FMT for active Crohn's disease, USA, open-label study
53 stool samples from USA patients with Crohn's disease, collected before and after a single fecal microbiota transplant from healthy donors via colonoscopy, in an uncontrolled, prospective open-label study. machine-written summary
53 samples · 53 runs · US · Age unknown · 2016 · 4.66 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 253 sample values (country, health condition, health condition detail, subject id, timepoint) |
| ✓ Abstract / description | 8 sample values (health condition, health condition detail) |
| ○ Full text | read; no usable statement or table · PMC11009399, PMC12180181, PMC12239758, PMC12268991, PMC12940132, PMC6759048, PMC7248251 |
| ○ 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
Faecal microbiota transplantation design single_arm_before_after · population crohns_disease · Single FMT via colonoscopy from healthy donors to active CD patients
“A single FMT was performed via colonoscopy” — bioproject.description (study level; per-sample arms are in the intervention column below)
longitudinalFMT donor → recipient — not resolved
18 of 22 people sampled more than once (49 samples; median 3, up to 3 per person) · follow-up median 28 d (max 28 d) · median interval between samples 28 d (time from timepoint labels). Schedule stated by the source: “Stool collected pre-FMT, 4 weeks after FMT, and 8 weeks after FMT in recipients; clinical follow-up 12 weeks, safety follow-up 26 weeks.” (time origin: FMT); stated follow-up 6 mo.
Each row is one person (3 shown of 18); dots are samples at days since that person's first sample.
FMT from healthy donors (D9001-D9005) to Crohn's disease recipients (R1001-R1022); donor->recipient mapping not in metadata.
Genera, mean relative abundance over 49 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 | 53 | 100% | 53 | |||
| health_condition | 53 | 100% | 49 | 4 | ||
| subject_id | 53 | 100% | 53 | |||
| health_condition_detail | 53 | 100% | 49 | 4 | ||
| timepoint_label | 49 | 92% | 49 |
- Impact of Microbiota Transplant on Resistome of Gut Microbiota in Gnotobiotic Piglets and Human Subjects. 2020 PMID 32508773 PMC7248251 own_data
- Microbial genes and pathways in inflammatory bowel disease. 2019 PMID 31249397 PMC6759048 unsure
- Plasmids in the human gut reveal neutral dispersal and recombination that is overpowered by inflammatory diseases. 2024 PMID 38605009 PMC11009399 unsure
- A meta-analysis of the gut microbiome in inflammatory bowel disease patients identifies disease-associated small molecules. 2025 PMID 39947133 PMC12268991 unsure
- Engrafting gut bacteriophages have potential to modulate microbial metabolism in fecal microbiota transplantation. 2025 PMID 40542451 PMC12180181 unsure
3 more
- Constructing inflammatory bowel disease diagnostic models based on k-mer and machine learning. 2025 PMID 40636504 PMC12239758
- Temporal dynamics of gut biosynthetic gene clusters link persistent colonization and engraftment in fecal microbiota transplantation. 2026 PMID 41741396 PMC12940132
- Plasmid dispersal and recombination across human gut microbiomes is neutral, but overpowered by inflammatory diseases 2023
Archive description
This is an uncontrolled, prospective open-label study of FMT from healthy donors to subjects with active CD. A single FMT was performed via colonoscopy. Stool samples were collected prior to FMT and at two time points, four and eight weeks after FMT. Recipients’ microbial diversity, mucosal T-cell phenotypes and clinical and inflammatory parameters were measured over 12 weeks, and safety over 26 weeks.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.85. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.description · “Stool samples were collected prior to FMT”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN05065727 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA |
| SAMN05065727 | health_condition | crohns_disease | R1 | 0.85 | biosample.attribute:gastroinstest_disord | gastroinstest_disord: Crohn's disease |
| SAMN05065738 | health_condition | crohns_disease | R4 | 0.50 | study.description | subjects with active CD |
| SAMN05065727 | health_condition_detail | Crohn's disease | R1 | 0.90 | sample.attr.gastroinstest_disord | Crohn's disease |
| SAMN05065738 | health_condition_detail | Active Crohn's disease | R4 | 0.50 | study.description | subjects with active CD |
| SAMN05065727 | subject_id | R1004 | R1 | 0.85 | sample.attr.host_subject_id | R1004 |
| SAMN05065727 | timepoint_label | pre-FMT | R1 | 0.85 | sample.attr.time_point | pre-FMT |
Sequencing
53 runs over 53 samples · mean 4.80 Gbp per run (median 4.66 Gbp, total 254.49 Gbp; 53 runs with a base count) · layout PAIRED 53 · platform ILLUMINA 53 · models Illumina HiSeq 2500 (53) · 92% of runs with a Sandpiper profile · first public 2016-05-31
Authors (40)
Liu H first · Wang HH last · Elmassry MM first · Sugihara K · Chankhamjon P · Kim Y · Camacho FR · Wang S · Sugimoto Y · Chatterjee S · Chen LA · Kamada N · Donia MS last · Ji S first · Ahmad F · Peng B · Yang Y · Su M · Zhao X · Vatanen T last · Li L first · Liu Z · Qin J · Xiong G · Yang C · Cai F · Huang J last · Garcia-Guevara F first · Resink T · Clasen F · Uhlén M · Achour A · Shoaie S last · Mizrahi I first · Zorea A · Pellow D · Levin L · Pilosof S · Friedman J · Shamir R last
Downloads
PRJNA321058.csv.gz (2.3 KB) · parquet (71.0 KB) — all 53 samples, every field with route and confidence · PRJNA321058_determinations.csv.gz (2.0 KB) — 261 evidence rows