Pediatric UC gut microbiome before/after FMT, Michigan
12 stool samples from children in Michigan, USA, including ulcerative colitis patients and healthy controls, studied in a fecal microbiota transplantation (FMT) intervention design. machine-written summary
12 samples · 12 runs · US · Child · 2018 · 0.35 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 108 sample values (collection date, country, health condition, health condition detail, intervention, latitude, location region, longitude) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC11650326, PMC12180181, PMC6454419, PMC9927247 |
| ✓ Supplementary tables | 4 sample values (subject id) |
| ✓ External resources | 8 sample values (health condition, health condition detail) · from GMrepo v3 |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
intervention · arms resolved
4 people have samples in more than one arm.
Faecal microbiota transplantation design single_arm_before_after · population ulcerative_colitis · Fecal microbiota transplantation in pediatric ulcerative colitis
“before and after fecal microbiota transplantation” — bioproject.description (study level; per-sample arms are in the intervention column below)
longitudinal — not resolvedFMT donor → recipient
4 of 8 people sampled more than once (8 samples; median 2, up to 2 per person). Schedule stated by the source: “stool samples collected before and after FMT (Baseline and PostFMT) from each patient, plus Donor sample” (time origin: intervention_start).
FMT in 4 paediatric UC responders: each with own donor stool, baseline and post-FMT samples.
donorrecipient · circles are people (pale = no sequenced sample), arrows run donor → recipient and parent → child, curved lines join twins, partners and siblings, squares are shared settings or families without recorded roles. Shown: 4 linked groups from explicit relations. 8 people in the project overall.
Genera, mean relative abundance over 10 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 | 12 | 100% | ||||
| country | 12 | 100% | 12 | |||
| health_condition | 12 | 100% | 8 | 4 | ||
| subject_id | 12 | 100% | 8 | 4 | ||
| collection_date | 12 | 100% | 12 | |||
| detailed_location | 12 | 100% | ||||
| health_condition_detail | 12 | 100% | 8 | 4 | ||
| intervention | 12 | 100% | 12 | |||
| latitude | 12 | 100% | 12 | |||
| location_region | 12 | 100% | 12 | |||
| longitude | 12 | 100% | 12 | |||
| timepoint_label | 12 | 100% | 12 |
- Gut microbial and metabolomic profiles after fecal microbiota transplantation in pediatric ulcerative colitis patients. 2018 PMID 30010747 PMC6454419 own_data
- A Matching Strategy To Guide Donor Selection for Ulcerative Colitis in Fecal Microbiota Transplantation: Meta-Analysis and Analytic Hierarchy Process. 2023 PMID 36472435 PMC9927247 unsure
- Gut-microbiota-based ensemble model predicts prognosis of pediatric inflammatory bowel disease. 2024 PMID 39691780 PMC11650326 unsure
- Engrafting gut bacteriophages have potential to modulate microbial metabolism in fecal microbiota transplantation. 2025 PMID 40542451 PMC12180181 unsure
Archive description
Gut microbial profiles from 7 children with ulcerative colitis were characterized by 16S rRNA gene sequencing before and after fecal microbiota transplantation.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of child by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage reason_code age_child_over_36m”
- body site study.title · “Gut microbial profiles after”
- body site study.description · “Gut microbial profiles from”
- life stage external_curation.infant_catalog · “infant triage reason_code age_child_over_36m”
- life stage study.title · “microbiota transplantation in pediatric ulcerative colitis patients”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN08707421 | collection_date | 2012 | R1 | 0.90 | biosample.attribute:collection_date | 2012 |
| SAMN08707421 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: Michigan |
| SAMN08707422 | health_condition | ulcerative_colitis | R1 | 0.85 | biosample.attribute:category | category: Baseline |
| SAMN08707423 | health_condition | ulcerative_colitis | R1 | 0.80 | biosample_attr | PostFMT |
| SAMN08707421 | health_condition | healthy_control | R2 | 0.75 | external.gmrepo source | phenotype: Health |
| SAMN08707422 | health_condition_detail | Baseline | R1 | 0.85 | biosample.attribute:category | category: Baseline |
| SAMN08707421 | health_condition_detail | Health | R2 | 0.75 | external.gmrepo source | phenotype: Health |
| SAMN08707421 | intervention | no_intervention | R1 | 0.85 | biosample.attribute:category | category: Donor |
| SAMN08707421 | latitude | 42.5800 | R1 | 0.90 | biosample.attribute:lat_lon | 42.58 N 85.39 W |
| SAMN08707421 | location_region | Michigan | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: Michigan |
| SAMN08707421 | longitude | -85.3900 | R1 | 0.90 | biosample.attribute:lat_lon | 42.58 N 85.39 W |
| SAMN08707422 | subject_id | Responder 1 | R1 | 0.85 | sample.attr.subject | Responder 1 |
| SAMN08707421 | subject_id | Responder 1 donor | R2 | 0.80 | archive | |
| SAMN08707421 | timepoint_label | Donor | R1 | 0.85 | biosample.attribute:category | category: Donor |
Sequencing
12 runs over 12 samples · mean 0.36 Gbp per run (median 0.35 Gbp, total 4.33 Gbp; 12 runs with a base count) · layout PAIRED 12 · platform ILLUMINA 12 · models NextSeq 500 (12) · 83% of runs with a Sandpiper profile · first public 2018-03-22
Authors (46)
Nusbaum DJ first · Sun F · Ren J · Zhu Z · Ramsy N · Pervolarakis N · Kunde S · England W · Gao B · Fiehn O · Michail S · Whiteson K last · Zhang B first · Yang L · Ning H · Cao M · Chen Z · Chen Q · Lian G · Tang H · Wang Q · Wang J · Lin Z · Wen J · Liu Y · Xuan J · Li X · Lin A · He J · Zhang L · Hou X · Zeng Q · Xiao C last · Ha SM first · Lee K · Kim GH · Hurych J · Cinek O · Shim JO last · Ji S first · Ahmad F · Peng B · Yang Y · Su M · Zhao X · Vatanen T last
Downloads
PRJNA438164.csv.gz (1.3 KB) · parquet (70.8 KB) — all 12 samples, every field with route and confidence · PRJNA438164_determinations.csv.gz (1.9 KB) — 120 evidence rows