Foundry120 atlas

← IBD microbiome

Additional file 5 of Tissue and stool microbiome in pediatric inflammatory bowel disease patients: diversity differs in patients with relapsing and non-relapsing Crohn’s disease

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Dataset overview

Participants 82
Samples None
Reuse readiness 6.0/10 evidence-backed score

Tissue and stool microbiome in pediatric inflammatory bowel disease patients: diversity differs in patients with relapsing and non-relapsing Crohn's disease.

Hrala M, Deissová T, Andrla P, Radová L, Zahornacká S, Bohošová J, Macháčková T, Křen L, et al. · Gut pathogens · 2025

Abstract

<h4>Background</h4>Inflammatory bowel diseases (IBD), including Crohn's disease (CD) and ulcerative colitis (UC), are chronic conditions characterized by periods of clinical remission and relapse. Pediatric cases (pIBD) often have a more complicated disease course, where approximately 30% will develop a relapse within a year of diagnosis. Identifying prognostic markers for pIBD is important to optimize treatment and improve long-term outcomes. Our aim was to analyze the tissue microbiome, identify microbial prognostic markers, and validate their predictive power in non-invasive fecal samples.<h4>Results</h4>Tissue and fecal microbiome were characterized from a prospective cohort comprising 33 therapeutically naïve pCD and 23 pUC patients, and 26 non-IBD pediatric controls, using amplicon 16S rRNA gene sequencing. Disease relapse was monitored for one year. At diagnosis, relapsing pCD patients exhibited a significantly decreased alpha diversity and altered beta diversity in tissue compared to non-relapsing pCD patients. Specific taxa were differentially abundant in relapsing pCD, with Barnesiella being the most depleted genus in tissue samples. Receiver Operating Characteristic (ROC) analysis identified Barnesiella (AUC = 0.818), Butyricimonas, and Collinsella as individual microbial tissue markers discriminating pCD relapse. Combining Barnesiella with the weighted Pediatric Crohn's Disease Activity Index (wPCDAI) further enhanced the specificity and sensitivity of the ROC analysis (AUC = 0.872 in tissue, 0.852 in feces), suggesting potential for non-invasive prognostic markers from stool.<h4>Conclusions</h4>Tissue and fecal microbial markers can predict relapse in pCD patients with high prognostic power, providing a basis for precision medicine and personalized treatment strategies in pIBD.

doi:10.1186/s13099-025-00766-5 ↗ PMID 41241730 ↗ PMC12619421 ↗

Study facts

Organism
—
Platform
Illumina MiSeq
Age group
paediatric
Disease groups
Crohn's disease, Non-IBD controls, Ulcerative colitis
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

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
Paired-end sequencing was then conducted

Section 16S rRNA sequencing library preparation, offset 10300
assay.platform Illumina MiSeq
Paired-end sequencing was then conducted using the MiSeq Sequencing System

Section 16S rRNA sequencing library preparation, offset 10300
assay.primers_reported True
Quick-16S™ Primer Set V1-V2 (Zymo Research) was employed

Section 16S rRNA sequencing library preparation, offset 9320
assay.read_length 300
generating reads with a length of 2 × 300 bp

Section 16S rRNA sequencing library preparation, offset 10420
assay.sequencing_type amplicon_16s
For the 16S rRNA library preparation

Section 16S rRNA sequencing library preparation, offset 9300
assay.target_region V1-V2
Quick-16S™ Primer Set V1-V2... to target the variable V1-V2 regions

Section 16S rRNA sequencing library preparation, offset 9360

Cohort

FieldValueEvidence
cohort.age_group paediatric
The pediatric cases (pIBD)

Section Background, offset 700
cohort.crohns_disease_participants 33
pediatric Crohn’s disease (pCD, N = 33)

Section Study participants and sample collection, offset 4050
cohort.disease_activity_metadata_available True
disease activity indices (weighted Pediatric Crohn’s Disease Activity Index [wPCDAI] and Pediatric Ulcerative Colitis Activity Index [PUCAI])

Section Study participants and sample collection, offset 4800
cohort.non_ibd_controls 26
The control group (non-IBD, N = 26) comprised children

Section Study participants and sample collection, offset 4270
cohort.total_participants 82 inferred
The case group consisted of children diagnosed with pediatric inflammatory bowel disease (pIBD, N = 56)... The control group (non-IBD, N = 26)

Section Study participants and sample collection, offset 3900
cohort.treatment_exposure_documented True
a therapeutically naïve cohort of 33 pCD patients, 23 pUC patients, and 26 non-IBD pediatric controls

Section Background, offset 1780
cohort.treatment_response_metadata_available True
disease relapse within 12 months post-diagnosis was monitored as a prognostic indicator of disease severity and/or treatment response

Section Study participants and sample collection, offset 5100
cohort.ulcerative_colitis_participants 23
pediatric ulcerative colitis (pUC, N = 23)

Section Study participants and sample collection, offset 4110

Data_Assets

FieldValueEvidence
data_assets.qc_or_negative_controls_reported True
Microbial DNA-free water... was used as a negative control.

Section Sample DNA extraction, offset 6900

Specimens

FieldValueEvidence
specimens.body_site terminal ileum, caecum-ascendens/right hemicolon, rectosigmoideum/left hemicolon, and stool
the terminal ileum (TEI), caecum-ascendens (right hemicolon, RHC), and rectosigmoideum (left hemicolon, LHC)

Section Study participants and sample collection, offset 4520
specimens.inflamed_status_available True
One biopsy from each region was evaluated... to confirm or exclude microscopic inflammation.

Section Study participants and sample collection, offset 4660
specimens.sample_type mixed
Two fresh-frozen tissue biopsies were obtained... Additionally, stool samples were collected

Section Study participants and sample collection, offset 4470