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The relevance of spatial composition in the microbial changes associated with ulcerative colitis, is unclear. We coupled luminal brush samples, mucosal biopsies and laser capture microdissection with deep sequencing of the gut microbiota to develop an integrated spatial assessment of the microbial community in health and ulcerative colitis.

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Dataset overview

Participants 9
Samples 97
Reuse readiness 6.4/10 evidence-backed score

Spatial variation of the colonic microbiota in patients with ulcerative colitis and control volunteers.

Lavelle A, Lennon G, O'Sullivan O, Docherty N, Balfe A, Maguire A, Mulcahy HE, Doherty G, et al. · Gut · 2015

Abstract

<h4>Objectives</h4>The relevance of spatial composition in the microbial changes associated with UC is unclear. We coupled luminal brush samples, mucosal biopsies and laser capture microdissection with deep sequencing of the gut microbiota to develop an integrated spatial assessment of the microbial community in controls and UC.<h4>Design</h4>A total of 98 samples were sequenced to a mean depth of 31,642 reads from nine individuals, four control volunteers undergoing routine colonoscopy and five patients undergoing surgical colectomy for medically-refractory UC. Samples were retrieved at four colorectal locations, incorporating the luminal microbiota, mucus gel layer and whole mucosal biopsies.<h4>Results</h4>Interpersonal variability accounted for approximately half of the total variance. Surprisingly, within individuals, asymmetric Eigenvector map analysis demonstrated differentiation between the luminal and mucus gel microbiota, in both controls and UC, with no differentiation between colorectal regions. At a taxonomic level, differentiation was evident between both cohorts, as well as between the luminal and mucosal compartments, with a small group of taxa uniquely discriminating the luminal and mucosal microbiota in colitis. There was no correlation between regional inflammation and a breakdown in this spatial differentiation or bacterial diversity.<h4>Conclusions</h4>Our study demonstrates a conserved spatial structure to the colonic microbiota, differentiating the luminal and mucosal communities, within the context of marked interpersonal variability. While elements of this structure overlap between UC and control volunteers, there are differences between the two groups, both in terms of the overall taxonomic composition and how spatial structure is ascribable to distinct taxa.

doi:10.1136/gutjnl-2014-307873 ↗ PMID 25596182 ↗ PMC4602252 ↗

Study facts

Organism
—
Platform
Roche 454 GS-FLX Titanium
Age group
adult
Disease groups
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.platform Roche 454 GS-FLX Titanium
Sequencing was performed on a Roche 454 GS-FLX using Titanium chemistry

Section Amplicon sequencing and bioinformatics analysis, offset 14900
assay.primers_reported True
520F (5′-AYTGGGYDTAAAG NG-3′) and 926R (5′-CCGTCAATTYYTTTRAGTTT-3′)

Section Amplicon sequencing and bioinformatics analysis, offset 14500
assay.read_depth_reported 31642
to a mean depth of 31,642 reads

Section study.description, offset 2800
assay.sequencing_type amplicon_16s inferred
deep sequencing of the gut microbiota

Section study.description, offset 3050
assay.target_region V4 region of the 16S SSU rRNA gene
The V4 region of the 16S SSU rRNA gene was amplified by PCR with universal primers

Section Amplicon sequencing and bioinformatics analysis, offset 14500

Cohort

FieldValueEvidence
cohort.age_group adult
Each gave informed, written consent prior to the procedure, was more than 18 years of age

Section Patient recruitment, offset 3500
cohort.disease_activity_metadata_available True
Inflammatory scores at each level and overall disease activity scores are presented in table 2.

Section Results, offset 10250
cohort.non_ibd_controls 4
nine individuals, four healthy volunteers undergoing routine colonoscopy and five patients

Section study.description, offset 2820
cohort.study_design cross_sectional inferred
how colonic ecology varies across multiple loci at a single time point within an individual

Section Introduction, offset 2100
cohort.total_participants 9
A total of 97 samples were sequenced to a mean depth of 31,642 reads from nine individuals

Section study.description, offset 2800
cohort.treatment_exposure_documented True
Patients with UC were undergoing total colectomies for either medically-refractory UC or an acute severe flair of UC, unresponsive to intravenous hydrocortisone and biological therapy.

Section Patient recruitment, offset 4100
cohort.treatment_response_metadata_available True
Inflammatory scores at each level and overall disease activity scores are presented in table 2.

Section Results, offset 10300
cohort.ulcerative_colitis_participants 5
five patients undergoing surgical colectomy for medically-refractory ulcerative colitis

Section study.description, offset 2860

Data_Assets

FieldValueEvidence
data_assets.qc_or_negative_controls_reported True
An extraction blank was used for each run

Section Sample collection, offset 8500

Specimens

FieldValueEvidence
specimens.body_site colon
Sampling levels were the caecum, transverse colon, descending colon and rectum

Section Sample collection, offset 5200
specimens.inflamed_status_available True
Inflammatory scores at each level and overall disease activity scores are presented in table 2.

Section Results, offset 10200
specimens.longitudinal_sampling False inferred
how colonic ecology varies across multiple loci at a single time point within an individual

Section Introduction, offset 2100
specimens.number_of_samples 97
A total of 97 samples were sequenced

Section study.description, offset 2800
specimens.participant_to_sample_mapping_available True inferred
This gave a total of 12 samples for each individual.

Section Sample collection, offset 5350
specimens.sample_type mixed
incorporating the luminal microbiota, the mucus gel layer and whole mucosal biopsies

Section study.description, offset 3000