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Data released on June 23, 2017

Supporting data for "Two distinct metacommunities characterize the gut microbiota in Crohn’s disease patients"

He, Q; Gao, Y; Jie, Z; Yu, X; Laursen, J, M; Xiao, L; Li, Y; Li, L; Zhang, F; Feng, Q; Li, X; Yu, J; Liu, C; Lan, P; Yan, T; Liu, X; Xu, X; Yang, H; Wang, J; Madsen, L; Brix, S; Wang, J; Kristiansen, K; Jia, H (2017): Supporting data for "Two distinct metacommunities characterize the gut microbiota in Crohn’s disease patients" GigaScience Database. http://dx.doi.org/10.5524/100317 RIS BibTeX Text

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 (EEN).
Based on signature taxa, CD microbiotas clustered into two 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 EEN 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 two 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.

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Related datasets:

doi:10.5524/100317 Cites doi:10.5524/100064

Additional information:

https://github.com/andriaYG/LDA-EffectSize

Accessions (data included in GigaDB):

BioProject: PRJEB15371

Metagenomic

http://gigadb.org/images/data/cropped/100317.jpg

Funding:

  • Funding body - Shenzhen Municipal Government of China
  • Location - China
  • Award ID - JCYJ20160229172757249
  • Funding body - Shenzhen Municipal Government of China
  • Location - China
  • Award ID - JSGG20160229172752028
  • Funding body - National Natural Science Foundation of China
  • Award ID - 81670606
  • Funding body - National Natural Science Foundation of China
  • Award ID - 81470795

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
ERS1343317408170Human gut metagenome human gut metagenome Description:DNA extracted from feces of 48 year ol...
Alternative names:SZAXPI029499-101
Anomynised name:GZCD001
...
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ERS1343318408170Human gut metagenome human gut metagenome Description:DNA extracted from feces of 22 year ol...
Alternative names:SZAXPI029500-102
Anomynised name:GZCD002
...
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ERS1343319408170Human gut metagenome human gut metagenome Description:DNA extracted from feces of 27 year ol...
Alternative names:SZAXPI029501-104
Anomynised name:GZCD003
...
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ERS1343320408170Human gut metagenome human gut metagenome Description:DNA extracted from feces of 16 year ol...
Alternative names:SZAXPI029502-105
Anomynised name:GZCD004
...
+
ERS1343321408170Human gut metagenome human gut metagenome Description:DNA extracted from feces of 22 year ol...
Alternative names:SZAXPI029503-106
Anomynised name:GZCD005
...
+
ERS1343322408170Human gut metagenome human gut metagenome Description:DNA extracted from feces of 39 year ol...
Alternative names:SZAXPI029541-107
Anomynised name:GZCD006
...
+
ERS1343323408170Human gut metagenome human gut metagenome Description:DNA extracted from feces of 17 year ol...
Alternative names:SZAXPI029542-108
Anomynised name:GZCD007
...
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ERS1343324408170Human gut metagenome human gut metagenome Description:DNA extracted from feces of 43 year ol...
Alternative names:SZAXPI029544-123
Anomynised name:GZCD009
...
+
ERS1343325408170Human gut metagenome human gut metagenome Description:DNA extracted from feces of 27 year ol...
Alternative names:SZAXPI029545-129
Anomynised name:GZCD010
...
+
ERS1343326408170Human gut metagenome human gut metagenome Description:DNA extracted from feces of 27 year ol...
Alternative names:SZAXPI029546-133
Anomynised name:GZCD011
...
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Displaying 1-10 of 165 Sample(s).

Files: (FTP site) Table Settings

Columns:

File Description
Sample ID
File Type
File Format
Size
Release Date
Download Link
File Attributes

File NameSample IDFile TypeFile FormatSizeRelease Date 
tabular dataUNKNOWN1.01 GB2017-06-13
tabular dataUNKNOWN7.66 MB2017-06-13
tabular dataUNKNOWN297.23 KB2017-06-13
tabular dataUNKNOWN10.08 MB2017-06-13
ReadmeTEXT1.19 KB2017-06-13
Displaying 1-5 of 5 File(s).

History:

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