Ulcerative colitis FMT donor & patient gut metagenomes (US)
59 fecal metagenome samples from a US fecal microbiota transplantation (FMT) study in active ulcerative colitis patients, collected before and 4 weeks after FMT, plus samples from the 2 donor fecal preparations used. machine-written summary
59 samples · 59 runs · US · Age unknown · 2021 · 22.04 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 470 sample values (collection date, country, health condition, health condition detail, intervention, latitude, location region, longitude) |
| ✓ Abstract / description | 40 sample values (health condition, health condition detail) |
| ○ Full text | read; no usable statement or table · PMC8678328 |
| – Supplementary tables | no supplementary tables available (or none open access) |
| – 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 single_arm_before_after · population ulcerative_colitis · Fecal microbiota transplantation, 2-donor preparation, sampled pre- and week 4 post-FMT
“before fecal microbiota transplantation (FMT)” — bioproject.description (study level; per-sample arms are in the intervention column below)
longitudinalFMT donor → recipient
19 of 20 people sampled more than once (38 samples; median 2, up to 2 per person) · follow-up median 41 d (max 56 d) · median interval between samples 41 d (time from collection dates).
Each row is one person (19 shown); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 51 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 | 59 | 100% | 59 | |||
| health_condition | 59 | 100% | 39 | 20 | ||
| subject_id | 39 | 66% | 39 | |||
| detailed_location | 59 | 100% | ||||
| health_condition_detail | 59 | 100% | 39 | 20 | ||
| latitude | 59 | 100% | 59 | |||
| location_region | 59 | 100% | 59 | |||
| longitude | 59 | 100% | 59 | |||
| collection_date | 39 | 66% | 39 | |||
| intervention | 39 | 66% | 39 | |||
| timepoint_label | 39 | 66% | 39 |
- Transferable Immunoglobulin A-Coated Odoribacter splanchnicus in Responders to Fecal Microbiota Transplantation for Ulcerative Colitis Limits Colonic Inflammation. 2022 PMID 34606847 PMC8678328 own_data
Archive description
Fecal samples were collected from 20 patients diagnosed with active ulcerative colitis (UC, Mayo score >= 3 and an endoscopic subscore >= 1) before fecal microbiota transplantation (FMT) and at week 4 post-FMT. Samples from the 2-donor fecal preparation used to treat the 20 UC patients were also collected and subjected to metagenomic shotgun sequencing.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.65. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.description · “Fecal samples were collected from 20 patients”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN22039206 | collection_date | 2015-08-27 | R1 | 0.90 | biosample.attribute:collection_date | 2015-08-27 |
| SAMN22039205 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA |
| SAMN22039206 | health_condition | ulcerative_colitis | R1 | 0.90 | biosample_attr | UC |
| SAMN22039205 | health_condition | ulcerative_colitis | R4 | 0.50 | study.description | patients diagnosed with active ulcerative colitis |
| SAMN22039206 | health_condition_detail | UC | R1 | 0.90 | sample.attr.host_disease | UC |
| SAMN22039205 | health_condition_detail | active ulcerative colitis, Mayo score >= 3, endoscopic subscore >= 1 | R4 | 0.50 | study.description | active ulcerative colitis (UC, Mayo score >= 3 and an endoscopic subscore |
| SAMN22039206 | intervention | no_intervention | R1 | 0.70 | sample.name_rule:source_material_id | Patient.1.PRE |
| SAMN22039205 | latitude | 40.7655 | R1 | 0.90 | biosample.attribute:lat_lon | 40.7655 N 73.9550 W |
| SAMN22039205 | location_region | New York | R1 | 0.60 | biosample.attribute:lat_lon | 40.7655 N 73.9550 W |
| SAMN22039205 | longitude | -73.9550 | R1 | 0.90 | biosample.attribute:lat_lon | 40.7655 N 73.9550 W |
| SAMN22039206 | subject_id | Patient_1 | R1 | 0.70 | sample.name_rule:source_material_id | Patient.1.PRE |
| SAMN22039206 | timepoint_label | baseline | R1 | 0.70 | sample.name_rule:source_material_id | Patient.1.PRE |
Sequencing
59 runs over 59 samples · mean 22.71 Gbp per run (median 22.04 Gbp, total 1,339.98 Gbp; 59 runs with a base count) · layout PAIRED 59 · platform ILLUMINA 59 · models Illumina HiSeq 2500 (59) · 86% of runs with a Sandpiper profile · first public 2021-11-01
Authors (0)
No author record.
Downloads
PRJNA768409.csv.gz (2.6 KB) · parquet (72.8 KB) — all 59 samples, every field with route and confidence · PRJNA768409_determinations.csv.gz (4.1 KB) — 510 evidence rows