Fecal microbiome in ICI-induced colitis with FMT, New York
69 fecal samples from patients with immune-checkpoint-inhibitor-induced colitis in New York, USA, including some treated with fecal microbiota transplantation, in a case-control study. machine-written summary
69 samples · 69 runs · US · Age unknown · 2023 · 6.30 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 423 sample values (country, intervention, intervention detail, latitude, location region, longitude, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 69 sample values (location site) · PMC10932930, PMC11636624 |
| ○ 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 single_arm_before_after · Healthy-donor fecal microbiota transplantation for refractory immune-related colitis
“received healthy-donor FMT” — abstract:38108398 (study level; per-sample arms are in the intervention column below)
longitudinal — not resolvedFMT donor → recipient — not resolved
1 of 58 people sampled more than once (2 samples; median 2, up to 2 per person). Schedule stated by the source: “Repeated stool samples per patient relative to colitis onset (day_relative_to_onset) and relative to first FMT (day_relative_to_fmt1), from -13 to 250 days” (time origin: fmt); stated follow-up 8 mo.
5 irColitis patients given healthy-donor FMT; donor samples sequenced but donor->recipient mapping not in metadata.
Genera, mean relative abundance over 60 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 | 69 | 100% | 69 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 59 | 86% | 59 | |||
| detailed_location | 69 | 100% | ||||
| latitude | 69 | 100% | 69 | |||
| location_region | 69 | 100% | 69 | |||
| location_site | 69 | 100% | 69 | |||
| longitude | 69 | 100% | 69 | |||
| timepoint_label | 60 | 87% | 60 | |||
| intervention | 14 | 20% | 14 | |||
| intervention_detail | 14 | 20% | 14 |
- Immune-Related Colitis Is Associated with Fecal Microbial Dysbiosis and Can Be Mitigated by Fecal Microbiota Transplantation. 2024 PMID 38108398 PMC10932930 own_data
- Baseline colitogenicity and acute perturbations of gut microbiota in immunotherapy-related colitis. 2025 PMID 39666007 PMC11636624 unsure
Archive description
Fecal microbiota profiling of patients with immune-related colitis
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.57. Assay shotgun_dna.
- host run.scientific_name · “human gut metagenome”
- body site study.title · “Fecal microbiota profiling”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN34353381 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: New York |
| SAMN34353428 | intervention | no_intervention | R1 | 0.80 | biosample.attribute:day_relative_to_fmt1 | day_relative_to_fmt1: -6 |
| SAMN34353428 | intervention_detail | day_relative_to_fmt1 = -6 (before intervention start) | R1 | 0.80 | biosample.attribute:day_relative_to_fmt1 | day_relative_to_fmt1: -6 |
| SAMN34353381 | latitude | 40.7641 | R1 | 0.90 | biosample.attribute:lat_lon | 40.7641 N 73.9568 W |
| SAMN34353381 | location_region | New York | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: New York |
| SAMN34353381 | location_site | Memorial Sloan Kettering Cancer Center | R3 | 0.70 | paper.fulltext.methods | prospectively enrolled at the Memorial Sloan Kettering Cancer Center (MSK) |
| SAMN34353381 | longitude | -73.9568 | R1 | 0.90 | biosample.attribute:lat_lon | 40.7641 N 73.9568 W |
| SAMN34353381 | subject_id | colitis_001 | R1 | 0.85 | biosample.attribute:col_id | colitis_001 |
| SAMN34353381 | timepoint_label | day -1 relative to onset | R1 | 0.85 | biosample.attribute:day_relative_to_onset | -1 |
| SAMN34353428 | timepoint_label | -6 | R1 | 0.85 | sample.attr.day_relative_to_fmt1 | -6 |
Sequencing
69 runs over 69 samples · mean 5.69 Gbp per run (median 6.30 Gbp, total 392.94 Gbp; 69 runs with a base count) · layout PAIRED 69 · platform ILLUMINA 69 · models Illumina HiSeq 4000 (69) · 87% of runs with a Sandpiper profile · first public 2023-05-05 – 2023-06-05
Authors (45)
Elkrief A first · Waters NR · Smith N · Dai A · Slingerland J · Aleynick N · Febles B · Gogia P · Socci ND · Lumish M · Giardina PA · Chaft JE · Eng J · Motzer RJ · Mendelsohn RB · Markey KA · Zhuang M · Li Y · Yang Z · Hollmann TJ · Rudin CM · van den Brink MRM · Shia J · DeWolf S · Schoenfeld AJ · Hellmann MD · Babady NE · Faleck DM · Peled JU last · Shang J first · Del Valle DM · Britton GJ · Mead KR · Rajpal U · Chen-Liaw A · Mogno I · Li Z · Menon R · Gonzalez-Kozlova E · Gonsalves TR · Shah NJ · Postow M · Colombel JF · Gnjatic S · Faith JJ last
Help complete this project
2 of the 4 core fields are below 50% coverage: age_category, health_condition. Share metadata
Downloads
PRJNA961175.csv.gz (3.1 KB) · parquet (74.3 KB) — all 69 samples, every field with route and confidence · PRJNA961175_determinations.csv.gz (4.5 KB) — 492 evidence rows