Gut metagenomic signature for advanced fibrosis in NAFLD
86 stool shotgun metagenome samples from a case-control study examining a gut-microbiota signature for detecting advanced (stage 3-4) liver fibrosis in NAFLD patients. machine-written summary
86 samples · 86 runs · US · Age unknown · 2017 · 6.30 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 308 sample values (collection date, health condition, health condition detail, subject id) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC11085954, PMC11882788, PMC12147647, PMC12677068, PMC12853991, PMC13170203, PMC13403911, PMC5502730, PMC8424563, PMC8485520, PMC8511818, PMC8548776, PMC8845349, PMC9426597 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 86 sample values (country) · from curatedMetagenomicData 3 (cMD 3) |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
health condition: sequence archive and GMrepo disagree for 36 samples (e.g. liver_disease vs healthy_control) — withheld.
The sources disagree on 36 samples. Where two incompatible values exist for one sample (or one person's samples disagree on sex), neither value is published: the field is left empty here, in the sample sheet and in the downloads. Both sides, with their sources, are in gut_metadata_contradictions.parquet of the data package (what counts as a contradiction).
Contradicted values (36)
| sample | field | value | other value | handling |
|---|---|---|---|---|
| SAMN06328466 | health condition | liver_disease (sequence archive) | healthy_control (GMrepo) | withheld: neither value published |
| SAMN06328467 | health condition | liver_disease (sequence archive) | healthy_control (GMrepo) | withheld: neither value published |
| SAMN06328468 | health condition | liver_disease (sequence archive) | healthy_control (GMrepo) | withheld: neither value published |
| SAMN06328469 | health condition | liver_disease (sequence archive) | healthy_control (GMrepo) | withheld: neither value published |
| SAMN06328470 | health condition | liver_disease (sequence archive) | healthy_control (GMrepo) | withheld: neither value published |
| SAMN06328471 | health condition | liver_disease (sequence archive) | healthy_control (GMrepo) | withheld: neither value published |
| SAMN06328472 | health condition | liver_disease (sequence archive) | healthy_control (GMrepo) | withheld: neither value published |
| SAMN06328473 | health condition | liver_disease (sequence archive) | healthy_control (GMrepo) | withheld: neither value published |
| SAMN06328474 | health condition | liver_disease (sequence archive) | healthy_control (GMrepo) | withheld: neither value published |
| SAMN06328475 | health condition | liver_disease (sequence archive) | healthy_control (GMrepo) | withheld: neither value published |
| SAMN06328476 | health condition | liver_disease (sequence archive) | healthy_control (GMrepo) | withheld: neither value published |
| SAMN06328477 | health condition | liver_disease (sequence archive) | healthy_control (GMrepo) | withheld: neither value published |
| SAMN06328478 | health condition | liver_disease (sequence archive) | healthy_control (GMrepo) | withheld: neither value published |
| SAMN06328479 | health condition | liver_disease (sequence archive) | healthy_control (GMrepo) | withheld: neither value published |
| SAMN06328480 | health condition | liver_disease (sequence archive) | healthy_control (GMrepo) | withheld: neither value published |
| SAMN06328481 | health condition | liver_disease (sequence archive) | healthy_control (GMrepo) | withheld: neither value published |
| SAMN06328482 | health condition | liver_disease (sequence archive) | healthy_control (GMrepo) | withheld: neither value published |
| SAMN06328483 | health condition | liver_disease (sequence archive) | healthy_control (GMrepo) | withheld: neither value published |
| SAMN06328484 | health condition | liver_disease (sequence archive) | healthy_control (GMrepo) | withheld: neither value published |
| SAMN06328485 | health condition | liver_disease (sequence archive) | healthy_control (GMrepo) | withheld: neither value published |
| SAMN06328486 | health condition | liver_disease (sequence archive) | healthy_control (GMrepo) | withheld: neither value published |
| SAMN06328487 | health condition | liver_disease (sequence archive) | healthy_control (GMrepo) | withheld: neither value published |
| SAMN06328488 | health condition | liver_disease (sequence archive) | healthy_control (GMrepo) | withheld: neither value published |
| SAMN06328489 | health condition | liver_disease (sequence archive) | healthy_control (GMrepo) | withheld: neither value published |
| SAMN06328490 | health condition | liver_disease (sequence archive) | healthy_control (GMrepo) | withheld: neither value published |
| SAMN06328491 | health condition | liver_disease (sequence archive) | healthy_control (GMrepo) | withheld: neither value published |
| SAMN06328492 | health condition | liver_disease (sequence archive) | healthy_control (GMrepo) | withheld: neither value published |
| SAMN06328493 | health condition | liver_disease (sequence archive) | healthy_control (GMrepo) | withheld: neither value published |
| SAMN06328494 | health condition | liver_disease (sequence archive) | healthy_control (GMrepo) | withheld: neither value published |
| SAMN06328495 | health condition | liver_disease (sequence archive) | healthy_control (GMrepo) | withheld: neither value published |
| SAMN06328496 | health condition | liver_disease (sequence archive) | healthy_control (GMrepo) | withheld: neither value published |
