Gut bacterial & fungal microbiota in decompensated cirrhosis
95 samples from adult patients with decompensated liver cirrhosis, prospectively collected 2017–2022, analyzed for bacterial/fungal microbiota, gut barrier integrity, and inflammation in relation to clinical outcomes. machine-written summary
95 samples · 95 runs · DE · Adult · 2024 · 1.45 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 285 sample values (collection date, country, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC12054929 |
| ○ 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 | 95 | 100% | ||||
| country | 95 | 100% | 95 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 0 | 0% | ||||
| collection_date | 95 | 100% | 95 | |||
| timepoint_label | 95 | 100% | 95 |
- Distinct clusters of bacterial and fungal microbiota in end-stage liver cirrhosis correlate with antibiotic treatment, intestinal barrier impairment, and systemic inflammation. 2025 PMID 40255076 PMC12054929 cites_accession
Archive description
Decompensated liver cirrhosis (dLC) is associated with intestinal dysbiosis, however, underlying reasons and clinical consequences remain largely unexplored. We investigated bacterial and fungal microbiota, their relation with gut barrier integrity, inflammation and cirrhosis-specific complications in dLC-patients. Competing-risk analyses were performed to investigate clinical outcomes within 90 days. Samples were collected prospectively from 95 dLC-patients between 2017-2022. Quantitative metagenomic analyses clustered patients into three groups (G1-G3) showing greatly distinct microbial patterns. G1 (n=39) displayed lowest diversity and highest Enterococcus abundance, G2 (n=24) was dominated by Bifidobacteria, G3 (n=29) was most diverse and clustered most closely with healthy controls (HC). Of note, bacterial concentrations were significantly lower in cirrhosis compared with HC, especially for G1 that also showed lowest capacity to produce short chain fatty acids and secondary bile acids. Consequently, fungal overgrowth, dominated by Candida spp (51.63%), was observed in G1. Moreover, G1-patients most frequently received antibiotics (n=33; 86.8%), had highest plasma levels of Zonulin (p=0.044), sCD163 (p=0.019), a proinflammatory cytokine profile and numerically higher incidences of subsequent infections (p=0.09). In conclusion, distinct bacterial clusters were observed at qualitative and quantitative levels and correlated with fungal abundances. Antibiotics contributed to dysbiosis, which translated into intestinal barrier impairment and systemic inflammation.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.62. Assay shotgun_dna.
- host study.title · “microbiota in cirrhosis”
- host study.description · “95 dLC-patients between 2017-2022”
- body site study.description · “intestinal dysbiosis”
- life stage study.description · “95 dLC-patients between 2017-2022”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA116351933 | collection_date | 2023 | R1 | 0.85 | biosample.attribute:collection_date | collection_date: 2023 |
| SAMEA116351933 | country | DE | R1 | 0.85 | biosample.attribute:geographic_location_country_and_or_sea | geographic_location_country_and_or_sea: Germany |
| SAMEA116351933 | timepoint_label | BLn | R1 | 0.70 | sample.name_rule:ena_files | GST001_I-01-23-016BLn_S68 |
Sequencing
95 runs over 95 samples · mean 1.52 Gbp per run (median 1.45 Gbp, total 144.52 Gbp; 95 runs with a base count) · layout PAIRED 95 · platform ILLUMINA 95 · models Illumina NovaSeq 6000 (95) · 0% of runs with a Sandpiper profile · first public 2024-11-07
Authors (0)
No author record.
Help complete this project
2 of the 4 core fields are below 50% coverage: health_condition, subject_id. Share metadata
Downloads
PRJEB81819.csv.gz (2.9 KB) · parquet (72.5 KB) — all 95 samples, every field with route and confidence · PRJEB81819_determinations.csv.gz (3.3 KB) — 285 evidence rows