Liver cirrhosis case-control cohort, UK
185 samples from a UK case-control study of paired oral and fecal metagenomes in liver cirrh machine-written summary
185 samples · 592 runs · GB · Age unknown · 2021 · 2.05 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 925 sample values (country, health condition, health condition detail, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC12075632, PMC13377410 |
| – 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 |
longitudinal
30 of 37 people sampled more than once (83 samples; median 3, up to 3 per person) · follow-up median 3 mo (max 3 mo) · median interval between samples 29 d (time from timepoint labels).
Each row is one person (30 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 | 0 | 0% | ||||
| country | 185 | 100% | 185 | |||
| health_condition | 185 | 100% | 185 | |||
| subject_id | 185 | 100% | 185 | |||
| health_condition_detail | 185 | 100% | 185 | |||
| timepoint_label | 185 | 100% | 185 |
- Extensively acquired antimicrobial-resistant bacteria restructure the individual microbial community in post-antibiotic conditions. 2025 PMID 40360555 PMC12075632 unsure
- Integrative host-microbiome modeling uncovers the implication of oral-gut translocation in advanced cirrhosis. 2026 PMID 42491347 PMC13377410 unsure
Archive description
Liver Cirrhosis cohort
How this project entered the registry
Classified as human gut / stool / oral cavity shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.57. Assay shotgun_dna.
- host run.scientific_name · “human gut metagenome”
- body site run.scientific_name · “human oral metagenome”
- body site run.scientific_name · “human gut metagenome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA7324778 | country | GB | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | United Kingdom |
| SAMEA7324778 | health_condition | liver_disease | R1 | 0.70 | sample.name_rule:alias | RS_01_d01_SA |
| SAMEA7324778 | health_condition_detail | RS: Project PRJEB38481 description states 'Liver Cirrhosis cohort' for the whole project with no mention of a separate healt | R1 | 0.70 | sample.name_rule:alias | RS_01_d01_SA |
| SAMEA7324778 | subject_id | RS_01 | R1 | 0.70 | sample.name_rule:alias | RS_01_d01_SA |
| SAMEA7324778 | timepoint_label | d01 | R1 | 0.70 | sample.name_rule:alias | RS_01_d01_SA |
Sequencing
592 runs over 185 samples · mean 0.65 Gbp per run (median 0.43 Gbp, total 385.67 Gbp; 592 runs with a base count) · layout SINGLE 592 · platform ION_TORRENT 592 · models Ion Torrent Proton (592) · 0% of runs with a Sandpiper profile · first public 2021-08-09
Authors (33)
Baek JW first · Lim S · Park N · Song B · Kirtipal N · Nielsen J · Mardinoglu A · Shoaie S · Kim JI · Son JW · Koh A · Lee S last · Jin Y first · Clasen F · Garcia-Guevara F · Arif S · Schierwagen R · Bidkhori G · Praktiknjo M · Brol MJ · Uschner FE · Castelli FA · Pons N · Quinquis B · Galleron N · Da Silva K · Junot C · Shawcross DL · Moyes DL · Jalan R · Ehrlich SD · Patel VC · Trebicka J
Downloads
PRJEB38481.csv.gz (5.7 KB) · parquet (76.4 KB) — all 185 samples, every field with route and confidence · PRJEB38481_determinations.csv.gz (9.6 KB) — 925 evidence rows