the Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, Jiangsu Province, China.
Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, BGI-Shenzhen, Shenzhen 518083, China.
James D. Watson Institute of Genome Sciences, Hangzhou 310058, China.
Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Universitetsparken 13, 2100 Copenhagen, Denmark.
National Institute of Nutrition and Seafood Research, Bergen, Norway.
Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI-Shenzhen, Shenzhen 518083, China.


The inflammatory intestinal disorder Crohn's disease (CD) has become a health challenge worldwide. The gut microbiota closely interacts with the host immune system, but its functional impact in CD is unclear. Except for studies on a small number of CD patients, analyses of the gut microbiota in CD have used 16S rDNA amplicon sequencing. Here we employed metagenomic shotgun sequencing to provide a detailed characterization of the compositional and functional features of the CD microbiota, comprising also unannotated bacteria, and investigated its modulation by exclusive enteral nutrition. Based on signature taxa, CD microbiotas clustered into 2 distinct metacommunities, indicating individual variability in CD microbiome structure. Metacommunity-specific functional shifts in CD showed enrichment in producers of the pro-inflammatory hexa-acylated lipopolysaccharide variant and a reduction in the potential to synthesize short-chain fatty acids. Disruption of ecological networks was evident in CD, coupled with reduction in growth rates of many bacterial species. Short-term exclusive enteral nutrition elicited limited impact on the overall composition of the CD microbiota, although functional changes occurred following treatment. The microbiotas in CD patients can be stratified into 2 distinct metacommunities, with the most severely perturbed metacommunity exhibiting functional potentials that deviate markedly from that of the healthy individuals, with possible implication in relation to CD pathogenesis.


Crohn's disease; exclusive enteral nutrition; gut microbe; metagenomics

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