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The taxonomic composition of the donor intestinal microbiota is a major factor influencing the efficacy of faecal microbiota transplantation in therapy refractory ulcerative colitis.

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Dataset overview

Participants 27
Samples 172
Reuse readiness 7.6/10 evidence-backed score

The taxonomic composition of the donor intestinal microbiota is a major factor influencing the efficacy of faecal microbiota transplantation in therapy refractory ulcerative colitis.

Kump P, Wurm P, Gröchenig HP, Wenzl H, Petritsch W, Halwachs B, Wagner M, Stadlbauer V, et al. · Alimentary pharmacology & therapeutics · 2017

Abstract

<h4>Background</h4>Faecal microbiota transplantation is an experimental approach for the treatment of patients with ulcerative colitis. Although there is growing evidence that faecal microbiota transplantation is effective in this disease, factors affecting its response are unknown.<h4>Aims</h4>To establish a faecal microbiota transplantation treatment protocol in ulcerative colitis patients, and to investigate which patient or donor factors are responsible for the treatment success.<h4>Methods</h4>This is an open controlled trial of repeated faecal microbiota transplantation after antibiotic pre-treatment (FMT-group, n = 17) vs antibiotic pre-treatment only (AB-group, n = 10) in 27 therapy refractory ulcerative colitis patients over 90 days. Faecal samples of donors and patients were analysed by 16SrRNA gene-based microbiota analysis.<h4>Results</h4>In the FMT-group, 10/17 (59%) of patients showed a response and 4/17 (24%) a remission to faecal microbiota transplantation. Response to faecal microbiota transplantation was mainly influenced by the taxonomic composition of the donor's microbiota. Stool of donors with a high bacterial richness (observed species remission 946 ± 93 vs no response 797 ± 181 at 15367 rps) and a high relative abundance of Akkermansia muciniphila (3.3 ± 3.1% vs 0.1 ± 0.2%), unclassified Ruminococcaceae (13.8 ± 5.0% vs 7.5 ± 3.7%), and Ruminococcus spp. (4.9 ± 3.5% vs 1.0 ± 0.7%) were more likely to induce remission. In contrast antibiotic treatment alone (AB-group) was poorly tolerated, probably because of a sustained decrease of intestinal microbial richness.<h4>Conclusions</h4>The taxonomic composition of the donor's intestinal microbiota is a major factor influencing the efficacy of faecal microbiota transplantation in ulcerative colitis patients. The design of specific microbial preparation might lead to new treatments for ulcerative colitis.

doi:10.1111/apt.14387 ↗ PMID 29052237 ↗ PMC5765501 ↗

Study facts

Organism
—
Platform
Illumina MiSeq
Age group
—
Disease groups
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 Illumina MiSeq from source
ENA instrument_model=Illumina MiSeq

Section ENA study report, offset —
assay.read_depth_reported 15376
For the analyses, samples were rarefied to at least 15376 sequences/sample.

Section Microbiota analysis, offset 800
assay.sequencing_type amplicon_16s
For amplification of bacterial 16S rRNA gene... targeting the hypervariable region V4

Section DNA extraction, 16S rRNA gene amplification and sequencing, offset 350
assay.target_region V4
targeting the hypervariable region V4 of the 16S rRNA gene

Section DNA extraction, 16S rRNA gene amplification and sequencing, offset 470

Cohort

FieldValueEvidence
cohort.disease_activity_metadata_available True
At each study visit, the total Mayo score, faecal calprotectin and a standard laboratory analysis were performed.

Section Study design, offset 2350
cohort.study_design longitudinal
Faecal samples for microbiota analyses were collected at each study visit

Section Study design, offset 2700
cohort.total_participants 27
From June 2012 to July 2014, twenty-seven patients were recruited.

Section Study design, offset 3500
cohort.treatment_exposure_documented True
All patients received antibiotic treatment... Subsequently, 5 faecal microbiota transplantation administrations were performed

Section Study design, offset 1200
cohort.treatment_response_metadata_available True
resulted in a clinical response in 10 out of 17 (59%) patients on day 90

Section Clinical outcomes, offset 12200
cohort.ulcerative_colitis_participants 27
in 27 therapy refractory UC patients over 90 days

Section study description, offset —

Data_Assets

FieldValueEvidence
data_assets.analysis_code True
More information on statistics and bioinformatic tools applied to the dataset and metadata information can one found at: https://github.com/LGPW/FMT_in_TRUC_APT2017

Section study.description, offset 1050
data_assets.open_access True from source
"isOpenAccess": "Y"

Section publication metadata, offset 1300
data_assets.pipeline_or_tool_versions True
Raw files from Illumina MiSeq were processed according to the standard MiSeq SOP of mothur... QIIME version 1.8.0.

Section Microbiota analysis, offset —
data_assets.qc_or_negative_controls_reported True
Sequencing errors were reduced... Chimeras were removed... nonbacterial contaminants... were removed

Section Microbiota analysis, offset —
data_assets.raw_reads True
The generated FASTQ files were used for microbiota analysis.

Section DNA extraction, 16S rRNA gene amplification and sequencing, offset 1000

Specimens

FieldValueEvidence
specimens.inflamed_status_available True inferred
Active ulcerative colitis was defined as a total Mayo score ≥4 and an endoscopic subscore ≥1.

Section Study population-patients, offset —
specimens.longitudinal_sampling True
Faecal samples for microbiota analyses were collected at each study visit

Section Study design, offset 2700
specimens.number_of_samples 172 from source
ENA sample_count=172

Section ENA study report, offset —
specimens.sample_type stool
Stool samples of patients and donors were immediately frozen and stored at −20°C.

Section DNA extraction, 16S rRNA gene amplification and sequencing, offset —