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

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Dataset overview

Participants 129
Samples 382
Reuse readiness 8.6/10 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
Illumina HiSeq 2500
Age group
—
Disease groups
Crohn's disease, Ulcerative colitis
Anatomical sites
—

Data availability

  • Analysis code

Strengths & limitations for reuse

Strengths

  • Raw reads are advertised
  • Taxonomic tables are advertised
  • Analysis code is available
  • Participant-to-sample mapping is available
  • Participant counts are documented
  • Sample counts are documented

Limitations

  • Not documented: feature/otu 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 Illumina HiSeq 2500 from source
ENA instrument_model=Illumina HiSeq 2500

Section ENA study report, offset —
assay.sequencing_type shotgun_metagenomics
we perform deep-coverage shotgun metagenomics

Section Shotgun Metagenomic Data Collection and Profiling, offset 5300

Cohort

FieldValueEvidence
cohort.crohns_disease_participants 79
(50 ulcerative colitis 79 Crohn’s disease)

Section study description, offset 2040
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 14700
cohort.study_design longitudinal
Stool samples for each subject were collected approximately every 6 months.

Section UCSD Inflammatory Bowel Disease Biobank, offset 4300
cohort.total_participants 129
prospectively collect 332 stool samples from 129 subjects

Section study description, offset 2000
cohort.treatment_exposure_documented True
95 (73.6%) patients have current or prior TNF inhibitor exposure.

Section RESULTS, offset 11300
cohort.treatment_response_metadata_available True
We did not identify differences based on response to TNF-inhibitors

Section RESULTS, offset 27500
cohort.ulcerative_colitis_participants 50
(50 ulcerative colitis 79 Crohn’s disease)

Section study description, offset 2040

Data_Assets

FieldValueEvidence
data_assets.analysis_code True
published as a collection of Jupyter notebooks (https://github.com/knightlab-analyses/ibd-surgery)

Section Statistical Analyses, offset 10500
data_assets.open_access True
isOpenAccess: "Y"

Section publication metadata, offset 7000
data_assets.pipeline_or_tool_versions True
atropos1.1.21 ... Bowtie2 2.3.0 ... MetaPhlan2 2.7.7 ... HUMAnN2 0.11.2

Section Shotgun Metagenomic Data Collection and Profiling, offset 5900
data_assets.qc_or_negative_controls_reported True
we trimmed the adaptors and performed quality filtering

Section Shotgun Metagenomic Data Collection and Profiling, offset 6000
data_assets.raw_reads True
The metagenomic sequencing data have been deposited to the European Bioinformatics Institute

Section Data Availability, offset 8800
data_assets.sample_metadata True
the full data set including sample metadata has been made public on Qiita

Section Data Availability, offset 9000
data_assets.taxonomic_table True
The taxonomic profiles were generated using MetaPhlan2 2.7.7

Section Shotgun Metagenomic Data Collection and Profiling, offset 6400

Specimens

FieldValueEvidence
specimens.body_site gut
long-term effect on the gut microbiome

Section CONCLUSION, offset 34800
specimens.inflamed_status_available True
active endoscopic disease vs inactive endoscopic disease activity

Section RESULTS, offset 14700
specimens.longitudinal_sampling True
Stool samples for each subject were collected approximately every 6 months.

Section UCSD Inflammatory Bowel Disease Biobank, offset 4300
specimens.number_of_samples 382 from source
ENA sample_count=382

Section ENA study report, offset —
specimens.participant_to_sample_mapping_available True
single sample from 18 patients; 2 samples from 36 patients; 3 samples from 40 patients

Section RESULTS, offset 11200
specimens.sample_type stool
Participants collected samples at home in Covidien 2450SA stool specimen containers

Section Specimen Collection, offset 3500