PRJEB6337 ERP005860
Gut microbiome in liver cirrhosis vs controls, China
Liver cirrhosis occurs as a consequence of many chronic liver diseases that are prevalent worldwide. Previous studies have shown an association between the gut microbiota and liver complications such as cirrhosis and other liver injuries. We therefore undertook a whole gut microbiome wide association study of stool samples from 98 liver cirrhosis patients and 83 healthy controls to characterise the faecal microbial communities and their functional composition. In total, we generated 860 Gb of high-quality sequence data and built a reference gene set for the liver cirrhosis cohort containing 2.69 million genes, 36.1% of which was not covered by previously published gene catalogues.
312 faecal metagenome samples from adults and elderly individuals in China, comparing liver disease patients (169) and healthy controls (143) in a case-control study of gut microbiota in liver cirrhosis. machine-written summary
312 samples · 314 runs · CN · Adult · 2014 · 3.10 Gbp / sample · cohort Quantitative metagenomics reveals unique gut micro
Sources
✓Sequence archive 2,184○Abstract / description✓Full text 312✓Supplementary tables 191✓External resources 1,057–User contribution–Human verified
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 2,184 sample values (collection date, country, health condition, health condition detail, latitude, longitude, subject id) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 312 sample values (location site) · PMC10170289, PMC10714505, PMC10972203, PMC11654977, PMC12065390, PMC12108083, PMC13522639, PMC5501583, PMC6315199, PMC6446249, PMC8625315 |
| ✓ Supplementary tables | 191 sample values (sex) |
| ✓ External resources | 1,057 sample values (age, antibiotic exposure, bmi, sex) · from curatedMetagenomicData 3 (cMD 3) |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Samples at a glance
1 sampling locations · 1 country
Age
adult292
elderly20
Condition
liver_disease169
healthy_control143
Sex
male204
female108
Country
CN312
Body site
primary312
Sequencing depth per sample · this project all projects
Sampling design and relatedness
longitudinal — not resolved
68 of 237 people sampled more than once (143 samples; median 2, up to 3 per person).
Community composition
Phocaeicola 17.2%Bacteroides 14.4%Prevotella 10.5%Faecalibacterium 6.2%Lachnospira 5.7%Roseburia 3.5%Alistipes 2.8%Veillonella 2.3%Acetatifactor 1.5%Streptococcus 1.5%Parabacteroides 1.4%Escherichia 1.3%not assigned to a genus 7.6%other genera 24.0%
Genera, mean relative abundance over 235 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).
Field coverage
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 312 | 100% | ||||
| country | 312 | 100% | 312 | |||
| health_condition | 312 | 100% | 312 | |||
| subject_id | 312 | 100% | 312 | |||
| age_at_collection_days | 312 | 100% | 312 | |||
| antibiotic_exposure | 312 | 100% | 312 | |||
| bmi | 312 | 100% | 312 | |||
| collection_date | 312 | 100% | 312 | |||
| detailed_location | 312 | 100% | ||||
| health_condition_detail | 312 | 100% | 312 | |||
| latitude | 312 | 100% | 312 | |||
| location_site | 312 | 100% | 312 | |||
| longitude | 312 | 100% | 312 | |||
| sex | 312 | 100% | 312 |
Papers (47)
- VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data. 2017 PMID 28683828 PMC5501583 own_data
- Disorganized Gut Microbiome Contributed to Liver Cirrhosis Progression: A Meta-Omics-Based Study. 2018 PMID 30631318 PMC6315199 own_data
- MGS-Fast: Metagenomic shotgun data fast annotation using microbial gene catalogs. 2019 PMID 30942867 PMC6446249 own_data
- Aryl Hydrocarbon Receptor (AhR) Activation by 2,3,7,8-Tetrachlorodibenzo-p-Dioxin (TCDD) Dose-Dependently Shifts the Gut Microbiome Consistent with the Progression of Non-Alcoholic Fatty Liver Disease. 2021 PMID 34830313 PMC8625315 own_data
- Alterations in the intestinal microbiome and metabolic profile of patients with cirrhosis supplemented with lactulose, Clostridium butyricum, and Bifidobacterium longum infantis: a randomized placebo-controlled trial. 2023 PMID 37180228 PMC10170289 own_data
42 more
- Frequentmers - a novel way to look at metagenomic next generation sequencing data and an application in detecting liver cirrhosis. 2023 PMID 38087204 PMC10714505
- MIGRENE: The Toolbox for Microbial and Individualized GEMs, Reactobiome and Community Network Modelling. 2024 PMID 38535292 PMC10972203
- OneNet-One network to rule them all: Consensus network inference from microbiome data. 2024 PMID 39642168 PMC11654977
- Small amounts of misassembly can have disproportionate effects on pangenome-based metagenomic analyses. 2025 PMID 40298412 PMC12108083
- Whole genome comparisons reveal gut-to-lung translocation of Escherichia coli and Burkholderia cenocepacia in two cases of ventilator-associated pneumonia in ICU patients. 2025 PMID 40346542 PMC12065390
- Oral Colonisation of the Gut May Explain the Cirrhosis Virome Signature. 2026 PMID 42661387 PMC13522639
- Unique Features of Ethnic Mongolian Gut Microbiome revealed by metagenomic analysis. 2016 PMID 27708392 PMC5052615
- Quantitative metagenomics reveals unique gut microbiome biomarkers in ankylosing spondylitis. 2017 PMID 28750650 PMC5530561
