Gut metagenomes in cholestatic liver fibrosis, case-control
62 fecal metagenome samples from adults, collected as part of a case-control study comparing healthy controls and liver disease patients to assess the clinical relevance of Phocaeicola dorei abundance. machine-written summary
62 samples · 62 runs · KR · Adult · 2026 · 8.24 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 124 sample values (collection date, country) |
| ✓ Abstract / description | 62 sample values (health condition detail) |
| ✓ Full text | 62 sample values (antibiotic exposure) · PMC13377085 |
| ○ 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 · share metadata |
| – 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 | 62 | 100% | ||||
| country | 62 | 100% | 62 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 0 | 0% | ||||
| antibiotic_exposure | 62 | 100% | 62 | |||
| collection_date | 62 | 100% | 62 | |||
| health_condition_detail | 62 | 100% | 62 |
- Pharmabiotics, Phocaeicola dorei, ameliorates cholestatic liver fibrosis by alleviating macrophage efferocytosis of neutrophils. 2026 PMID 42143054 PMC13377085 own_data
Archive description
Phocaeicola dorei has been reported to ameliorate metabolic diseases. Its role in liver fibrosis remains unclear. We evaluated the hepatoprotective effect of P. dorei in liver fibrosis. Fecal samples were collected from healthy controls and patients (n=285) to assess the clinical relevance of P. dorei. In mice models (3,5-diethoxycarbonyl-1.4-dihydrocollidine [DDC] diet), P. dorei (109 CFU/g twice/week) was orally administered. Primary HSCs, LX-2, THP-1, and HL-60 cell lines were used for mechanical validation. The relative abundance of P. dorei increased with worsing liver disease in human. P. dorei administration significantly reduced neutrophil degranulation and efferocytosis pathways (Ly6g and F4/80). The dysregulated expression of neutrophil-associated chemokines (Cx3cl1, and Cx3cr1) was restored by P. dorei. P. dorei culture supernatant inhibited macrophage-mediated efferocytosis. P. dorei attenuates liver fibrosis by suppressing neutrophil and macrophage infiltration and disrupting efferocytosis. Our results identify P. dorei as a potential microbiome-based therapeutic candidate for liver fibrosis.
How this project entered the registry
Classified as human blood / tissue / internal fluids / gut / stool 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 · “dorei, ameliorates cholestatic liver fibrosis by alleviating”
- body site study.description · “Its role in liver fibrosis remains unclear.”
- body site study.description · “in liver fibrosis. Fecal samples were collected”
- 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 |
|---|---|---|---|---|---|---|
| SAMN56710721 | antibiotic_exposure | no | R3 | 0.70 | paper.fulltext.methods | continuously taking antibiotics within the last 2 months |
| SAMN56710721 | collection_date | 2018 | R1 | 0.90 | biosample.attribute:collection_date | 2018 |
| SAMN56710721 | country | KR | R1 | 0.90 | sample.attr.geo_loc_name | South Korea |
| SAMN56710721 | health_condition_detail | mixed_case_control: healthy controls vs cholestatic liver fibrosis patients | R4 | 0.40 | study.description | healthy controls and patients (n=285) |
Sequencing
62 runs over 62 samples · mean 8.21 Gbp per run (median 8.24 Gbp, total 509.28 Gbp; 62 runs with a base count) · layout PAIRED 62 · platform ILLUMINA 62 · models Illumina NovaSeq 6000 (62) · 0% of runs with a Sandpiper profile · first public 2026-04-02
Authors (13)
Eom JA first · Park IG · Hyun JY · Lee NY · Kwon GH · Yoon SJ · Won SM · Ham YL · Lee KJ · Han SH · Yang DH · Kim DJ · Suk KT last
Help complete this project
2 of the 4 core fields are below 50% coverage: health_condition, subject_id. Share metadata
Downloads
PRJNA1399671.csv.gz (2.5 KB) · parquet (71.2 KB) — all 62 samples, every field with route and confidence · PRJNA1399671_determinations.csv.gz (1.9 KB) — 248 evidence rows