Baseline gut microbiota in NAFLD prospective cohort
176 baseline faecal samples from a Shanghai, China cohort followed 4.6 years, comparing individuals who progressed to NAFLD versus matched controls who remained NAFLD-free, in a case-control design. machine-written summary
176 samples · 176 runs · CN · Age unknown · 2022 · 7.36 Gbp / sample · cohort Risk assessment with gut microbiome and metabolite
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,142 sample values (collection date, country, health condition, health condition detail, latitude, location locality, longitude) |
| ✓ Abstract / description | 176 sample values (subject id) |
| ✓ Full text | 176 sample values (location region) · PMC12763994, PMC9746350 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 176 sample values (antibiotic exposure) · from BugSigDB |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
intervention — arms not resolved
design observational_with_procedure
Genera, mean relative abundance over 155 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 | 176 | 100% | ||||
| country | 176 | 100% | 176 | |||
| health_condition | 86 | 49% | 86 | |||
| subject_id | 176 | 100% | 176 | |||
| antibiotic_exposure | 176 | 100% | 176 | |||
| collection_date | 176 | 100% | 176 | |||
| detailed_location | 176 | 100% | ||||
| health_condition_detail | 176 | 100% | 176 | |||
| latitude | 176 | 100% | 176 | |||
| location_locality | 176 | 100% | 176 | |||
| location_region | 176 | 100% | 176 | |||
| longitude | 176 | 100% | 176 |
- Risk assessment with gut microbiome and metabolite markers in NAFLD development. 2022 PMID 35675435 PMC9746350 own_data
- Discovery of robust and highly specific microbiome signatures of non-alcoholic fatty liver disease. 2025 PMID 39810263 PMC11730835 unsure
- Characterization of the gut mycobiome in patients with non-alcoholic fatty liver disease and correlations with serum metabolome. 2025 PMID 41087898 PMC12522779 unsure
- Characterization of the gut virome in patients with nonalcoholic fatty liver disease. 2025 PMID 41316248 PMC12763994 unsure
Archive description
A 4.6-year non-alcoholic fatty liver disease prospective (NAFLD) study. Faecal samples of individuals were collected at baseline where no one was diagnosed with NAFLD.
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”
- body site study.description · “Faecal samples of individuals were collected”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN19107326 | antibiotic_exposure | no | R2 | 0.60 | external.bugsigdb source | Antibiotics exclusion: 2 weeks |
| SAMN19107326 | collection_date | 2014-05 | R1 | 0.90 | biosample.attribute:collection_date | 2014-05 |
| SAMN19107326 | country | CN | R1 | 0.90 | sample.attr.geo_loc_name | China: Shanghai |
| SAMN19107326 | health_condition | cardiometabolic_other | R1 | 0.90 | biosample_attr | NAFLD |
| SAMN19107326 | health_condition_detail | NAFLD | R1 | 0.90 | sample.attr.group_by_nafld_status_in_2018 | NAFLD |
| SAMN19107326 | latitude | 30.5300 | R1 | 0.90 | biosample.attribute:lat_lon | 30.53 N 121.48 E |
| SAMN19107326 | location_locality | Shanghai | R1 | 0.85 | biosample.attribute:geo_loc_name | China: Shanghai |
| SAMN19107326 | location_region | Shanghai | R3 | 0.70 | paper.fulltext.methods | a suburb of Shanghai, China |
| SAMN19107326 | longitude | 121.4800 | R1 | 0.90 | biosample.attribute:lat_lon | 30.53 N 121.48 E |
| SAMN19107326 | subject_id | SAMN19107326 | R4 | 0.65 | design.one_sample_per_subject:description | Faecal samples of individuals were collected at baseline where no one was diagnosed with NAFLD. |
Sequencing
176 runs over 176 samples · mean 7.46 Gbp per run (median 7.36 Gbp, total 1,312.93 Gbp; 176 runs with a base count) · layout PAIRED 176 · platform ILLUMINA 176 · models Illumina NovaSeq 6000 (176) · 88% of runs with a Sandpiper profile · first public 2022-07-12 – 2022-09-30
Authors (39)
Leung H first · Long X · Ni Y · Qian L · Nychas E · Siliceo SL · Pohl D · Hanhineva K · Liu Y · Xu A · Nielsen HB · Belda E · Clément K · Loomba R · Li H · Jia W · Panagiotou G last · Marfil-Sánchez A · Chen X · Mirhakkak M · Nieuwdorp M · Zheng N first · Wang D · Xing G · Gao Y · Li S · Liu J · Kang J · Sha S · Cheng L · Fan S · Yu J · Yan Q · Jiang C last · Wang L first · Liu M · Yuan Q · Chen H · Mao S
Downloads
PRJNA728908.csv.gz (5.5 KB) · parquet (78.2 KB) — all 176 samples, every field with route and confidence · PRJNA728908_determinations.csv.gz (10.4 KB) — 1,670 evidence rows