- Identifying Group-Specific Sequences for Microbial Communities Using Long k-mer Sequence Signatures. 2018 PMID 29774017 PMC5943621
- Adaptive Evolution within Gut Microbiomes of Healthy People. 2019 PMID 31028005 PMC6749991
- MicroPro: using metagenomic unmapped reads to provide insights into human microbiota and disease associations. 2019 PMID 31387630 PMC6683435
- Establishing a novel colorectal cancer predictive model based on unique gut microbial single nucleotide variant markers. 2021 PMID 33430705 PMC7808391
- Compositional and genetic alterations in Graves' disease gut microbiome reveal specific diagnostic biomarkers. 2021 PMID 34079079 PMC8528855
- Comprehensive Strain-Level Analysis of the Gut Microbe Faecalibacterium prausnitzii in Patients with Liver Cirrhosis. 2021 PMID 34342541 PMC8407477
- Metagenomic analysis revealed the potential role of gut microbiome in gout. 2021 PMID 34373464 PMC8352958
- MetaGeneBank: a standardized database to study deep sequenced metagenomic data from human fecal specimen. 2021 PMID 34592929 PMC8485520
- Characterizing Enterotypes in Human Metagenomics: A Viral Perspective. 2021 PMID 34659174 PMC8511818
- Disentangling the Progression of Non-alcoholic Fatty Liver Disease in the Human Gut Microbiota. 2021 PMID 34721326 PMC8548776
- Multimodal deep learning applied to classify healthy and disease states of human microbiome. 2022 PMID 35039534 PMC8763943
- Investigation and characterization of human gut phageome in advanced liver cirrhosis of defined etiologies. 2022 PMID 35168645 PMC8845349
- Human disease prediction from microbiome data by multiple feature fusion and deep learning. 2022 PMID 35372808 PMC8971930
- More Positive or More Negative? Metagenomic Analysis Reveals Roles of Virome in Human Disease-Related Gut Microbiome. 2022 PMID 35493727 PMC9040671
- MegaD: Deep Learning for Rapid and Accurate Disease Status Prediction of Metagenomic Samples. 2022 PMID 35629336 PMC9143510
- Identification and Characterization of Major Bile Acid 7α-Dehydroxylating Bacteria in the Human Gut. 2022 PMID 35736002 PMC9426597
- Gut microbiota insights into human adaption to high-plateau diet. 2022 PMID 35989883 PMC9387673
- Faecal microbiome-based machine learning for multi-class disease diagnosis. 2022 PMID 36357393 PMC9649010
- Machine learning for data integration in human gut microbiome. 2022 PMID 36419034 PMC9685977
- 2 Hydroxybutyric Acid-Producing Bacteria in Gut Microbiome and Fusobacterium nucleatum Regulates 2 Hydroxybutyric Acid Level In Vivo. 2023 PMID 36984891 PMC10059959
- Toward an improved definition of a healthy microbiome for healthy aging. 2022 PMID 37118093 PMC10154212
- Microbial genes outperform species and SNVs as diagnostic markers for Crohn's disease on multicohort fecal metagenomes empowered by artificial intelligence. 2023 PMID 37278203 PMC10246480
- Gene-based microbiome representation enhances host phenotype classification. 2023 PMID 37404032 PMC10469787
- Four functional profiles for fibre and mucin metabolism in the human gut microbiome. 2023 PMID 37858269 PMC10588041
- Cross-cohort single-nucleotide-variant profiling of gut microbiota suggests a novel gut-health assessment approach. 2023 PMID 37905808 PMC10734426
- Multi-kingdom microbial signatures in excess body weight colorectal cancer based on global metagenomic analysis. 2024 PMID 38182885 PMC10770074
- The gut microbiome of Baka forager-horticulturalists from Cameroon is optimized for wild plant foods. 2024 PMID 38433907 PMC10904984
- Microbes with higher metabolic independence are enriched in human gut microbiomes under stress. 2025 PMID 40377187 PMC12084026
- Chinese soy-based microbiome and associated microbial risks: a metagenomic investigation. 2025 PMID 40681522 PMC12274573
- gutMSNP: a comprehensive database for human gut microbial single-nucleotide polymorphisms. 2026 PMID 41359024 PMC12807719
- Bacterial metabolic signatures in MASLD predicted through gene-centric studies in stool metagenomes. 2025 PMID 41413769 PMC12853991
- Multi-kingdom profiling reveals altered gut phage-bacteria-metabolite interactions in MASLD. 2026 PMID 42000726 PMC13275893
- CroCoDeEL: accurate control-free detection of cross-sample contamination in metagenomic data. 2026 PMID 42103726 PMC13377033
- Disrupted Gut Viral-Bacterial Ecology of Patients With Liver Cirrhosis. 2026 PMID 42587419 PMC13469701
Details
Archive description
Liver cirrhosis occurs as a consequence of many chronic liver diseases that are prevalent worldwide. Previous studies have shown an association between the gut microbiota and liver complications such as cirrhosis and other liver injuries. We therefore undertook a whole gut microbiome wide association study of stool samples from 98 liver cirrhosis patients and 83 healthy controls to characterise the faecal microbial communities and their functional composition. In total, we generated 860 Gb of high-quality sequence data and built a reference gene set for the liver cirrhosis cohort containing 2.69 million genes, 36.1% of which was not covered by previously published gene catalogues.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.75. Assay shotgun_dna.
