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Structural robustness of the gut mucosal microbiota is associated with Crohn's disease remission after surgery

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Dataset overview

Participants 20
Samples 46
Reuse readiness 5.3/10 evidence-backed score

Structural robustness of the gut mucosal microbiota is associated with Crohn's disease remission after surgery.

Mondot S, Lepage P, Seksik P, Allez M, Tréton X, Bouhnik Y, Colombel JF, Leclerc M, et al. · Gut · 2015

Abstract

<h4>Objectives</h4>Preventing postoperative recurrence after ileocolonic resection (ICR) for Crohn's disease (CD) is challenging. Defining the disturbances of the microbial composition and community structure after ICR and their link with early disease recurrence is crucial.<h4>Design</h4>Microbiota composition (fingerprinting and 16S rDNA sequencing) and community structure (correlation networks of bacterial species) were assessed from ileal mucosa sampled in 20 patients undergoing ICR and 6 months later during endoscopy from above (neoterminal ileum) and below (subanastomotic colon) the surgical anastomosis.<h4>Results</h4>ICR had a dramatic effect on gut microbial ecosystem. At surgery, CD mucosa harboured a dysbiotic microbiota with high proportions of α/β Proteobacteria and Bacilli. Six months later, half of the patients had recurrent lesions at ileocolonoscopy and presented higher numbers of Lachnospiraceae. Recurrence of endoscopic lesions was associated with enrichment in Enterococcus durans while patients in remission had increased proportions of Dorea longicatena and Bacteroides plebeius. Structural differences were striking between recurrence and remission microbiota; while the microbiota of patients with CD recurrence exhibited a loose community structure, the microbiota of patients in remission displayed communities that were robustly correlated to each other. Microbiota colonising the neoterminal ileum and subanastomotic colon 6 months after ICR only differed in patients with recurrence.<h4>Conclusions</h4>ICR modifies the gut microbiome. Remission after 6 months was associated with homogenous bacterial distribution around the anastomosis. Community structure and bacterial networks highlight target species, including Faecalibacterium prausnitzii and Ruminococcus gnavus, which may allow precise modulations of the overall microbial ecosystem towards remission pattern.

doi:10.1136/gutjnl-2015-309184 ↗ PMID 26628508 ↗ PMC4893116 ↗

Study facts

Organism
human gut metagenome
Platform
454 GS-FLX-Titanium (Roche) and MiSeq (Illumina)
Age group
—
Disease groups
Crohn's disease
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
  • 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.platform 454 GS-FLX-Titanium (Roche) and MiSeq (Illumina)
454 pyrosequencing using GS-FLX-Titanium technology ... for mucosal samples or MiSeq (Illumina) for faecal samples

Section Microbial composition assessment by high-throughput sequencing, offset 7050
assay.primers_reported True
V3fwd: 5′-TACGGRAGGCAGCAG-3′, V4rev: 5′-GGACTACCAGGGTATCTAAT-3′

Section DNA preparation, offset 6600
assay.sequencing_type amplicon_16s
bacterial 16S rRNA gene was amplified ... for sequencing

Section DNA preparation, offset 6500
assay.target_region V3-V4
the V3-V4 region for sequencing (V3fwd: 5′-TACGGRAGGCAGCAG-3′, V4rev: 5′-GGACTACCAGGGTATCTAAT-3′)

Section DNA preparation, offset 6600

Cohort

FieldValueEvidence
cohort.crohns_disease_participants 20
Twenty patients with active CD were included in this study.

Section Patients and samples, offset 3500
cohort.disease_activity_metadata_available True
Endoscopic status was determined (recurrence of inflammatory lesions (REC); remission (REM)). Endoscopic recurrence was defined by a Rutgeerts score >2.

Section Patients and samples, offset 4700
cohort.study_design longitudinal
Patients were examined 6 months after ICR (month 6 (M6)), provided faecal samples and an ileocolonoscopy was performed.

Section Patients and samples, offset 4400
cohort.total_participants 20
Microbiota composition ... was assessed from ileal mucosa sampled in 20 patients undergoing ICR

Section study.description, offset —
cohort.treatment_exposure_documented True
They were part of a double-blind, randomised, placebo-controlled, 6-month clinical study ... assessing the efficacy of the probiotic strain Lactobacillus johnsonii LA1

Section Patients and samples, offset 3650

Specimens

FieldValueEvidence
specimens.body_site ileal mucosa, subanastomotic colon, and faeces
Biopsies were sampled ... at the ileal level ... Patients ... provided faecal samples ... Biopsies were sampled from the neoterminal ileum ... and the subanastomotic colon

Section Patients and samples, offset 4200
specimens.inflamed_status_available True
Biopsies were sampled ... in macroscopically ulcerated regions.

Section Patients and samples, offset 4550
specimens.longitudinal_sampling True
At time of surgery (month 0 (M0)) ... Patients were examined 6 months after ICR (month 6 (M6))

Section Patients and samples, offset 4200
specimens.number_of_samples 46
Ten patients (ie, 46 samples: 26 mucosal samples and 20 faecal samples; see online supplementary table S1)

Section Microbial composition assessment by high-throughput sequencing, offset 6900
specimens.sample_type mixed
Ten patients (ie, 46 samples: 26 mucosal samples and 20 faecal samples; see online supplementary table S1)

Section Microbial composition assessment by high-throughput sequencing, offset 6900