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Gut multi-omics profiling in Crohn’s disease: A preliminary study

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Dataset overview

Participants 24
Samples 24
Reuse readiness 8.9/10 evidence-backed score

In search for interplay between stool microRNAs, microbiota and short chain fatty acids in Crohn's disease - a preliminary study.

Ambrozkiewicz F, Karczmarski J, Kulecka M, Paziewska A, Niemira M, Zeber-Lubecka N, Zagorowicz E, Kretowski A, et al. · BMC gastroenterology · 2020

Abstract

<h4>Background</h4>Inflammatory bowel diseases are classic polygenic disorders, with genetic loads that reflect immunopathological processes in response to the intestinal microbiota. Herein we performed the multiomics analysis by combining the large scale surveys of gut bacterial community, stool microRNA (miRNA) and short chain fatty acid (SCFA) signatures to correlate their association with the activity of Crohn's disease (CD).<h4>Methods</h4>DNA, miRNA, and metabolites were extracted from stool samples of 15 CD patients, eight with active disease and seven in remission, and nine healthy individuals. Microbial, miRNA and SCFA profiles were assessed using datasets from 16S rRNA sequencing, Nanostring miRNA and GC-MS targeted analysis, respectively.<h4>Results</h4>Pairwise comparisons showed that 9 and 23 taxa differed between controls and CD patients with active and inactive disease, respectively. Six taxa were common to both comparisons, whereas four taxa differed in CD patients. α-Diversity was lower in both CD groups than in controls. The levels of 13 miRNAs differed (p-value < 0.05; FC > 1.5) in CD patients and controls before FDR correction and 4 after. Of six SCFAs, the levels of two differed significantly (p-value < 0.05, FC > 1.5) in CD patients and controls, and the levels of four differed in patients with active and inactive CD. PLS-DA revealed models with smallest error rate for controls in bacterial component and inactive disease in metabolites.<h4>Conclusion</h4>A complex interrelationship may exist between gut dysbiosis, miRNA profiling and SCFA level in response to intestinal inflammation.

doi:10.1186/s12876-020-01444-3 ↗ PMID 32958038 ↗ PMC7507689 ↗

Study facts

Organism
Homo sapiens
Platform
Ion Torrent Personal Genome Machine (PGM)
Age group
adult
Disease groups
Crohn's disease, Non-IBD controls
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

  • Raw reads are advertised
  • Feature/OTU tables are advertised
  • Taxonomic tables are advertised
  • Participant-to-sample mapping is available
  • Participant counts are documented
  • Sample counts are documented
Extraction evidence & provenance

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

Assay

FieldValueEvidence
assay.platform Ion Torrent Personal Genome Machine (PGM)
16S rRNA was sequenced on an Ion Torrent Personal Genome Machine (PGM) platform

Section Methods—Fecal DNA extraction and 16S rRNA sequencing, offset 11700
assay.read_depth_reported 92000
An average of 92,000 reads were generated

Section Results—16S rRNA microbiome survey, offset 17100
assay.sequencing_type amplicon_16s
16S rRNA was sequenced on an Ion Torrent Personal Genome Machine (PGM) platform

Section Methods—Fecal DNA extraction and 16S rRNA sequencing, offset 11700
assay.target_region V2, V3, V4, V6–7, V8 and V9
a consensus view across 6 regions V2, V3, V4, V6–7, V8 and V9

Section Methods—Fecal DNA extraction and 16S rRNA sequencing, offset 12000

Cohort

FieldValueEvidence
cohort.age_group adult inferred
median age 32 years (range, 20–62 years) ... median age 36 years (range, 26–41 years)

Section Methods—Samples, offset 8550
cohort.crohns_disease_participants 15
The study cohort consisted of 15 CD patients

Section Methods—Samples, offset 8500
cohort.disease_activity_metadata_available True
seven patients in remission or with mild CD ... eight patients with moderate to severe CD

Section Methods—Samples, offset 8900
cohort.non_ibd_controls 9
and nine healthy control individuals

Section Methods—Samples, offset 8500
cohort.study_design cross_sectional inferred
A stool sample from a single bowel movement was collected and immediately frozen

Section Methods—Stool collection and preparation, offset 10700
cohort.total_participants 24 computed
The study cohort consisted of 15 CD patients... and nine healthy control individuals.

Section Methods — Samples, offset —
cohort.treatment_exposure_documented True
Previous treatment Immunosupressants Glucocorticoids Biological therapy

Section Methods—Samples, offset 9200

Data_Assets

FieldValueEvidence
data_assets.feature_or_otu_table True inferred
Of the 432 taxa identified in these samples, 81 were present at level higher than 0.1% of reads

Section Results—16S rRNA microbiome survey, offset 19500
data_assets.open_access True
"isOpenAccess": "Y"

Section publication metadata, offset 1500
data_assets.pipeline_or_tool_versions True
Additional steps of the analysis were performed using Mothur version 1.38 software.

Section Statistical analysis — 16S rRNA analysis, offset —
data_assets.qc_or_negative_controls_reported True
only the sequences that were 200–300 bases in length, with an average base quality of 20... were kept

Section Statistical analysis—16S rRNA analysis, offset 12600
data_assets.raw_reads True
Unmapped BAM files were converted to FASTQ using Picard’s SamToFastq

Section Statistical analysis—16S rRNA analysis, offset 16800
data_assets.sample_metadata True
The study cohort consisted of 15 CD patients ... and nine healthy control individuals

Section Methods—Samples, offset 7900
data_assets.taxonomic_table True
Of the 432 taxa identified in these samples

Section Results—16S rRNA microbiome survey, offset 19500

Specimens

FieldValueEvidence
specimens.body_site gastrointestinal tract
Microbial communities of the gastro-intestinal tract

Section Background, offset —
specimens.inflamed_status_available True
Disease activity was determined by measuring the CD activity index (CDAI)

Section Methods—Samples, offset 9000
specimens.longitudinal_sampling False inferred
A stool sample from a single bowel movement was collected

Section Stool collection and preparation, offset 8700
specimens.number_of_samples 24 inferred
stool samples of 15 CD patients... and nine healthy individuals

Section study.description, offset —
specimens.participant_to_sample_mapping_available True inferred
A stool sample from a single bowel movement was collected

Section Methods—Stool collection and preparation, offset 7600
specimens.sample_type stool
A stool sample from a single bowel movement was collected

Section Methods—Stool collection and preparation, offset 11000