Gut microbiome and liver fibrosis risk, Hispanic adults
Cross-sectional study of 341 stool samples from a Hispanic cohort in the USA (269 adults, 72 elderly; 125 with type 2 diabetes), examining gut bacteria associated with liver fibrosis risk in NAFLD/MASH. machine-written summary
341 samples · 341 runs · US · Adult · 2023 · 2.83 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 2,853 sample values (age, collection date, country, health condition, health condition detail, latitude, longitude, sex) |
| ✓ Abstract / description | 341 sample values (location locality) |
| ✓ Full text | 341 sample values (antibiotic exposure) · PMC11382720, PMC11406975, PMC7109342, PMC8930512, PMC9238400 |
| ○ 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 303 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 | 341 | 100% | ||||
| country | 341 | 100% | 341 | |||
| health_condition | 125 | 37% | 125 | |||
| subject_id | 341 | 100% | 341 | |||
| age_at_collection_days | 341 | 100% | 341 | |||
| antibiotic_exposure | 341 | 100% | 341 | |||
| collection_date | 341 | 100% | 341 | |||
| detailed_location | 341 | 100% | ||||
| health_condition_detail | 341 | 100% | 341 | |||
| latitude | 341 | 100% | 341 | |||
| location_locality | 341 | 100% | 341 | |||
| longitude | 341 | 100% | 341 | |||
| sex | 341 | 100% | 341 |
- Gut microbiome features associated with liver fibrosis in Hispanics, a population at high risk for fatty liver disease. 2022 PMID 34633706 PMC8930512 own_data
- Gut Microbiome Alterations Associated with Diabetes in Mexican Americans in South Texas. 2022 PMID 35477306 PMC9238400 own_data
- Gut phageome in Mexican Americans: a population at high risk for metabolic dysfunction-associated steatotic liver disease and diabetes. 2024 PMID 39166873 PMC11406975 own_data
- Protection against fibrosis by a bacterial consortium in metabolic dysfunction-associated steatohepatitis and the role of amino acid metabolism. 2024 PMID 39239875 PMC11382720 own_data
- Bile Acid Changes Associated With Liver Fibrosis and Steatosis in the Mexican-American Population of South Texas 2020 PMID 32258950 PMC7109342 own_data
Archive description
This study aimed to identify microbiome signatures and microbial functions associated with NAFLD and common co-morbidities in the Hispanic population.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult and elderly by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- body site study.title · “Stool microbiome of Hispanics”
- body site external_curation.infant_catalog · “body_site_call gut”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- life stage sample.attr.age · “64 (n=83/341)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN19547594 | age_at_collection_days | 21549.8 | R1 | 0.70 | sample.attr.age | 59 |
| SAMN19547594 | antibiotic_exposure | no | R3 | 0.70 | paper.fulltext.methods | antibiotic, probiotic, or proton pump inhibitor use within 30 days, were excluded |
| SAMN19547594 | collection_date | 2018-08-06 | R1 | 0.90 | biosample.attribute:collection_date | 2018-08-06 |
| SAMN19547594 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA |
| SAMN19547594 | health_condition | type2_diabetes | R1 | 0.70 | biosample_attr | Diabetic |
| SAMN19547594 | health_condition_detail | Diabetic | R1 | 0.90 | sample.attr.diabetes_status | Diabetic |
| SAMN19547594 | latitude | 25.9000 | R1 | 0.90 | biosample.attribute:lat_lon | 25.90 N 97.49 W |
| SAMN19547594 | location_locality | Cameron County | R4 | 0.40 | ena.study_title | Cameron County Hispanic Cohort |
| SAMN19547594 | longitude | -97.4900 | R1 | 0.90 | biosample.attribute:lat_lon | 25.90 N 97.49 W |
| SAMN19547594 | sex | male | R1 | 0.90 | sample.attr.gender | male |
| SAMN19547594 | subject_id | 5Y1156 | R1 | 0.85 | biosample.attribute:DESCRIPTION | CCHC participant 5Y1156 |
Sequencing
341 runs over 341 samples · mean 2.92 Gbp per run (median 2.83 Gbp, total 994.06 Gbp; 341 runs with a base count) · layout PAIRED 341 · platform ILLUMINA 341 · models Illumina NovaSeq 6000 (198), Illumina HiSeq X (143) · 89% of runs with a Sandpiper profile · first public 2023-01-01 – 2024-07-23
Authors (26)
Kwan SY first · Jiao J · Qi J · Wang Y · Wei P · McCormick JB · Fisher-Hoch SP · Beretta L last · Joon A · Petty LE · Below JE · Daniel CR · Wu X · Zhang J · Jenq RR · Futreal PA · Hawk ET · Sabotta CM · Cruz LR · Wong MC · Ajami NJ · Gonzales KA · Jamal MA · Stevenson HL · Tan L · Lorenzi PL
Downloads
PRJNA734860.csv.gz (12.4 KB) · parquet (86.9 KB) — all 341 samples, every field with route and confidence · PRJNA734860_determinations.csv.gz (25.3 KB) — 3,535 evidence rows