FMT trial in IBS patients, Finland
133 fecal samples from a randomized, placebo-controlled FMT trial in IBS patients in Finland, studying microbiota composition and functional changes after FMT. machine-written summary
133 samples · 133 runs · FI · Age unknown · 2024 · 1.01 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,197 sample values (country, health condition, health condition detail, intervention, latitude, location region, longitude, subject id) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC11349920 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 133 sample values (antibiotic exposure) · from BugSigDB |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
intervention · arms resolved
Faecal microbiota transplantation design randomized_controlled_trial · population ibs · FMT vs placebo in IBS patients from healthy donor
“randomized, placebo controlled FMT trial on 49 IBS patients” — abstract:39191760 (study level; per-sample arms are in the intervention column below)
longitudinalFMT donor → recipient
31 of 31 people sampled more than once (133 samples; median 4, up to 5 per person) · follow-up median 12 mo (max 12 mo) · median interval between samples 56 d (time from timepoint numbers, unit from the stated sampling schedule). Schedule stated by the source: “Baseline and follow-up samples at weeks 0,1,2,3,4,5,12,26,52 relative to FMT/placebo treatment” (time origin: treatment start (FMT/placebo)); stated follow-up 12 mo.
Each row is one person (31 shown); dots are samples at days since that person's first sample.
FMT trial: 17 FMT-arm IBS recipients of one universal donor (donor 'Do' sampled 4x); 13 placebo (autologous) recipients.
donorrecipient · circles are people (pale = no sequenced sample), arrows run donor → recipient and parent → child, curved lines join twins, partners and siblings, squares are shared settings or families without recorded roles. Shown: 1 linked group from explicit relations. 31 people in the project overall.
Genera, mean relative abundance over 62 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 0 | 0% | ||||
| country | 133 | 100% | 133 | |||
| health_condition | 133 | 100% | 133 | |||
| subject_id | 133 | 100% | 133 | |||
| antibiotic_exposure | 133 | 100% | 133 | |||
| detailed_location | 133 | 100% | ||||
| health_condition_detail | 133 | 100% | 133 | |||
| intervention | 133 | 100% | 133 | |||
| latitude | 133 | 100% | 133 | |||
| location_region | 133 | 100% | 133 | |||
| longitude | 133 | 100% | 133 | |||
| timepoint_label | 133 | 100% | 133 |
- Fecal microbiota transplantation influences microbiota without connection to symptom relief in irritable bowel syndrome patients. 2024 PMID 39191760 PMC11349920 own_data
Archive description
Imbalanced microbiota may contribute to the pathophysiology of irritable bowel syndrome, and fecal microbiota transplantation has been studied as a treatment option. We used both 16S rRNA gene amplicon and shotgun metagenomics data from a previous randomized, placebo controlled FMT trial on 49 IBS patients. The aim of this study was to analyze post-FMT changes in microbiota composition and functional potential.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.68. Assay shotgun_dna.
- host run.scientific_name · “Homo sapiens”
- body site study.title · “Fecal microbiota transplantation”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA115958304 | antibiotic_exposure | no | R2 | 0.60 | external.bugsigdb source | Antibiotics exclusion: 1 year |
| SAMEA115958304 | country | FI | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Finland |
| SAMEA115958304 | health_condition | ibs | R1 | 0.85 | biosample.attribute:TITLE | TITLE: Adult IBS |
| SAMEA115958304 | health_condition_detail | Adult IBS | R1 | 0.85 | biosample.attribute:TITLE | TITLE: Adult IBS |
| SAMEA115958304 | intervention | fmt | R1 | 0.85 | biosample.attribute:DESCRIPTION | DESCRIPTION: FMT |
| SAMEA115958304 | latitude | 60.1666 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 60.166641 24.943537 |
| SAMEA115958304 | location_region | Uusimaa | R1 | 0.60 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 60.166641 24.943537 |
| SAMEA115958304 | longitude | 24.9435 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 60.166641 24.943537 |
| SAMEA115958304 | subject_id | B1 | R1 | 0.70 | sample.name_rule:alias | B1x0 |
| SAMEA115958304 | timepoint_label | 0 | R1 | 0.70 | sample.name_rule:alias | B1x0 |
Sequencing
133 runs over 133 samples · mean 1.09 Gbp per run (median 1.01 Gbp, total 145.13 Gbp; 133 runs with a base count) · layout PAIRED 133 · platform ILLUMINA 133 · models Illumina MiSeq (133) · 47% of runs with a Sandpiper profile · first public 2024-08-31
Authors (10)
Hartikainen AK first · Jalanka J · Lahtinen P · Ponsero AJ · Mertsalmi T · Finnegan L · Crispie F · Cotter PD · Arkkila P · Satokari R last
Downloads
PRJEB65418.csv.gz (4.3 KB) · parquet (75.1 KB) — all 133 samples, every field with route and confidence · PRJEB65418_determinations.csv.gz (9.7 KB) — 1,330 evidence rows