Stool metagenome in primary biliary cholangitis, USA
558 stool samples from adults in the USA: 280 with primary biliary cholangitis (PBC) and 278 age- and sex-matched healthy controls, analyzed by shotgun metagenomic sequencing in a case-control design. machine-written summary
558 samples · 558 runs · US · Adult · 2026 · 1.53 Gbp / sample · cohort Compositional and functional differences of gut mi
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 2,790 sample values (country, health condition, latitude, location region, longitude) |
| ✓ Abstract / description | 1,116 sample values (health condition detail, subject id) |
| ○ Full text | read; no usable statement or table · PMC13078198 |
| ○ 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 |
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 558 | 100% | ||||
| country | 558 | 100% | 558 | |||
| health_condition | 558 | 100% | 558 | |||
| subject_id | 558 | 100% | 558 | |||
| detailed_location | 558 | 100% | ||||
| health_condition_detail | 558 | 100% | 558 | |||
| latitude | 558 | 100% | 558 | |||
| location_region | 558 | 100% | 558 | |||
| longitude | 558 | 100% | 558 |
- Compositional and functional differences of gut microbiome and metabolome inform pathogenesis of cholestatic liver disease. 2026 PMID 41975274 PMC13078198 unsure
Archive description
Stool metagenomic sequencing of patients with PBC. The cohort comprised of: 280 patients with primary biliary cholangitis (PBC) and 278 age- and sex- matched controls.
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 · “Stool metagenome in primary”
- body site study.description · “Stool metagenomic sequencing of”
- body site study.description · “patients with primary biliary cholangitis (PBC) and”
- 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 |
|---|---|---|---|---|---|---|
| SAMN55419033 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA |
| SAMN55419033 | health_condition | liver_disease | R1 | 0.85 | biosample_attr | PBC |
| SAMN55419033 | health_condition_detail | mixed_case_control: PBC patients vs. age- and sex-matched controls | R4 | 0.40 | study.description | 280 patients with primary biliary cholangitis |
| SAMN55419033 | latitude | 44.0228 | R1 | 0.90 | biosample.attribute:lat_lon | 44.02275279 N 92.46684038 W |
| SAMN55419033 | location_region | Minnesota | R1 | 0.60 | biosample.attribute:lat_lon | 44.02275279 N 92.46684038 W |
| SAMN55419033 | longitude | -92.4668 | R1 | 0.90 | biosample.attribute:lat_lon | 44.02275279 N 92.46684038 W |
| SAMN55419033 | subject_id | SAMN55419033 | R4 | 0.60 | design.one_sample_per_subject:description | 280 patients with primary biliary cholangitis (PBC) and 278 age- and sex- matched controls |
Sequencing
558 runs over 558 samples · mean 1.55 Gbp per run (median 1.53 Gbp, total 864.73 Gbp; 558 runs with a base count) · layout PAIRED 558 · platform ILLUMINA 558 · models Illumina NovaSeq 6000 (558) · 0% of runs with a Sandpiper profile · first public 2026-05-05
Authors (29)
Nikolaidis M first · Hu C · Juran BD · McCauley BM · Schlicht EM · Bianchi JK · Ali AH · Tragaki V · Atkinson EJ · Johnson S · Mars RA · Eaton JE · Carey EJ · Franke A · Schramm C · Kashyap PC · Go YM · Tran V · Teeny S · Jones DP · Grant CW · Athreya AP · Miller GW · LaRusso NF · Gores GJ · Karlsen TH · Hov JR · Amoutzias GD · Lazaridis KN last
Downloads
PRJNA1425466.csv.gz (14.1 KB) · parquet (93.4 KB) — all 558 samples, every field with route and confidence · PRJNA1425466_determinations.csv.gz (20.6 KB) — 3,906 evidence rows