Encapsulated FMT in ulcerative colitis, Burlington, Vermont
215 fecal samples from adults with ulcerative colitis in Burlington, Vermont, USA, from a randomized trial comparing colonoscopic FMT plus 12 weeks of daily frozen encapsulated oral FMT versus sham treatment. machine-written summary
215 samples · 215 runs · US · Age unknown · 2019 · 0.80 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 2,308 sample values (country, health condition, health condition detail, intervention, intervention detail, latitude, location locality, location region) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 221 sample values (collection date, health condition, health condition detail) · PMC8268596, PMC8406238 |
| ○ 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 resolved
12 people have samples in more than one arm.
Faecal microbiota transplantation design randomized_controlled_trial · population ulcerative_colitis · Colonoscopy FMT induction + 12wk daily encapsulated oral FMT vs sham
“randomized 1:1 to receive FMT induction” — abstract:34238227 (study level; per-sample arms are in the intervention column below)
longitudinalFMT donor → recipient — not resolved
14 of 14 people sampled more than once (212 samples; median 16, up to 22 per person) · follow-up median 5 mo (max 5 mo) · median interval between samples 7 d (time from visit codes mapped to the stated schedule). Schedule stated by the source: “Stool collected weekly from before antibiotic pretreatment through 18-week follow-up; clinic visits/blood at baseline and weeks 4, 8, 12, 18, 36” (time origin: transplant); stated follow-up 8 mo.
Each row is one person (12 shown of 14); dots are samples at days since that person's first sample.
2 stool donors (Donor am, Donor az) sampled; FMT-arm patients received capsule/colonoscopic material from them.
Genera, mean relative abundance over 190 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 | 215 | 100% | ||||
| country | 215 | 100% | 215 | |||
| health_condition | 215 | 100% | 212 | 3 | ||
| subject_id | 212 | 99% | 212 | |||
| collection_date | 215 | 100% | 215 | |||
| detailed_location | 215 | 100% | ||||
| health_condition_detail | 215 | 100% | 212 | 3 | ||
| latitude | 215 | 100% | 215 | |||
| location_locality | 215 | 100% | 215 | |||
| location_region | 215 | 100% | 215 | |||
| longitude | 215 | 100% | 215 | |||
| intervention | 199 | 93% | 199 | |||
| intervention_detail | 199 | 93% | 199 | |||
| timepoint_label | 199 | 93% | 199 |
- Daily, oral FMT for long-term maintenance therapy in ulcerative colitis: results of a single-center, prospective, randomized pilot study. 2021 PMID 34238227 PMC8268596 own_data
- Dynamic Colonization of Microbes and Their Functions after Fecal Microbiota Transplantation for Inflammatory Bowel Disease. 2021 PMID 34281401 PMC8406238 own_data
Archive description
Data generated from a thorough characterization of the host and gut microbiome response to fecal transplant in a small cohort of ulcerative colitis patients. The aims were to establish the downstream effects of fecal transplant on the gut microbiome, stool and blood metabolome, and the local and systemic immune system.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.68. Assay shotgun_dna.
- host run.scientific_name · “human gut metagenome(215)”
- body site study.title · “Fecal transplant for ulcerative colitis”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN11654460 | collection_date | 2016-02/2017-09 | R3 | 0.60 | paper.fulltext.results | From February 2016 to September 2017, 154 UC patients were assessed |
| SAMN11654460 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA:Vermont,Burlington |
| SAMN11654460 | health_condition | ulcerative_colitis | R1 | 0.85 | biosample.attribute:patient_pub | patient_pub: FMT N |
| SAMN11654696 | health_condition | ulcerative_colitis | R3 | 0.70 | paper.fulltext.abstract | Twelve subjects with active UC were randomized |
| SAMN11654460 | health_condition_detail | FMT N | R1 | 0.85 | biosample.attribute:patient_pub | patient_pub: FMT N |
| SAMN11654696 | health_condition_detail | active ulcerative colitis undergoing FMT trial | R3 | 0.70 | paper.fulltext.abstract | Twelve subjects with active UC were randomized |
| SAMN11654460 | intervention | no_intervention | R1 | 0.80 | biosample.attribute:days_past_fmt | days_past_fmt: -7 |
| SAMN11654463 | intervention | fmt | R1 | 0.90 | biosample.attribute:treatment | treatment: fmt |
| SAMN11654460 | intervention_detail | days_past_fmt = -7 (before intervention start); assigned arm: FMT treatment arm | R1 | 0.80 | biosample.attribute:days_past_fmt | days_past_fmt: -7 |
| SAMN11654463 | intervention_detail | FMT treatment arm | R1 | 0.90 | biosample.attribute:treatment | treatment: fmt |
| SAMN11654460 | latitude | 44.4759 | R1 | 0.90 | biosample.attribute:lat_lon | 44.4759 N 73.2121 W |
| SAMN11654460 | location_locality | Burlington | R1 | 0.85 | biosample.attribute:geo_loc_name | USA:Vermont,Burlington |
| SAMN11654460 | location_region | Vermont | R1 | 0.85 | biosample.attribute:geo_loc_name | USA:Vermont,Burlington |
| SAMN11654460 | longitude | -73.2121 | R1 | 0.90 | biosample.attribute:lat_lon | 44.4759 N 73.2121 W |
| SAMN11654460 | subject_id | FMT N | R1 | 0.85 | biosample.attribute:patient_pub | patient_pub: FMT N |
| SAMN11654460 | timepoint_label | -7 | R1 | 0.85 | sample.attr.days_past_fmt | -7 |
Sequencing
215 runs over 215 samples · mean 1.12 Gbp per run (median 0.80 Gbp, total 241.73 Gbp; 215 runs with a base count) · layout PAIRED 215 · platform ILLUMINA 215 · models NextSeq 500 (215) · 88% of runs with a Sandpiper profile · first public 2019-10-02
Authors (24)
Crothers JW first · Chu ND · Nguyen LTT · Phillips M · Collins C · Fortner K · Del Rio-Guerra R · Lavoie B · Callas P · Velez M · Cohn A · Elliott RJ · Wong WF · Vo E · Wilcox R · Smith M · Kassam Z · Budd R · Alm EJ · Mawe GM · Moses PL last · Kearney SM · Smith MB · Xavier R
Downloads
PRJNA475599.csv.gz (7.1 KB) · parquet (79.7 KB) — all 215 samples, every field with route and confidence · PRJNA475599_determinations.csv.gz (19.0 KB) — 2,529 evidence rows