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Relating the transcriptome and microbiome by paired terminal ileal Crohn's disease

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Dataset overview

Participants 10
Samples 20
Reuse readiness 6.4/10 evidence-backed score

Relating the transcriptome and microbiome by paired terminal ileal Crohn disease.

Cai C, Zhu S, Tong J, Wang T, Feng Q, Qiao Y, Shen J. · iScience · 2021

Abstract

Management of terminal ileal Crohn disease (CD) is difficult due to fibrotic prognosis and failure to achieve mucosal healing. A limited number of synchronous analyses have been conducted on the transcriptome and microbiome in unpaired terminal ileum tissues. Therefore, our study focused on the transcriptome and mucosal microbiome in terminal ileal tissues of patients with CD with the aim of determining the role of cross-talk between the microbiome and transcriptome in the pathogenesis of terminal ileal CD. Mucosa-attached microbial communities were significantly associated with segmental inflammation status. Interaction-related transcription factors (TFs) are the panel nodes for cross-talk between the gene patterns and microbiome for terminal ileal CD. The transcriptome and microbiome in terminal ileal CD can be differently related to the local inflammatory status, and specific differentially expressed genes may be targeted for mucosal healing. TFs connect gene patterns with the microbiome by reflecting environmental stimuli and signals from microbiota.

doi:10.1016/j.isci.2021.102516 ↗ PMID 34113837 ↗ PMC8170125 ↗

Study facts

Organism
Homo sapiens
Platform
—
Age group
—
Disease groups
—
Anatomical sites
—

Data availability

  • Analysis code

Strengths & limitations for reuse

Strengths

  • Feature/OTU tables are advertised
  • Analysis code is available
  • Participant-to-sample mapping is available
  • Participant counts are documented
  • Sample counts are documented

Limitations

  • Not documented: raw reads are advertised
  • Not documented: taxonomic tables are advertised
Extraction evidence & provenance

Each extracted field is shown with the source excerpt and location used to resolve it.

Assay

FieldValueEvidence
assay.sequencing_type amplicon_16s
Analysis of 20 ileal mucosa-attached bacterial samples resulted in a total of 44.7 million 16S rRNA amplicons...

Section Results—Microbiome analysis detected subtle alteration in the ileal mucosa-attached microbiome, offset —

Cohort

FieldValueEvidence
cohort.disease_activity_metadata_available True
A total of 10 paired tissue samples from inflamed and proximal non-inflamed ileum of patients with new-onset CD were analyzed.

Section Results—Identification of functional genes and inflammation-associated genes using transcriptome analysis, offset 6000
cohort.study_design cross_sectional inferred
A total of 10 paired tissue samples from inflamed and proximal non-inflamed ileum of patients with new-onset CD were analyzed.

Section Results, offset 9000
cohort.total_participants 10
four mucosal biopsies ... from ... CD patients (n=10)

Section study.description, offset 520
cohort.treatment_exposure_documented True
all patients were instructed to avoid antibiotics, steroids, immunosuppressants, and biologics

Section study.description, offset 690

Data_Assets

FieldValueEvidence
data_assets.analysis_code True
All data and code supporting the findings of this study are available within the paper and its supplemental information files

Section Data availability, offset 24880
data_assets.feature_or_otu_table True
A total of 19 phyla and 3,120 operational taxonomical units (OTUs) were detected

Section Results—Microbiome analysis detected subtle alteration in the ileal mucosa-attached microbiome, offset 8400
data_assets.open_access True from source
"license": "cc by-nc-nd"

Section publication_metadata, offset —
data_assets.sample_metadata True
Characteristics of the included samples are listed in Table S1.

Section Results, offset 9000

Specimens

FieldValueEvidence
specimens.body_site terminal ileum
Analysis of 20 ileal mucosa-attached bacterial samples

Section Results—Microbiome analysis, offset 11900
specimens.inflamed_status_available True
distinct clusters based on the inflamed or non-inflamed mucosa of CD

Section Results—Microbiome analysis, offset 12500
specimens.longitudinal_sampling False
this study did not analyze the differences between pre- and post-treatment

Section Limitations of the study, offset 39000
specimens.number_of_samples 20
Analysis of 20 ileal mucosa-attached bacterial samples resulted in a total of 44.7 million 16S rRNA amplicons...

Section Results—Microbiome analysis detected subtle alteration in the ileal mucosa-attached microbiome, offset —
specimens.participant_to_sample_mapping_available True
A total of 10 paired tissue samples from inflamed and proximal non-inflamed ileum of patients with new-onset CD were analyzed.

Section Results—Identification of functional genes and inflammation-associated genes using transcriptome analysis, offset —
specimens.sample_type mucosal_biopsy
four mucosal biopsies

Section study.description, offset 420