Gut metagenome in UDCA-naive PBC patients vs healthy controls
263 stool metagenome samples from a case-control study comparing UDCA treatment-naive primary biliary cholangitis patients and matched healthy controls, geography not specified (data agreement established pre-2023). machine-written summary
263 samples · 263 runs · Age unknown · 2026 · 8.86 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 789 sample values (collection date, health condition, health condition detail) |
| ✓ Abstract / description | 263 sample values (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 · share metadata |
| – Human verified | not yet checked by a person · I checked this project — verify it |
intervention — arms not resolved
Non-antibiotic pharmaceutical given as the study intervention (metformin design single_arm_before_after · population liver_disease · UDCA treatment in treatment-naive PBC patients, samples before and after
“samples obtained before (n = 132) and after (n = 59) treatment” — abstract:39305900 (study level; per-sample arms are in the intervention column below)
longitudinal — not resolved
Schedule stated by the source: “Stool/serum collected before (n=132) and after (n=59) UDCA treatment; no specific interval given” (time origin: treatment_start).
Genera, mean relative abundance over 260 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 | 0 | 0% | ||||
| health_condition | 263 | 100% | 263 | |||
| subject_id | 263 | 100% | 263 | |||
| collection_date | 263 | 100% | 263 | |||
| health_condition_detail | 263 | 100% | 263 |
- Gut microbiome pattern impacts treatment response in primary biliary cholangitis 2025 PMID 39305900 own_data
Archive description
To dissect the gut microbiome dysbiosis in PBC, we performed stool metagenome, metabolome, and serum metabolome profiling and collected detailed metadata from a cohort of 132 UDCA naive-patients with PBC and 131 healthy controls matched for geography, age, sex, and BMI.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by opus_adjudicated with confidence 0.85. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.description · “we performed stool metagenome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMD00931150 | collection_date | 2019-09-23 | R1 | 0.90 | biosample.attribute:collection_date | 2019-09-23 |
| SAMD00931150 | health_condition | liver_disease | R1 | 0.70 | sample.name_rule:TITLE | TITLE: MXC001 (SAMC2954021) |
| SAMD00931150 | health_condition_detail | C | R1 | 0.70 | sample.name_rule:TITLE | TITLE: MXC001 (SAMC2954021) |
| SAMD00931150 | subject_id | SAMD00931150 | R4 | 0.55 | design.one_sample_per_subject:description | a cohort of 132 UDCA naive-patients with PBC and 131 healthy controls |
Sequencing
263 runs over 263 samples · mean 9.80 Gbp per run (median 8.86 Gbp, total 2,576.26 Gbp; 263 runs with a base count) · layout PAIRED 263 · platform ILLUMINA 263 · models Illumina NovaSeq 6000 (263) · 99% of runs with a Sandpiper profile · first public 2026-09-05
Authors (22)
Liu Q first · Huang B · Zhou Y · Wei Y · Li Y · Li B · Zhang J · Qian Q · Chen R · Lyu Z · Wang R · Cao Q · Xu Q · Wang Q · Miao Q · You Z · Lian M · Gershwin ME · Jin Q · Xiao X · Ma X · Tang R last
Help complete this project
2 of the 4 core fields are below 50% coverage: age_category, country. Share metadata
Downloads
PRJDB28938.csv.gz (7.0 KB) · parquet (80.4 KB) — all 263 samples, every field with route and confidence · PRJDB28938_determinations.csv.gz (10.5 KB) — 1,052 evidence rows