Oral-gut microbiome in cirrhosis severity, case-control
186 paired saliva and faecal samples from healthy controls and patients with stable cirrhosis, decompensated cirrhosis, acute-on-chronic liver failure, or severe infection without cirrhosis, studying oral-gut microbiome overlap and metabolism; case-control design. machine-written summary
186 samples · 186 runs · Adult · 2024 · 12.37 Gbp / sample · cohort Microbial collagenase activity is linked to oral-g
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 182 sample values (subject id) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC12768972, PMC13377410 |
| ✓ Supplementary tables | 630 sample values (age, antibiotic exposure, health condition, health condition detail, sex) |
| – 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 — not resolved
70 of 112 people sampled more than once (140 samples; median 2, up to 2 per person).
Genera, mean relative abundance over 164 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 | 186 | 100% | ||||
| country | 0 | 0% | ||||
| health_condition | 182 | 98% | 182 | |||
| subject_id | 182 | 98% | 182 | |||
| health_condition_detail | 182 | 98% | 182 | |||
| sex | 182 | 98% | 182 | |||
| age_at_collection_days | 42 | 23% | 42 | |||
| antibiotic_exposure | 42 | 23% | 42 |
- Pathogenic entero- and salivatypes harbour changes in microbiome virulence and antimicrobial resistance genes with increasing chronic liver disease severity 2023 own_data
- Microbial collagenase activity is linked to oral-gut translocation in advanced chronic liver disease. 2026 PMID 41461922 PMC12768972 unsure
- Integrative host-microbiome modeling uncovers the implication of oral-gut translocation in advanced cirrhosis. 2026 PMID 42491347 PMC13377410 unsure
Archive description
Cirrhosis complications are often triggered by bacterial infections with multidrug-resistant organisms. Alterations in the gut and oral microbiome in decompensated cirrhosis (DC) influence clinical outcomes. We interrogated: (i) gut and oral microbiome community structures, (ii) virulence factors (VFs) and antimicrobial resistance genes (ARGs) and (iii) oral-gut microbial overlap in patients with differing cirrhosis severity. Fifteen healthy controls (HCs), as well as 26 patients with stable cirrhosis (SC), 46 with DC, 14 with acute-on-chronic liver failure (ACLF) and 14 with severe infection without cirrhosis participated. Metagenomic sequencing was undertaken on paired saliva and faecal samples. ‘Salivatypes’ and ‘enterotypes’ based on genera clustering were assessed against cirrhosis severity and clinical parameters. VFs and ARGs were evaluated in oral and gut niches, and distinct resistotypes identified. Salivatypes and enterotypes revealed a greater proportion of pathobionts with concomitant reduction in autochthonous genera with increasing cirrhosis severity and hyperammonaemia. Increasing overlap between oral and gut microbiome communities was observed in DC and ACLF vs. SC and HCs, independent of antimicrobial, beta-blocker and gastric acid-suppressing therapies. Two distinct gut microbiome clusters harboured genes encoding for the PTS (phosphoenolpyruvate:sugar phosphotransferase system) and other VFs in DC and ACLF. Substantial ARGs (oral: 1,218 and gut: 672) were detected (575 common to both sites). The cirrhosis resistome was distinct, with three oral and four gut resistotypes identified, respectively.
How this project entered the registry
Classified as human gut / stool / oral cavity / 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 · “Oral- gut microbiome interactions in”
- body site study.description · “Alterations in the gut and oral microbiome”
- body site study.title · “Oral -gut microbiome interactions”
- body site study.description · “the gut and oral microbiome in decompensated”
- body site study.description · “14 with acute-on-chronic liver failure (ACLF) 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 |
|---|---|---|---|---|---|---|
| SAMEA14408392 | age_at_collection_days | 23010.8 | R2 | 0.75 | paper.supp.41564_2025_2223_MOESM4_ESM.xlsx[patient info][age] | 363: age = 63 |
| SAMEA14408392 | antibiotic_exposure | yes | R2 | 0.75 | paper.supp.41564_2025_2223_MOESM4_ESM.xlsx[patient info][receive_antibiotic] | 363: receive_antibiotic = 1 |
| SAMEA14408380 | health_condition | liver_disease | R2 | 0.75 | paper.supp.41564_2025_2223_MOESM4_ESM.xlsx[metadata table][disease_state] | 193: disease_state = cACLD |
| SAMEA14408380 | health_condition_detail | cACLD | R2 | 0.75 | paper.supp.41564_2025_2223_MOESM4_ESM.xlsx[metadata table][disease_state] | 193: disease_state = cACLD |
| SAMEA14408380 | sex | male | R2 | 0.75 | paper.supp.41564_2025_2223_MOESM4_ESM.xlsx[patient info][gender] | 193: gender = male |
| SAMEA14408380 | subject_id | 193 | R1 | 0.70 | sample.name_rule:DESCRIPTION | DESCRIPTION: 193fecal in STABLE |
| SAMEA14408396 | subject_id | 440 | R1 | 0.70 | sample.name_rule:TITLE | TITLE: 440fecal |
Sequencing
186 runs over 186 samples · mean 12.48 Gbp per run (median 12.37 Gbp, total 2,321.75 Gbp; 186 runs with a base count) · layout PAIRED 186 · platform ILLUMINA 186 · models Illumina NovaSeq 6000 (186) · 88% of runs with a Sandpiper profile · first public 2024-12-02
Authors (46)
Jin S first · Cenier A · Wetzel D · Arefaine B · Moreno-Gonzalez M · Stamouli M · Mohamad M · Lupatsii M · Ríos E · Lee S · Zamalloa A · Chokshi S · Mardinoglu A · Shoaie S · Beraza N · Patel VC · Schirmer M 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 · Trebicka J · Begum N · Witherden E · Harzandi A · Cai H · Edwards LA · Williams R · Proctor G · Moyes D · Uhlen M
Downloads
PRJEB52891.csv.gz (5.9 KB) · parquet (77.1 KB) — all 186 samples, every field with route and confidence · PRJEB52891_determinations.csv.gz (9.1 KB) — 812 evidence rows