FMT in UC patients, Bacteroidetes engraftment, Massachusetts
72 gut metagenome samples from an intervention study in Massachusetts, USA, involving patients with inflammatory bowel disease (IBD) treated with fecal microbiota transplant (FMT). machine-written summary
72 samples · 72 runs · US · Age unknown · 2019 · 76.5 Mbp / sample · cohort Invertible promoters mediate bacterial phase varia
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 504 sample values (collection date, country, latitude, location region, longitude, subject id, timepoint) |
| ✓ Abstract / description | 144 sample values (health condition, health condition detail) |
| ○ Full text | read; no usable statement or table · PMC6543533 |
| – Supplementary tables | no supplementary tables available (or none open access) |
| – 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 ulcerative_colitis · Endoscopic FMT then oral capsule maintenance for 12 weeks
“treated initially with endoscopic FMT” — bioproject.description (study level; per-sample arms are in the intervention column below)
longitudinal
4 of 4 people sampled more than once (72 samples; median 18, up to 22 per person) · follow-up median 5 mo (max 5 mo) · median interval between samples 7 d (time from collection dates). Schedule stated by the source: “Before FMT (day 1) and after FMT at multiple timepoints (e.g. days 5,12,21,27,30,35,40,48,130,138,145) through 12-week oral capsule maintenance”.
Each row is one person (4 shown); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 24 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 | 72 | 100% | 72 | |||
| health_condition | 72 | 100% | 72 | |||
| subject_id | 72 | 100% | 72 | |||
| collection_date | 72 | 100% | 72 | |||
| detailed_location | 72 | 100% | ||||
| health_condition_detail | 72 | 100% | 72 | |||
| latitude | 72 | 100% | 72 | |||
| location_region | 72 | 100% | 72 | |||
| longitude | 72 | 100% | 72 | |||
| timepoint_label | 72 | 100% | 72 |
- Invertible promoters mediate bacterial phase variation, antibiotic resistance, and host adaptation in the gut. 2019 PMID 30630933 PMC6543533 unsure
Archive description
We performed an FMT study where Patients with UC were selectively enrolled and treated initially with endoscopic FMT and then take the oral capsules with fecal microbiota for maintenance for 12 weeks. This project provides alignments of the metagenomic samples from the FMT study to Bacteroides fragilis, Bacteroides vulgatus and Bacteroides ovatus genomes.
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.scientific_name · “human gut metagenome”
- body site study.description · “fecal microbiota transplant study”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN10409892 | collection_date | 2016-04-04 | R1 | 0.90 | biosample.attribute:collection_date | 2016-04-04 |
| SAMN10409892 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: Massachusetts |
| SAMN10409892 | health_condition | ibd_unspecified | R4 | 0.50 | study.description | Patients with UC were selectively enrolled |
| SAMN10409892 | health_condition_detail | UC (ulcerative colitis) patients treated with FMT | R4 | 0.50 | study.description | Patients with UC were selectively enrolled |
| SAMN10409892 | latitude | 42.3700 | R1 | 0.90 | biosample.attribute:lat_lon | 42.37 N 71.08 W |
| SAMN10409892 | location_region | Massachusetts | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: Massachusetts |
| SAMN10409892 | longitude | -71.0800 | R1 | 0.90 | biosample.attribute:lat_lon | 42.37 N 71.08 W |
| SAMN10409892 | subject_id | patient 001 | R1 | 0.85 | biosample.attribute:host | host: patient 001 |
| SAMN10409892 | timepoint_label | before 1 day | R1 | 0.85 | biosample.attribute:isolation_source | isolation_source: before 1 day |
Sequencing
72 runs over 72 samples · mean 0.11 Gbp per run (median 76.5 Mbp, total 7.59 Gbp; 72 runs with a base count) · layout PAIRED 72 · platform ILLUMINA 72 · models Illumina HiSeq 2500 (72) · 33% of runs with a Sandpiper profile · first public 2019-01-02
Authors (12)
Jiang X first · Hall AB · Arthur TD · Plichta DR · Covington CT · Poyet M · Crothers J · Moses PL · Tolonen AC · Vlamakis H · Alm EJ · Xavier RJ last
Downloads
PRJNA474024.csv.gz (3.0 KB) · parquet (74.1 KB) — all 72 samples, every field with route and confidence · PRJNA474024_determinations.csv.gz (5.6 KB) — 648 evidence rows