Gut metagenomes in MASLD vs controls, female nurses, USA
713 stool samples from a case-control study of women (Nurses' Health Study II) comparing metabolic dysfunction-associated steatotic liver disease (MASLD) cases to matched healthy controls, sampled in Utah, USA. machine-written summary
713 samples · 713 runs · US · Adult · 2025 · 3.96 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 3,565 sample values (collection date, country, latitude, location region, longitude) |
| ✓ Abstract / description | 713 sample values (subject id) |
| ✓ Full text | 713 sample values (sex) · PMC12320953, PMC13275893 |
| ○ 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 |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Genera, mean relative abundance over 702 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 | 713 | 100% | ||||
| country | 713 | 100% | 713 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 713 | 100% | 713 | |||
| collection_date | 713 | 100% | 713 | |||
| detailed_location | 713 | 100% | ||||
| latitude | 713 | 100% | 713 | |||
| location_region | 713 | 100% | 713 | |||
| longitude | 713 | 100% | 713 | |||
| sex | 713 | 100% | 713 |
- Multi-omic analysis reveals transkingdom gut dysbiosis in metabolic dysfunction-associated steatotic liver disease. 2025 PMID 40604156 PMC12320953 own_data
- Multi-kingdom profiling reveals altered gut phage-bacteria-metabolite interactions in MASLD. 2026 PMID 42000726 PMC13275893 unsure
Archive description
Leveraging a large-scale collection of stool specimens in the Micro-N study within the prospective cohort study (Nurses' Health Study II), we performed shotgun metagenomic sequencing and untargeted metabolomics profiling among 211 women with metabolic dysfunction-associated steatotic liver disease (MASLD), matched to age-, body mass index-, and location-matched healthy controls (total N with matched and unmatched controls=713). We found microbiome and metabolomic profiles to be altered in MASLD cases compared to controls. Data deposited include metagenomic sequencing data (after removing the human sequences) and metabolomics data.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.70. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.description · “large-scale collection of stool specimens in the Micro-N study”
- life stage study.description · “211 women with metabolic dysfunction-associated steatotic liver disease”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN47769379 | collection_date | 2022-04-12 | R1 | 0.90 | biosample.attribute:collection_date | 2022-04-12 |
| SAMN47769379 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA:Utah |
| SAMN47769379 | latitude | 40.7600 | R1 | 0.90 | biosample.attribute:lat_lon | 40.76 N 111.89 W |
| SAMN47769379 | location_region | Utah | R1 | 0.85 | biosample.attribute:geo_loc_name | USA:Utah |
| SAMN47769379 | longitude | -111.8900 | R1 | 0.90 | biosample.attribute:lat_lon | 40.76 N 111.89 W |
| SAMN47769379 | sex | female | R3 | 0.70 | paper.fulltext.methods | includes 116,429 female nurses aged 25–42 years |
| SAMN47769379 | subject_id | SAMN47769379 | R4 | 0.60 | design.one_sample_per_subject:abstract | 211 MASLD cases and 502 controls from a cohort of female nurses |
Sequencing
713 runs over 713 samples · mean 4.03 Gbp per run (median 3.96 Gbp, total 2,873.73 Gbp; 713 runs with a base count) · layout SINGLE 713 · platform ILLUMINA 713 · models Illumina HiSeq 4000 (713) · 98% of runs with a Sandpiper profile · first public 2025-04-05
Authors (34)
Kim H first · Nelson P · Nzabarushimana E · Shen J · Jensen J · Bhosle A · Li C · Lee N · Everett C · Berdy B · Frongillo G · Livny J · Hu FB · Simon TG · McIver L · Franzosa EA · Chan AT · Hayete B · Thompson KN · Huttenhower C · Nguyen LH last · Zhou X first · Zhou D · Pu Y · Sun Z · Qi W · Jin J · Zhang W · Xia M · Wang C · Hong S · Jiao N · Zheng Y · Liu T last
Downloads
PRJNA1246224.csv.gz (17.9 KB) · parquet (99.5 KB) — all 713 samples, every field with route and confidence · PRJNA1246224_determinations.csv.gz (28.8 KB) — 4,991 evidence rows