Foundry120 atlas

← IBD microbiome

Gastrointestinal Surgery for Inflammatory Bowel Disease Persistently Lowers Microbiome and Metabolome Diversity

Download from source ↗

Dataset overview

Participants 129
Samples 300
Reuse readiness 8.0/10 evidence-backed score

Gastrointestinal Surgery for Inflammatory Bowel Disease Persistently Lowers Microbiome and Metabolome Diversity.

Fang X, Vázquez-Baeza Y, Elijah E, Vargas F, Ackermann G, Humphrey G, Lau R, Weldon KC, et al. · Inflammatory bowel diseases · 2021

Abstract

<h4>Background</h4>Many studies have investigated the role of the microbiome in inflammatory bowel disease (IBD), but few have focused on surgery specifically or its consequences on the metabolome that may differ by surgery type and require longitudinal sampling. Our objective was to characterize and contrast microbiome and metabolome changes after different surgeries for IBD, including ileocolonic resection and colectomy.<h4>Methods</h4>The UC San Diego IBD Biobank was used to prospectively collect 332 stool samples from 129 subjects (50 ulcerative colitis; 79 Crohn's disease). Of these, 21 with Crohn's disease had ileocolonic resections, and 17 had colectomies. We used shotgun metagenomics and untargeted liquid chromatography followed by tandem mass spectrometry metabolomics to characterize the microbiomes and metabolomes of these patients up to 24 months after the initial sampling.<h4>Results</h4>The species diversity and metabolite diversity both differed significantly among groups (species diversity: Mann-Whitney U test P value = 7.8e-17; metabolomics, P-value = 0.0043). Escherichia coli in particular expanded dramatically in relative abundance in subjects undergoing surgery. The species profile was better able to classify subjects according to surgery status than the metabolite profile (average precision 0.80 vs 0.68).<h4>Conclusions</h4>Intestinal surgeries seem to reduce the diversity of the gut microbiome and metabolome in IBD patients, and these changes may persist. Surgery also further destabilizes the microbiome (but not the metabolome) over time, even relative to the previously established instability in the microbiome of IBD patients. These long-term effects and their consequences for health outcomes need to be studied in prospective longitudinal trials linked to microbiome-involved phenotypes.

doi:10.1093/ibd/izaa262 ↗ PMID 33026068 ↗ PMC8047854 ↗

Study facts

Organism
—
Platform
HiSeq 4000
Age group
—
Disease groups
Crohn's disease, Ulcerative colitis
Anatomical sites
—

Data availability

  • Analysis code

Strengths & limitations for reuse

Strengths

  • Raw reads are advertised
  • Analysis code is available
  • Participant counts are documented
  • Sample counts are documented

Limitations

  • 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.platform HiSeq 4000
sequenced using HiSeq 4000 platform.

Section Shotgun Metagenomic Data Collection and Profiling, offset 6800
assay.sequencing_type shotgun_metagenomics
we perform deep-coverage shotgun metagenomics

Section INTRODUCTION, offset 3900

Cohort

FieldValueEvidence
cohort.crohns_disease_participants 79
332 stool samples from 129 subjects (50 ulcerative colitis 79 Crohn’s disease).

Section ena_study.study.description, offset 6550
cohort.disease_activity_metadata_available True
We separated samples into those from patients with active endoscopic disease vs inactive endoscopic disease activity.

Section RESULTS, offset 18200
cohort.study_design longitudinal
Stool samples for each subject were collected approximately every 6 months.

Section UCSD Inflammatory Bowel Disease Biobank, offset 6100
cohort.total_participants 129
The UC San Diego IBD Biobank was used to prospectively collect 332 stool samples from 129 subjects (50 ulcerative colitis 79 Crohn’s disease).

Section ena_study.study.description, offset 6500
cohort.treatment_exposure_documented True
95 (73.6%) patients have current or prior TNF inhibitor exposure.

Section RESULTS, offset 12300
cohort.treatment_response_metadata_available True
We did not identify differences based on response to TNF-inhibitors with and without stratifying based on prior surgery.

Section RESULTS, offset 31500
cohort.ulcerative_colitis_participants 50
332 stool samples from 129 subjects (50 ulcerative colitis 79 Crohn’s disease).

Section ena_study.study.description, offset 6550

Data_Assets

FieldValueEvidence
data_assets.analysis_code True
A detailed description of the individual steps has been published as a collection of Jupyter notebooks

Section Statistical Analyses, offset 10800
data_assets.open_access True from source
"isOpenAccess": "Y"

Section publication metadata, offset —
data_assets.pipeline_or_tool_versions True
MetaPhlan2 2.7.7 ... HUMAnN2 0.11.2

Section Shotgun Metagenomic Data Collection and Profiling, offset 7350
data_assets.qc_or_negative_controls_reported True
we trimmed the adaptors and performed quality filtering ... and filtered out host reads

Section Shotgun Metagenomic Data Collection and Profiling, offset 7100
data_assets.raw_reads True
The metagenomic sequencing data have been deposited to the European Bioinformatics Institute (EBI accession is ERP121770)

Section Data Availability, offset 11200
data_assets.sample_metadata True
the full data set including sample metadata has been made public on Qiita

Section Data Availability, offset 11350

Specimens

FieldValueEvidence
specimens.body_site gut inferred
Participants collected samples at home in Covidien 2450SA stool specimen containers.

Section Specimen Collection, offset 5200
specimens.inflamed_status_available True
active endoscopic disease vs inactive endoscopic disease activity

Section RESULTS, offset 18400
specimens.longitudinal_sampling True
Stool samples for each subject were collected approximately every 6 months.

Section UCSD Inflammatory Bowel Disease Biobank, offset 6100
specimens.number_of_samples 300
After filtering out low-quality samples, we worked with 300 metagenomics samples.

Section Shotgun Metagenomic Data Collection and Profiling, offset 7200
specimens.sample_type stool
Participants collected samples at home in Covidien 2450SA stool specimen containers.

Section Specimen Collection, offset 5200