FMT for recurrent C. diff and IBD, Stony Brook trial
118 stool samples from donors and recipients (rCDI, rCDI+IBD, UC, or CD) in two single-arm FMT clinical trials at Stony Brook University Medical Center, collected pre-FMT, 1 week, and 3 months post-FMT. machine-written summary
118 samples · 118 runs · Age unknown · 2022 · 6.53 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 118 sample values (subject id) |
| ✓ Abstract / description | 354 sample values (collection date, health condition detail, location site) |
| ○ Full text | read; no usable statement or table · PMC9817289 |
| ○ 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 · population ibd_or_gi_disease · Single colonoscopic FMT, pre/1wk/3mo post, rCDI and/or IBD
“single colonoscopic FMT on microbial composition and function” — abstract:36618438 (study level; per-sample arms are in the intervention column below)
longitudinal — not resolvedFMT donor → recipient — not resolved
33 of 34 people sampled more than once (117 samples; median 4, up to 4 per person). Schedule stated by the source: “Stool collected pre-FMT, 1 week post-FMT, and 3 months post-FMT from each recipient; donor stool collected for transplant” (time origin: FMT procedure); stated follow-up 3 mo.
55 FMT donor-recipient pairs: 27 rCDI, 8 rCDI+IBD, 11 UC, 9 CD recipients paired with healthy donors.
Genera, mean relative abundance over 106 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 | 118 | 100% | ||||
| country | 0 | 0% | ||||
| health_condition | 0 | 0% | ||||
| subject_id | 118 | 100% | 118 | |||
| collection_date | 118 | 100% | 118 | |||
| detailed_location | 118 | 100% | ||||
| health_condition_detail | 118 | 100% | 118 | |||
| location_site | 118 | 100% | 118 |
- Metagenomic and bile acid metabolomic analysis of fecal microbiota transplantation for recurrent Clostridiodes difficile and/or inflammatory bowel diseases. 2022 PMID 36618438 PMC9817289 own_data
Archive description
This project has parallel 16S V3V4 rRNA gene sequencing and shotgun DNA sequencing data generated from human stool samples collected during two colonoscopic single donor fecal microbial transplant clinical trials conducted at Stony Brook University Medical Center (2015 -2019). These trials included: 1.) recipients with recurrent C. difficile (rCDI) infections and or ulcerative colitis (UC) without rCDI [ClinicalTrials.gov ID:NCT03268213, 479696, UC only Investigational New Drug (IND) 15642] and 2.) Crohn's disease (CD) without rCDI). For each FMT in these clinical trials, stools were collected from each paired healthy donor, who was prescreened for pathogens and antibiotic resistant organisms, to be transplanted into four groups of recipients: 1.) rCDI no IBD, n = 27 2.) rCDI + IBD, n = 8 3.) UC no rCDI, n = 11 4.)CD no rCDI, n =9. From each recipient, stools were collected before the procedure (pre-FMT), 1 week after (1 wk post-FMT), and 3 months after (3 mo post-FMT).
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.72. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- host study.description · “human stool samples collected during”
- body site study.description · “stools were collected from each”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN19775068 | collection_date | 2015/2019 | R4 | 0.45 | ena.study_description | clinical trials conducted at Stony Brook University Medical Center (2015 -2019) |
| SAMN19775068 | health_condition_detail | mixed_case_control: recipients with rCDI and/or IBD (UC or CD) vs healthy donors | R4 | 0.50 | study.title | recurrent C. difficile and or IBD |
| SAMN19775068 | location_site | Stony Brook University Medical Center | R4 | 0.45 | ena.study_description | conducted at Stony Brook University Medical Center |
| SAMN19775068 | subject_id | FMT-1 | R1 | 0.70 | sample.name_rule:experiment_title | HiSeq X Ten sequencing: FMT-1 R_Pre-Transpl |
Sequencing
118 runs over 118 samples · mean 6.28 Gbp per run (median 6.53 Gbp, total 740.58 Gbp; 118 runs with a base count) · layout PAIRED 118 · platform ILLUMINA 118 · models HiSeq X Ten (118) · 90% of runs with a Sandpiper profile · first public 2022-01-01
Authors (21)
Ramos RJ first · Zhu C · Joseph DF · Thaker S · Lacomb JF · Markarian K · Lee HJ · Petrov JC · Monzur F · Buscaglia JM · Chawla A · Small-Harary L · Gathungu G · Morganstern JA · Yang J · Li J · Pamer EG · Robertson CE · Frank DN · Cross JR · Li E last
Help complete this project
2 of the 4 core fields are below 50% coverage: country, health_condition. Share metadata
Downloads
PRJNA739170.csv.gz (3.8 KB) · parquet (74.0 KB) — all 118 samples, every field with route and confidence · PRJNA739170_determinations.csv.gz (3.9 KB) — 472 evidence rows