| SAMN06328497 | health condition | liver_disease (sequence archive) | healthy_control (GMrepo) | withheld: neither value published |
| SAMN06328498 | health condition | liver_disease (sequence archive) | healthy_control (GMrepo) | withheld: neither value published |
| SAMN06328499 | health condition | liver_disease (sequence archive) | healthy_control (GMrepo) | withheld: neither value published |
| SAMN06328500 | health condition | liver_disease (sequence archive) | healthy_control (GMrepo) | withheld: neither value published |
| SAMN06328501 | health condition | liver_disease (sequence archive) | healthy_control (GMrepo) | withheld: neither value published |
Genera, mean relative abundance over 76 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 | 0 | 0% | ||||
| country | 86 | 100% | 86 | |||
| health_condition | 50 | 58% | 50 | |||
| subject_id | 86 | 100% | 86 | |||
| collection_date | 86 | 100% | 86 | |||
| health_condition_detail | 86 | 100% | 86 |
- Gut Microbiome-Based Metagenomic Signature for Non-invasive Detection of Advanced Fibrosis in Human Nonalcoholic Fatty Liver Disease. 2017 PMID 28467925 PMC5502730 own_data
- Anti-diabetic effect of dicaffeoylquinic acids is associated with the modulation of gut microbiota and bile acid metabolism. 2025 PMID 38969095 PMC12147647 own_data
- Microbiota-derived H<sub>2</sub>S induces c-kit<sup>+</sup> cDC1 autophagic cell death and liver inflammation in metabolic dysfunction-associated steatohepatitis. 2025 PMID 40044736 PMC11882788 own_data
- Alterations in bile acid metabolizing gut microbiota and specific bile acid genes as a precision medicine to subclassify NAFLD. 2021 PMID 34151600 PMC8424563 unsure
- MetaGeneBank: a standardized database to study deep sequenced metagenomic data from human fecal specimen. 2021 PMID 34592929 PMC8485520 unsure
9 more
- 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
- Investigation and characterization of human gut phageome in advanced liver cirrhosis of defined etiologies. 2022 PMID 35168645 PMC8845349
- Identification and Characterization of Major Bile Acid 7α-Dehydroxylating Bacteria in the Human Gut. 2022 PMID 35736002 PMC9426597
- Christensenella strain resources, genomic/metabolomic profiling, and association with host at species level. 2024 PMID 38722028 PMC11085954
- <i>Christensenella intestinihominis</i> MNO-863 improve obesity and related metabolic disorders via SCFAs-induced GLP-1 hormone secretion. 2025 PMID 41356823 PMC12677068
- Bacterial metabolic signatures in MASLD predicted through gene-centric studies in stool metagenomes. 2025 PMID 41413769 PMC12853991
- Multicohort Validation of Gut Microbiome Signatures for Cholangiocarcinoma Diagnosis and Functional Characterization of Bifidobacterium Pseudocatenulatum. 2026 PMID 41816992 PMC13170203
- Gut-Liver Translocation of Bacteroides Uniformis Alleviates Advanced Metabolic Dysfunction-Associated Steatotic Liver Disease by Suppressing Hepatocyte Ferroptosis via Propionic Acid Secretion. 2026 PMID 42505071 PMC13403911
Archive description
The presence of advanced fibrosis in nonalcoholic fatty liver disease (NAFLD) is the most important predictor of liver mortality. The aim of this study was to examine the diagnostic</p><p>accuracy of a gut-microbiota derived metagenomic signature for detecting the presence of advanced fibrosis in NAFLD. In this prospective study, we characterized the microbiome signatures associated with advanced fibrosis (defined as stage 3 or 4 fibrosis) in uniquely well characterized biopsy- and imaging-phenotyped patients with NAFLD. Gut microbiome</p><p>compositions of the patients were determined using whole-genome shotgun sequencing of DNA extracted from stool samples.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by opus_adjudicated with confidence 0.85. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- host study.description · “phenotyped patients with NAFLD”
- body site study.description · “DNA extracted from stool samples”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN06328416 | collection_date | 2014-09-10 | R1 | 0.90 | biosample.attribute:collection_date | 2014-09-10 |
| SAMN06328416 | country | US | R2 | 0.75 | external.cmd source | country: United States |
| SAMN06328416 | health_condition | liver_disease | R1 | 0.85 | biosample.attribute:description | Fibrosis stage 4 |
| SAMN06328416 | health_condition_detail | Fibrosis stage 4 | R1 | 0.90 | sample.attr.liver_disord | Fibrosis stage 4 |
| SAMN06328416 | subject_id | subject-0006 | R1 | 0.85 | sample.attr.host_subject_id | subject-0006 |
Sequencing
86 runs over 86 samples · mean 7.21 Gbp per run (median 6.30 Gbp, total 620.28 Gbp; 86 runs with a base count) · layout PAIRED 86 · platform ILLUMINA 86 · models Illumina HiSeq 2500 (86) · 88% of runs with a Sandpiper profile · first public 2017-02-28
Authors (52)
Naseri M first · Palizban F · Yadegar A · Khodarahmi M · Asadzadeh Aghdaei H · Houri H · Zahiri J last · Kong P first · Xian Y · Lao C · Huang B · Zhang D · Tai L · Zhao Y · Pu Z · Lan Z · Zhang C · Liu Z · Xiao C · Zhao G · Zhu R · Liang Y · Lin CS · Lin JH · Sun JZ · Wang T · Liu HW · Jiang X last · Medina-Méndez JM first · Iruzubieta P · Fernández-López R · Crespo J · de la Cruz F last · Rao B first · Jiang J · Zhang R · Li A · Lu H · Zhang H · Zhou L · Guo W · Wen P · Xue J · Pan J · Aji T · Zheng S · Yu Z · Ren Z last · Liu H first · Fan Z · Qin L · Zhao X last
Downloads
PRJNA373901.csv.gz (3.5 KB) · parquet (74.0 KB) — all 86 samples, every field with route and confidence · PRJNA373901_determinations.csv.gz (4.9 KB) — 394 evidence rows