Shotgun metagenomics of FMT in active ulcerative colitis
284 fecal samples from adults with active ulcerative colitis, collected in a randomized controlled trial of faecal microbiota transplantation, used to identify bacterial and phage determinants of treatment outcome. machine-written summary
284 samples · 284 runs · Adult · 2018 · 1.71 Gbp / sample · cohort Fungal Trans-kingdom Dynamics Linked to Responsive
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ○ Sequence archive | records read; no usable sample values |
| ✓ Abstract / description | 568 sample values (health condition, health condition detail) |
| ○ Full text | read; no usable statement or table · PMC11487140, PMC12547691, PMC12710892, PMC8647676 |
| ○ 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 · share metadata |
| – 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 (donor faecal microbiota) vs placebo in FOCUS trial for active UC
“randomised, controlled FOCUS Study of FMT” — bioproject.description (study level; per-sample arms are in the intervention column below)
FMT donor → recipient — not resolved
Evidence of fmt donor recipient structure.
Genera, mean relative abundance over 259 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 | 284 | 100% | ||||
| country | 0 | 0% | ||||
| health_condition | 284 | 100% | 284 | |||
| subject_id | 0 | 0% | ||||
| health_condition_detail | 284 | 100% | 284 |
- Fungal Trans-kingdom Dynamics Linked to Responsiveness to Fecal Microbiota Transplantation (FMT) Therapy in Ulcerative Colitis. 2020 PMID 32298656 PMC8647676 unsure
- The phageome of patients with ulcerative colitis treated with donor fecal microbiota reveals markers associated with disease remission. 2024 PMID 39420033 PMC11487140 unsure
- Gut microbiota strain richness is species specific and affects engraftment. 2025 PMID 39604726 PMC12547691 unsure
- Cohort-specific determinants of donor strain engraftment following multi-donor faecal microbiota transplantation in two randomised clinical trials. 2025 PMID 41378445 PMC12710892 unsure
Archive description
Faecal Microbiota Transplantation (FMT) effectively induces remission in ulcerative colitis (UC). In the randomised, controlled FOCUS Study of FMT in active UC we aimed to identify the bacterial taxonomic and functional determinants of therapeutic outcome.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- body site study.title · “OF OUTCOME IN FAECAL MICROBIOTA TRANSPLANTATION FOR”
- body site study.description · “Faecal Microbiota Transplantation (FMT)”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA4672320 | health_condition | ulcerative_colitis | R4 | 0.50 | study.title | ACTIVE ULCERATIVE COLITIS |
| SAMEA4672320 | health_condition_detail | active ulcerative colitis | R4 | 0.50 | study.title | ACTIVE ULCERATIVE COLITIS |
Sequencing
284 runs over 284 samples · mean 1.72 Gbp per run (median 1.71 Gbp, total 487.65 Gbp; 284 runs with a base count) · layout PAIRED 284 · platform ILLUMINA 284 · models Illumina HiSeq 2500 (284) · 92% of runs with a Sandpiper profile · first public 2018-12-18
Authors (43)
Leonardi I first · Paramsothy S · Doron I · Semon A · Kaakoush NO · Clemente JC · Faith JJ · Borody TJ · Mitchell HM · Colombel JF · Kamm MA · Iliev ID last · Majzoub ME first · Haifer C · Parthasarathy R · Leong RW · Chen-Liaw A first · Aggarwala V · Mogno I · Li Z · Eggers J · Helmus D · Hart A · Wehkamp J · Lamousé-Smith ESN · Kerby RL · Rey FE · Olle B · Norman JM · Menon R · Watson AR · Crossette E · Terveer EM · Keller JJ · Grinspan A · Dubinsky MC · Behling AH first · Portlock T · Ho D · Wilson BC · Cutfield WS · O'Sullivan JM · Vatanen T last
Help complete this project
2 of the 4 core fields are below 50% coverage: country, subject_id. Share metadata
Downloads
PRJEB26357.csv.gz (6.9 KB) · parquet (78.8 KB) — all 284 samples, every field with route and confidence · PRJEB26357_determinations.csv.gz (2.4 KB) — 568 evidence rows