- host study.description · “stool samples from 98 liver cirrhosis patients”
- body site study.description · “faecal microbial communities and their functional composition”
- life stage study.description · “98 liver cirrhosis patients and 83 healthy controls”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA2581875 | age_at_collection_days | 14610.0 | R2 | 0.75 | external.cmd source | age: 40; age_unit: Year; age_group: Adult |
| SAMEA2581875 | antibiotic_exposure | no | R2 | 0.75 | external.cmd source | antibiotics_current_use: No |
| SAMEA2581875 | bmi | 20.03 | R2 | 0.75 | external.cmd source | bmi: 20.03 |
| SAMEA2581875 | collection_date | 2011 | R1 | 0.90 | biosample.attribute:collection_date | 2011 |
| SAMEA2581875 | country | CN | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea_region | China |
| SAMEA2581875 | health_condition | healthy_control | R1 | 0.85 | biosample.attribute:DESCRIPTION | DESCRIPTION: Healthy samples for discovery |
| SAMEA2581875 | health_condition_detail | Healthy samples for discovery | R1 | 0.85 | biosample.attribute:DESCRIPTION | DESCRIPTION: Healthy samples for discovery |
| SAMEA2581875 | latitude | 30.0000 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 30 120 |
| SAMEA2581875 | location_site | First Affiliated Hospital, School of Medicine, Zhejiang University | R3 | 0.70 | paper.fulltext.methods | recruited at the First Affiliated Hospital, School of Medicine, Zhejiang University |
| SAMEA2581875 | longitude | 120.0000 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 30 120 |
| SAMEA2581875 | sex | female | R2 | 0.85 | paper.supp.metabolites-14-00132-s001.zip::SupplementaryTable.xlsx[Supplementary Table S1!Gender] | Female |
| SAMEA2581879 | sex | female | R2 | 0.75 | external.cmd source | sex: Female |
| SAMEA2581875 | subject_id | HD-1 | R1 | 0.70 | sample.name_rule:alias | HD-1_Run4 |
Sequencing
314 runs over 312 samples · mean 3.85 Gbp per run (median 3.08 Gbp, total 1,207.97 Gbp; 314 runs with a base count) · layout PAIRED 314 · platform ILLUMINA 314 · models Illumina HiSeq 2000 (314) · 75% of runs with a Sandpiper profile · first public 2014-06-13 – 2014-06-16
Authors (41)
Medina-Méndez JM first · Iruzubieta P · Fernández-López R · Crespo J · de la Cruz F last · Zhou X first · Zhou D · Pu Y · Kim H · Sun Z · Qi W · Jin J · Zhang W · Xia M · Wang C · Hong S · Nguyen LH · Jiao N · Zheng Y · Liu T last · Goulet L first · Plaza Oñate F · Famechon A · Quinquis B · Belda E · Prifti E · Le Chatelier E · Gautreau G last · Chang H first · Yang Y · Zhang P · Lei Z · Zhang Y · Li S · Wang L · Wang Y · Jiang J · Li L · Shi H · Shi A last · Zavos C first last
Downloads
PRJEB6337.csv.gz (10.5 KB) · parquet (85.3 KB) — all 312 samples, every field with route and confidence · PRJEB6337_determinations.csv.gz (31.9 KB) — 3,744 evidence rows
Samples (312 · every field this project has values for · hover a cell for its source)
Loading the sample table…