FMT for Ulcerative Colitis RCT, Netherlands
89 fecal samples from adults in a double-blind randomized controlled trial in the Netherlands comparing fecal microbiota transplantation from healthy donors to autologous transplantation in patients with ulcerative colitis. machine-written summary
89 samples · 178 runs · NL · Age unknown · 2022 · 5.36 Gbp / sample · cohort Drivers and determinants of strain dynamics follow
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 498 sample values (collection date, country, latitude, longitude, subject id, timepoint) |
| ✓ Abstract / description | 178 sample values (location locality, location site) |
| ○ Full text | read; no usable statement or table · PMC10424414, PMC9499871 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
intervention — arms not resolved
Faecal microbiota transplantation design randomized_controlled_trial · population ulcerative_colitis · FMT via nasoduodenal tube vs autologous (control) in UC, double-blind RCT
“underwent FMT with feces from healthy donors or were given autologous fecal” — abstract:25836986 (study level; per-sample arms are in the intervention column below)
longitudinalFMT donor → recipient — not resolved
24 of 27 people sampled more than once (68 samples; median 3, up to 3 per person) · follow-up median 12 mo (max 12 mo) · median interval between samples 3 mo (time from timepoint labels). Schedule stated by the source: “Samples collected at day 0, day 84 (~12 weeks), and day 365 after transplant, per alias day-offset suffixes (0, 84, 365).”; stated follow-up 12 mo.
Each row is one person (24 shown); dots are samples at days since that person's first sample.
FMT RCT: donor-material samples (TURN_DON_*) sequenced; donor vs autologous origin not separable from archive, no per-sample links emitted.
Genera, mean relative abundance over 87 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 | 89 | 100% | ||||
| country | 89 | 100% | 89 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 71 | 80% | 71 | |||
| collection_date | 89 | 100% | 89 | |||
| detailed_location | 89 | 100% | ||||
| latitude | 89 | 100% | 89 | |||
| location_locality | 89 | 100% | 89 | |||
| location_site | 89 | 100% | 89 | |||
| longitude | 89 | 100% | 89 | |||
| timepoint_label | 71 | 80% | 71 |
- Findings From a Randomized Controlled Trial of Fecal Transplantation for Patients With Ulcerative Colitis. 2015 PMID 25836986 own_data
- Drivers and determinants of strain dynamics following fecal microbiota transplantation. 2022 PMID 36109636 PMC9499871 unsure
- Recipient-independent, high-accuracy FMT-response prediction and optimization in mice and humans. 2023 PMID 37580821 PMC10424414 unsure
Archive description
Longitudinal metagenomic sequencing data for a Randomized-Controlled Trial of Fecal Microbiota Transplantation in ulcerative colitis. For a detailed sample description, see Rosen et al, 2015 (PMID:25836986).
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by opus_adjudicated with confidence 0.75. Assay shotgun_dna.
- host run.scientific_name · “human gut metagenome”
- host study.description · “Randomized-Controlled Trial of Fecal Microbiota Transplantation”
- body site study.title · “Fecal Microbiota Transplantation for Ulcerative Colitis”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA9457539 | collection_date | 2011/2014 | R1 | 0.90 | biosample.attribute:collection_date | 2011/2014 |
| SAMEA9457539 | country | NL | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Netherlands |
| SAMEA9457539 | latitude | 52.0000 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 52 5 |
| SAMEA9457539 | location_locality | Amsterdam | R4 | 0.50 | paper.abstract | at the Academic Medical Center in Amsterdam |
| SAMEA9457539 | location_site | Academic Medical Center | R4 | 0.50 | paper.abstract | performed at the Academic Medical Center in Amsterdam |
| SAMEA9457539 | longitude | 5.0000 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 52 5 |
| SAMEA9457539 | subject_id | 903 | R1 | 0.70 | sample.name_rule:alias | TURN_903-22-0-0 |
| SAMEA9457539 | timepoint_label | day 0 | R1 | 0.70 | sample.name_rule:alias | TURN_903-22-0-0 |
Sequencing
178 runs over 89 samples · mean 2.68 Gbp per run (median 1.08 Gbp, total 476.20 Gbp; 178 runs with a base count) · layout PAIRED 89, SINGLE 89 · platform ILLUMINA 178 · models Illumina HiSeq 4000 (178) · 87% of runs with a Sandpiper profile · first public 2022-04-28
Authors (42)
Rossen NG first · Fuentes S · van der Spek MJ · Tijssen JG · Hartman JH · Duflou A · Löwenberg M · van den Brink GR · Mathus-Vliegen EM · de Vos WM · Zoetendal EG · D'Haens GR · Ponsioen CY last · Schmidt TSB first · Li SS · Maistrenko OM · Akanni W · Coelho LP · Dolai S · Fullam A · Glazek AM · Hercog R · Herrema H · Jung F · Kandels S · Orakov A · Thielemann R · von Stetten M · Van Rossum T · Benes V · Borody TJ · Nieuwdorp M · Bork P last · Shtossel O first · Turjeman S · Riumin A · Goldberg MR · Elizur A · Bekor Y · Mor H · Koren O · Louzoun Y last
Downloads
PRJEB46777.csv.gz (3.4 KB) · parquet (73.9 KB) — all 89 samples, every field with route and confidence · PRJEB46777_determinations.csv.gz (5.3 KB) — 676 evidence rows