FMT for Ulcerative Colitis Fecal Metagenomes, Leiden
209 fecal metagenome samples from a Leiden University Medical Center study of fecal microbiota transplantation (FMT) in ulcerative colitis patients and healthy donors, an intervention study combining drug therapy and FMT. machine-written summary
209 samples · 209 runs · NL · Age unknown · 2024 · 0.29 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 2,060 sample values (collection date, country, health condition, health condition detail, latitude, location locality, location region, longitude) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 209 sample values (location site) · PMC11369067, PMC11836888, PMC12378841, PMC13376552 |
| ○ 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
Non-antibiotic pharmaceutical given as the study intervention (metformin Faecal microbiota transplantation design randomized_controlled_trial · population ulcerative_colitis · Budesonide or placebo pretreatment then 4 FMT infusions from selected donors
“randomly assigned to 3 weeks of budesonide [9 mg] or placebo followed” — abstract:38572716 (study level; per-sample arms are in the intervention column below)
longitudinalFMT donor → recipient — not resolved
25 of 26 people sampled more than once (207 samples; median 9, up to 14 per person) · follow-up median 3 mo (max 2.1 y) · median interval between samples 8 d (time from collection dates).
Each row is one person (25 shown); dots are samples at days since that person's first sample.
Evidence of fmt donor recipient structure.
Genera, mean relative abundance over 186 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 | 209 | 100% | 209 | |||
| health_condition | 209 | 100% | 209 | |||
| subject_id | 208 | 100% | 208 | |||
| collection_date | 209 | 100% | 209 | |||
| detailed_location | 209 | 100% | ||||
| health_condition_detail | 209 | 100% | 209 | |||
| latitude | 209 | 100% | 209 | |||
| location_locality | 209 | 100% | 209 | |||
| location_region | 209 | 100% | 209 | |||
| location_site | 209 | 100% | 209 | |||
| longitude | 209 | 100% | 209 | |||
| timepoint_label | 180 | 86% | 180 |
- Fecal Microbiota Transplantation engraftment after budesonide or placebo in patients with active ulcerative colitis using pre-selected donors: a randomized pilot study. 2024 PMID 38572716 PMC11369067 own_data
- Dynamics of Gut Microbiota After Fecal Microbiota Transplantation in Ulcerative Colitis: Success Linked to Control of Prevotellaceae. 2025 PMID 39225490 PMC11836888 own_data
- Ecological resilience in ulcerative colitis: microbial dynamics of donor and resident species in a longitudinal fecal microbiota transplantation study. 2025 PMID 40873786 PMC12378841 own_data
- Inorganic nitrogen metabolic reprogramming of the gut microbiome drives fecal microbiota transplantation in ulcerative colitis. 2026 PMID 42151161 PMC13376552 own_data
Archive description
Human fecal metagenomic sequences from the FECBUD clinical study conducted at the Leiden University Medical Center.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.70. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.title · “Fecal Metagenomes”
- body site run.scientific_name · “gut metagenome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN39710385 | collection_date | 2020-05-15 | R1 | 0.90 | biosample.attribute:collection_date | 2020-05-15 |
| SAMN39710385 | country | NL | R1 | 0.90 | sample.attr.geo_loc_name | Netherlands:Leiden |
| SAMN39710385 | health_condition | ulcerative_colitis | R1 | 0.85 | biosample.attribute:gastrointest_disord | gastrointest_disord: Ulcerative Colitis |
| SAMN39710385 | health_condition_detail | Ulcerative Colitis | R1 | 0.90 | sample.attr.gastrointest_disord | Ulcerative Colitis |
| SAMN39710385 | latitude | 52.1636 | R1 | 0.90 | biosample.attribute:lat_lon | 52.1636 N 4.4802 E |
| SAMN39710385 | location_locality | Leiden | R1 | 0.85 | biosample.attribute:geo_loc_name | Netherlands:Leiden |
| SAMN39710385 | location_region | South Holland | R1 | 0.60 | biosample.attribute:lat_lon | 52.1636 N 4.4802 E |
| SAMN39710385 | location_site | Department of Gastroenterology, Leiden University Medical Center | R3 | 0.70 | paper.fulltext.methods | treated at the Department of Gastroenterology at Leiden University Medical Center |
| SAMN39710385 | longitude | 4.4802 | R1 | 0.90 | biosample.attribute:lat_lon | 52.1636 N 4.4802 E |
| SAMN39710385 | subject_id | 115 | R1 | 0.70 | sample.name_rule:sample_title | Subject _115_Week 14 |
| SAMN39710385 | timepoint_label | Week 14 | R1 | 0.70 | sample.name_rule:sample_title | Subject _115_Week 14 |
Sequencing
209 runs over 209 samples · mean 0.31 Gbp per run (median 0.29 Gbp, total 64.59 Gbp; 209 runs with a base count) · layout SINGLE 209 · platform ILLUMINA 209 · models Illumina NovaSeq 6000 (209) · 89% of runs with a Sandpiper profile · first public 2024-06-07
Authors (34)
van Lingen E first · Nooij S · Terveer EM · Crossette E · Prince AL · Bhattarai SK · Watson A · Galazzo G · Menon R · Szabady RL · Bucci V · Norman JM · van der Woude CJ · van der Marel S · Verspaget HW · van der Meulen-de Jong AE · Keller JJ last · Pinto S first · Šajbenová D · Benincà E · Bogaards JA · Steyerberg EW last · Wang Y first · Hou Q · Lv X · Liu J · Wang H · Zhao Y · Tong H · Liu Y · Du J · Yang X · Wu S · He S
Downloads
PRJNA1071720.csv.gz (7.2 KB) · parquet (80.1 KB) — all 209 samples, every field with route and confidence · PRJNA1071720_determinations.csv.gz (17.7 KB) — 2,269 evidence rows