Gut microbiome in PSC patient on vancomycin, Minnesota
4 fecal and mucosal biopsy samples from an adult with primary sclerosing cholangitis in Minnesota, USA, studied longitudinally during vancomycin antibiotic treatment using 16S rRNA sequencing and shotgun metagenomics. machine-written summary
4 samples · 4 runs · US · Adult · 2026 · 13.86 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 28 sample values (country, intervention, intervention detail, latitude, location region, longitude, timepoint) |
| ✓ Abstract / description | 16 sample values (antibiotic exposure, health condition, health condition detail, subject id) |
| – Full text | no open-access full text linked |
| – 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 resolved
1 people have samples in more than one arm.
Antibiotic given as the study intervention (incl. eradication therapy design single_arm_before_after · population autoimmune_inflammatory · Vancomycin treatment, longitudinal case study
“patient undergoing vancomycin treatment” — bioproject.description (study level; per-sample arms are in the intervention column below)
longitudinal
1 of 1 people sampled more than once (4 samples; median 4, up to 4 per person) · follow-up median 7 mo (max 7 mo) · median interval between samples 3 mo (time from timepoint labels). Schedule stated by the source: “Fecal samples collected at baseline, day 28, day 112, and day 222 during vancomycin treatment”; stated follow-up 7 mo.
Each row is one person (1 shown); dots are samples at days since that person's first sample.
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 4 | 100% | ||||
| country | 4 | 100% | 4 | |||
| health_condition | 4 | 100% | 4 | |||
| subject_id | 4 | 100% | 4 | |||
| antibiotic_exposure | 4 | 100% | 4 | |||
| detailed_location | 4 | 100% | ||||
| health_condition_detail | 4 | 100% | 4 | |||
| intervention | 4 | 100% | 4 | |||
| intervention_detail | 4 | 100% | 4 | |||
| latitude | 4 | 100% | 4 | |||
| location_region | 4 | 100% | 4 | |||
| longitude | 4 | 100% | 4 | |||
| timepoint_label | 4 | 100% | 4 |
- Rapid resolution of colon inflammation and microbiome remodeling with vancomycin therapy in a patient with primary sclerosing cholangitis. 2026 PMID 42490468 own_data
Archive description
Longitudinal case study of gut microbiome changes in a primary sclerosing cholangitis patient undergoing vancomycin treatment. 16S rRNA gene sequencing was performed on fecal and mucosal biopsy samples. Shotgun metagenomics was performed on fecal samples.
How this project entered the registry
Classified as human gut / stool / blood / tissue / internal fluids shotgun DNA metagenome of adult by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- body site study.title · “Gut microbiome dynamics in”
- body site study.description · “case study of gut microbiome changes in”
- body site study.description · “fecal and mucosal biopsy samples. Shotgun metagenomics”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN60297422 | antibiotic_exposure | yes | R4 | 0.50 | study.description | undergoing vancomycin treatment |
| SAMN60297422 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA:Minnesota |
| SAMN60297422 | health_condition | liver_disease | R4 | 0.50 | study.title | primary sclerosing cholangitis patient |
| SAMN60297422 | health_condition_detail | primary sclerosing cholangitis (PSC) | R4 | 0.50 | study.title | primary sclerosing cholangitis patient |
| SAMN60297422 | intervention | no_intervention | R1 | 0.90 | biosample.attribute:timepoint | timepoint: baseline |
| SAMN60297422 | intervention_detail | baseline before vancomycin treatment | R1 | 0.90 | biosample.attribute:timepoint | timepoint: baseline |
| SAMN60297422 | latitude | 44.9723 | R1 | 0.90 | biosample.attribute:lat_lon | 44.9723 N 93.2335 W |
| SAMN60297422 | location_region | Minnesota | R1 | 0.85 | biosample.attribute:geo_loc_name | USA:Minnesota |
| SAMN60297422 | longitude | -93.2335 | R1 | 0.90 | biosample.attribute:lat_lon | 44.9723 N 93.2335 W |
| SAMN60297422 | subject_id | PRJNA1468588:single_subject | R4 | 0.75 | design.single_subject_case_study:description | Longitudinal case study of gut microbiome changes in a primary sclerosing cholangitis patient |
| SAMN60297422 | timepoint_label | baseline | R1 | 0.85 | sample.attr.timepoint | baseline |
Sequencing
4 runs over 4 samples · mean 17.79 Gbp per run (median 13.86 Gbp, total 71.17 Gbp; 4 runs with a base count) · layout PAIRED 4 · platform ELEMENT 4 · models Element AVITI (4) · 0% of runs with a Sandpiper profile · first public 2026-08-13
Downloads
PRJNA1468588.csv.gz (1.1 KB) · parquet (71.0 KB) — all 4 samples, every field with route and confidence · PRJNA1468588_determinations.csv.gz (1.2 KB) — 44 evidence rows