Foundry120 atlas

← IBD microbiome

Metagenomes of the gut microbiota of CD patients that required resection from a Belgian cohort

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Dataset overview

Participants 49
Samples 98
Reuse readiness 5.1/10 evidence-backed score

Dysbiosis and relapse-related microbiome in inflammatory bowel disease: A shotgun metagenomic approach.

Serrano-Gómez G, Mayorga L, Oyarzun I, Roca J, Borruel N, Casellas F, Varela E, Pozuelo M, et al. · Computational and structural biotechnology journal · 2021

Abstract

Crohn's disease (CD) and ulcerative colitis (UC), the two main forms of inflammatory bowel disease (IBD), affect several million people worldwide. CD and UC are characterized by periods of clinical remission and relapse. Although IBD patients present chronic alterations of the gut microbiome, called dysbiosis, little attention has been devoted to the relapse-related microbiome. To address this gap, we generated shotgun metagenomic data from the stools of two European cohorts-134 Spanish (followed up for one year) and 49 Belgian (followed up for 6 months) subjects-to characterize the microbial taxonomic and metabolic profiles present. To assess the predictive value of microbiome data, we added the taxonomic profiles generated from a previous study of 130 Americans. Our results revealed that CD was more dysbiotic than UC compared to healthy controls (HC) and that strategies for energy extraction and propionate production were different in CD compared to UC and HC. Remarkably, CD and UC relapses were not associated with alpha- or beta-diversity, or with a dysbiotic score. However, CD relapse was linked to alterations at the species and metabolic pathway levels, including those involved in propionate production. The random forest method using taxonomic profiles allowed the prediction of CD vs. non-CD with an AUC = 0.938, UC vs. HC with an AUC = 0.646, and CD relapse vs. remission with an AUC = 0.769. Our study validates previous taxonomic findings, points to different relapse-related growth and defence mechanisms in CD compared to UC and HC and provides biomarkers to discriminate IBD subtypes and predict disease activity.

doi:10.1016/j.csbj.2021.11.037 ↗ PMID 34938418 ↗ PMC8665270 ↗

Study facts

Organism
—
Platform
Illumina HiSeq
Age group
—
Disease groups
Crohn's disease
Anatomical sites
—

Data availability

Specific data assets have not been resolved from the source yet — see the source repository below for the full file listing.

Strengths & limitations for reuse

Strengths

  • Participant counts are documented
  • Sample counts are documented

Limitations

  • Not documented: raw reads are advertised
  • Not documented: feature/otu tables 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.paired_end True
The sequencing process provided an average of 95 million paired-end sequence reads per sample.

Section Methods > DNA shotgun sequencing, offset 5800
assay.platform Illumina HiSeq
the Illumina HiSeq sequencing platform

Section Methods > DNA shotgun sequencing, offset 5700
assay.sequencing_type shotgun_metagenomics
were processed for DNA shotgun sequencing

Section Methods > Study cohorts, offset 4650

Cohort

FieldValueEvidence
cohort.crohns_disease_participants 49
The Belgian cohort consisted of CD patients (n = 49)

Section Methods > Study cohorts, offset 4500
cohort.disease_activity_metadata_available True
CD patients who underwent POR (n = 21) ... compared to those who remained in remission (n = 28)

Section Results > Differentially abundant species in IBD subtypes and disease activity, offset 12500
cohort.study_design longitudinal
A total of 98 faecal samples were provided before surgery and at month 6 post-surgery

Section Methods > Study cohorts, offset 4650
cohort.total_participants 49
The Belgian cohort consisted of CD patients (n = 49)

Section Methods > Study cohorts, offset 4500
cohort.treatment_response_metadata_available True
Patients’ characteristics can be found in Supplementary Table 2. These patients were at risk of developing POR, which was defined by a Rutgeerts score ≥ i2b.

Section Methods > Study cohorts, offset 4450

Data_Assets

FieldValueEvidence
data_assets.pipeline_or_tool_versions True
The KneadData v0.7.4 pipeline was used to pre-process and decontaminate the sequence reads.

Section Methods > Upstream sequence analysis: Quality control, decontamination and profiling, offset 6900
data_assets.qc_or_negative_controls_reported True
The KneadData v0.7.4 pipeline was used to pre-process and decontaminate the sequence reads.

Section Methods > Upstream sequence analysis: Quality control, decontamination and profiling, offset 6900

Specimens

FieldValueEvidence
specimens.longitudinal_sampling True
A total of 98 faecal samples were provided before surgery and at month 6 post-surgery

Section Methods > Study cohorts, offset 4650
specimens.number_of_samples 98
A total of 98 faecal samples were provided before surgery and at month 6 post-surgery and were processed for DNA shotgun sequencing.

Section Methods > Study cohorts, offset 4650
specimens.sample_type stool
A total of 98 faecal samples were provided before surgery and at month 6 post-surgery

Section Methods > Study cohorts, offset 4650