Oral vancomycin trial in PSC-IBD, Birmingham, UK
60 gut samples from patients with PSC-associated IBD in Birmingham, UK, in a single-arm interventional study of oral vancomycin treatment followed by withdrawal. machine-written summary
60 samples · 60 runs · GB · Elderly · 2024 · 2.08 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 294 sample values (age, country, location locality, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 240 sample values (antibiotic exposure, collection date, health condition, health condition detail) · PMC11831226 |
| ○ 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
Antibiotic given as the study intervention (incl. eradication therapy design single_arm_before_after · Oral vancomycin 125mg QID for 4 weeks
“treated with OV (125 mg QID) for 4 weeks” — abstract:39673746 (study level; per-sample arms are in the intervention column below)
longitudinal
15 of 15 people sampled more than once (60 samples; median 4, up to 4 per person) · follow-up median 3.0 y (max 3.1 y) · median interval between samples 12 mo (time from age at collection). Schedule stated by the source: “Stool collected at Weeks 0, 2, 4, and 8 (baseline, during 4-week OV treatment, and 4-week withdrawal).” (time origin: intervention_start); stated follow-up 56 d.
Each row is one person (13 shown of 15); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 36 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 | 60 | 100% | ||||
| country | 60 | 100% | 60 | |||
| health_condition | 60 | 100% | 60 | |||
| subject_id | 60 | 100% | 60 | |||
| antibiotic_exposure | 60 | 100% | 60 | |||
| collection_date | 60 | 100% | 60 | |||
| detailed_location | 60 | 100% | ||||
| health_condition_detail | 60 | 100% | 60 | |||
| location_locality | 60 | 100% | 60 | |||
| timepoint_label | 60 | 100% | 60 | |||
| age_at_collection_days | 54 | 90% | 54 |
- Open Label Vancomycin in Primary Sclerosing Cholangitis-Inflammatory Bowel Disease: Improved Colonic Disease Activity and Associations With Changes in Host-Microbiome-Metabolomic Signatures. 2025 PMID 39673746 PMC11831226 own_data
Archive description
16S and metatranscriptomic dataset from PSC-Vanc study
How this project entered the registry
Classified as human gut / stool mixed assays of elderly by sonnet_x2 with confidence 0.50. Assay mixed.
- host run.scientific_name · “Homo sapiens”
- body site study.title · “PSC-Vanc Clinical Trial”
- life stage sample.attr.age · “100 (n=56/60)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN42687847 | age_at_collection_days | 22280.2 | R1 | 0.70 | sample.attr.age | 61 |
| SAMN42687847 | antibiotic_exposure | no | R3 | 0.70 | paper.fulltext.methods | use of antibiotics or probiotics in the 3 months prior |
| SAMN42687847 | collection_date | 2022-02/2022-11 | R3 | 0.70 | paper.fulltext.methods | conducted from February 2022 to November 2022 |
| SAMN42687847 | country | GB | R1 | 0.90 | sample.attr.geo_loc_name | United Kingdom: Birmingham |
| SAMN42687847 | health_condition | ibd_unspecified | R3 | 0.70 | paper.fulltext.abstract | patients with PSC and active colitis |
| SAMN42687847 | health_condition_detail | PSC and active colonic IBD (PSC-IBD) | R3 | 0.70 | paper.fulltext.abstract | patients with PSC and active colitis |
| SAMN42687847 | location_locality | Birmingham | R1 | 0.85 | biosample.attribute:geo_loc_name | United Kingdom: Birmingham |
| SAMN42687847 | subject_id | SN10 | R1 | 0.85 | biosample.attribute:isolate | SN10 |
| SAMN42687847 | timepoint_label | VISIT1 | R1 | 0.70 | sample.name_rule:alias | SN10_DNA_VISIT1 |
Sequencing
60 runs over 60 samples · mean 5.07 Gbp per run (median 2.08 Gbp, total 304.21 Gbp; 60 runs with a base count) · layout PAIRED 60 · platform ILLUMINA 60 · models NextSeq 2000 (60) · 60% of runs with a Sandpiper profile · first public 2024-09-28
Authors (24)
Quraishi MN first · Cheesbrough J · Rimmer P · Mullish BH · Sharma N · Efstathiou E · Acharjee A · Gkoutus G · Patel A · Marchesi JR · Camuzeaux S · Chappell K · Valdivia-Garcia MA · Ferguson J · Brookes MJ · Walmsley M · Rossiter AE · van Schaik W · McInnes RS · Cooney R · Trauner M · Beggs AD · Iqbal TH · Trivedi PJ last
Downloads
PRJNA1138254.csv.gz (2.9 KB) · parquet (72.8 KB) — all 60 samples, every field with route and confidence · PRJNA1138254_determinations.csv.gz (4.7 KB) — 534 evidence rows