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

Dataset overview

Participants 27

Samples 172

Reuse readiness 7.7/10 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: mixed
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

Field	Value	Evidence
`assay.platform`	Illumina MiSeq from source	ENA instrument_model=Illumina MiSeq Section `ENA study report`, offset —
`assay.read_depth_reported`	15376	samples were rarefied to at least 15376 sequences/sample Section `Microbiota analysis`, offset 15380
`assay.sequencing_type`	amplicon_16s	For amplification of bacterial 16S rRNA gene Section `DNA extraction, 16S rRNA gene amplification and sequencing`, offset 13800
`assay.target_region`	V4	targeting the hypervariable region V4 of the 16S rRNA gene Section `DNA extraction, 16S rRNA gene amplification and sequencing`, offset 13920

Cohort

Field	Value	Evidence
`cohort.age_group`	mixed inferred	Eligible patients with chronic active ulcerative colitis were aged between 16 and 80 years. Section `Study population-patients`, offset 7240
`cohort.disease_activity_metadata_available`	True	Active ulcerative colitis was defined as a total Mayo score ≥4 and an endoscopic subscore ≥1. Section `Study population-patients`, offset 7470
`cohort.study_design`	longitudinal	This is an open prospective trial of repeated faecal microbiota transplantation ... End of follow-up was after 90 days. Section `Study design`, offset 3690
`cohort.total_participants`	27	From June 2012 to July 2014, twenty-seven patients were recruited. Section `Study design`, offset 5070
`cohort.treatment_exposure_documented`	True	repeated faecal microbiota transplantation after antibiotic pre-treatment (FMT-group) with a nonrandomised control group with antibiotic pre-treatment only (AB-group) Section `Study design`, offset 3690
`cohort.treatment_response_metadata_available`	True	Primary end point was the reduction of the total Mayo score on day 90. Section `Study design`, offset 4610
`cohort.ulcerative_colitis_participants`	27	27 therapy refractory UC patients over 90 days. Section `study description`, offset —

Data_Assets

Field	Value	Evidence
`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 1450
`data_assets.open_access`	True from source	isOpenAccess: "Y" Section `publication metadata`, offset 1800
`data_assets.qc_or_negative_controls_reported`	True	Sequencing errors were reduced ... Chimeras were removed with UCHIME Section `Microbiota analysis`, offset 14700
`data_assets.raw_reads`	True	The datasets generated and analysed during the current study are available in the European nucleotide archive (ENA) repository under the Primary accession number PRJEB11841 Section `AVAILABILITY OF DATA AND MATERIAL`, offset 36000
`data_assets.sample_metadata`	True	metadata information can one found at: https://github.com/LGPW/FMT_in_TRUC_APT2017 Section `study.description`, offset 900

Specimens

Field	Value	Evidence
`specimens.body_site`	gastrointestinal tract inferred	the faecal suspension was applied into the terminal ileum and the right colon Section `Donor stool preparation and protocol for faecal microbiota transplantation`, offset 10120
`specimens.inflamed_status_available`	True	Active ulcerative colitis was defined as a total Mayo score ≥4 and an endoscopic subscore ≥1. Section `Study population-patients`, offset 7470
`specimens.longitudinal_sampling`	True	Faecal samples for microbiota analyses were collected at each study visit Section `Study design`, offset 4290
`specimens.number_of_samples`	172 from source	ENA sample_count=172 Section `ENA study report`, offset —
`specimens.sample_type`	stool	Faecal samples for microbiota analyses were collected at each study visit Section `Study design`, offset 4290