Foundry120 atlas

← IBD microbiome

Epigenomic alterations are associated with mucosal microbiota and inflammation in inflammatory bowel disease

Download from source ↗

Dataset overview

Participants 161
Samples 48
Reuse readiness 7.6/10 evidence-backed score

Colonic microbiota is associated with inflammation and host epigenomic alterations in inflammatory bowel disease.

Ryan FJ, Ahern AM, Fitzgerald RS, Laserna-Mendieta EJ, Power EM, Clooney AG, O'Donoghue KW, McMurdie PJ, et al. · Nature communications · 2020

Abstract

Studies of inflammatory bowel disease (IBD) have been inconclusive in relating microbiota with distribution of inflammation. We report microbiota, host transcriptomics, epigenomics and genetics from matched inflamed and non-inflamed colonic mucosa [50 Crohn's disease (CD); 80 ulcerative colitis (UC); 31 controls]. Changes in community-wide and within-patient microbiota are linked with inflammation, but we find no evidence for a distinct microbial diagnostic signature, probably due to heterogeneous host-microbe interactions, and show only marginal microbiota associations with habitual diet. Epithelial DNA methylation improves disease classification and is associated with both inflammation and microbiota composition. Microbiota sub-groups are driven by dominant Enterbacteriaceae and Bacteroides species, representative strains of which are pro-inflammatory in vitro, are also associated with immune-related epigenetic markers. In conclusion, inflamed and non-inflamed colonic segments in both CD and UC differ in microbiota composition and epigenetic profiles.

doi:10.1038/s41467-020-15342-5 ↗ PMID 32251296 ↗ PMC7089947 ↗

Study facts

Organism
Homo sapiens
Platform
Illumina MiSeq
Age group
adult
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-to-sample mapping is available
  • 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
on an Illumina MiSeq for 2 × 300 bp reads

Section Methods, offset 68100
assay.platform Illumina MiSeq
sent for sequencing at Eurofins Genomics on an Illumina MiSeq

Section Methods, offset 68100
assay.primers_reported True
The primers (forward TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGCCTACGGGNGGCWGCAG; reverse GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGGACTACHVGGGTATCTAATCC)

Section Methods, offset 65100
assay.read_length 300
on an Illumina MiSeq for 2 × 300 bp reads

Section Methods, offset 68100
assay.sequencing_type amplicon_16s
reads of the amplified 16S rRNA V3-V4 gene region

Section Results, offset 3500
assay.target_region 16S rRNA V3-V4
the amplified 16S rRNA V3-V4 gene region

Section Results, offset 3500

Cohort

FieldValueEvidence
cohort.age_group adult
We studied paired biopsies from inflamed and non-inflamed mucosa of 80 adult patients

Section Results, offset 1060
cohort.crohns_disease_participants 50
80 adult patients with ulcerative colitis and 50 with Crohn’s disease

Section Results, offset 3200
cohort.disease_activity_metadata_available True
samples from areas of active (lesions) inflammation and from normal-appearing areas

Section Methods, offset 60300
cohort.non_ibd_controls 31
along with paired biopsies of 31 non-IBD (here: healthy) controls

Section Results, offset 1280
cohort.study_design cross_sectional
While our study is based on a single time-point

Section Discussion, offset —
cohort.total_participants 161
Fig. 1 Overall microbiota composition ... from 161 subjects

Section Results, offset 2870
cohort.treatment_exposure_documented True
Of the 15 patients on biologics (anti-TNFs: Adalimumab and Infliximab)

Section Results, offset 10700
cohort.ulcerative_colitis_participants 80
80 adult patients with ulcerative colitis and 50 with Crohn’s disease

Section Results, offset 3200

Data_Assets

FieldValueEvidence
data_assets.open_access True
"isOpenAccess": "Y"

Section publication metadata, offset —
data_assets.pipeline_or_tool_versions True
FastQC v0.11.3 ... Trimmomatic v0.33 ... R v3.3.0 ... DADA2 package (v1.03)

Section Methods—Bioinformatic and statistical analysis, offset 60600
data_assets.qc_or_negative_controls_reported True
the quality of the raw reads was visualized with FastQC v0.11.3 followed by read trimming and filtering with Trimmomatic v0.33

Section Bioinformatic and statistical analysis, offset —

Specimens

FieldValueEvidence
specimens.body_site colon
endoscopically-targeted biopsies from paired inflamed and non-inflamed segments of the colon

Section Introduction, offset 1800
specimens.inflamed_status_available True
samples from areas of active (lesions) inflammation and from normal-appearing areas

Section Methods, offset 60300
specimens.longitudinal_sampling False
While our study is based on a single time-point

Section Discussion, offset —
specimens.number_of_samples 48
Bisulphite converted DNA from the 48 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip

Section study, offset —
specimens.participant_to_sample_mapping_available True
For those with CD, colonic biopsies were taken ... (n = 50 biopsy pairs)

Section Methods, offset 60600
specimens.sample_type mucosal_biopsy
Microbiota composition of 346 colonic biopsies were analyzed

Section Results, offset 3200