Fecal metagenome in non-cirrhotic NASH vs controls, USA
Case-control study of 307 fecal samples from US adults, comparing biopsy-proven non-cirrhotic NASH (F1-F3 fibrosis) patients to healthy controls using shotgun metagenomics and fecal bile acid metabolomics. machine-written summary
307 samples · 307 runs · US · Adult · 2023 · 3.05 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,535 sample values (country, latitude, location region, longitude, subject id) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC10674038 |
| – Supplementary tables | no supplementary tables available (or none open access) |
| ✓ External resources | 558 sample values (health condition, health condition detail) · from GMrepo v3 |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Genera, mean relative abundance over 260 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 | 307 | 100% | ||||
| country | 307 | 100% | 307 | |||
| health_condition | 279 | 91% | 279 | |||
| subject_id | 307 | 100% | 307 | |||
| detailed_location | 307 | 100% | ||||
| latitude | 307 | 100% | 307 | |||
| location_region | 307 | 100% | 307 | |||
| longitude | 307 | 100% | 307 | |||
| health_condition_detail | 279 | 91% | 279 |
- An integrated analysis of fecal microbiome and metabolomic features distinguish non-cirrhotic NASH from healthy control populations. 2023 PMID 37222264 PMC10674038 own_data
Archive description
There is great interest in identifying microbiome features as reliable noninvasive diagnostic and/or prognostic biomarkers for non-cirrhotic NASH fibrosis. Several cross-sectional studies have reported gut microbiome features associated with advanced NASH fibrosis and cirrhosis, where the most prominent features are associated with cirrhosis. However, no large, prospectively collected data exist establishing microbiome features that discern non-cirrhotic NASH fibrosis, integrate the fecal metabolome as disease biomarkers, and are unconfounded by BMI and age. Results from shotgun metagenomic sequencing performed on fecal samples prospectively collected from 279 US patients with biopsy-proven NASH (F1-F3 fibrosis) enrolled in the REGENERATE I303 study were compared to those from three healthy control cohorts and integrated with the absolute quantification of fecal bile acids. Microbiota beta-diversity was different, and BMI- and age-adjusted logistic regression identified 12 NASH-associated species. Random forest prediction models resulted in an AUC of 0.75 to 0.81 in a receiver operator characteristic analysis. Additionally, specific fecal bile acids were significantly lower in NASH and correlated with plasma C4 levels. Microbial gene abundance analysis revealed 127 genes increased in controls, many involving protein synthesis, whereas 362 genes were increased in NASH many involving bacterial environmental responses (FDR < 0.01). Finally, we provide evidence that fecal bile acid levels may be a better discriminator of non-cirrhotic NASH versus health than either plasma bile acids or gut microbiome features. These results may have value as a set of baseline characteristics of non-cirrhotic NASH against which therapeutic interventions to prevent cirrhosis can be compared and microbiome-based diagnostic biomarkers identified.
How this project entered the registry
Classified as human gut / stool / blood / tissue / internal fluids shotgun DNA metagenome of adult 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 · “integrated analysis of fecal microbiome and metabolomic”
- body site study.description · “studies have reported gut microbiome features associated”
- body site study.description · “US patients with biopsy -proven NASH (F1-F3”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN36736951 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA |
| SAMN36736979 | health_condition | cardiometabolic_other | R2 | 0.75 | external.gmrepo source | phenotype: Non-alcoholic Fatty Liver Disease |
| SAMN36736979 | health_condition_detail | Non-alcoholic Fatty Liver Disease | R2 | 0.75 | external.gmrepo source | phenotype: Non-alcoholic Fatty Liver Disease |
| SAMN36736951 | latitude | 39.9473 | R1 | 0.90 | biosample.attribute:lat_lon | 39.9473 N 75.1958 W |
| SAMN36736951 | location_region | Pennsylvania | R1 | 0.60 | biosample.attribute:lat_lon | 39.9473 N 75.1958 W |
| SAMN36736951 | longitude | -75.1958 | R1 | 0.90 | biosample.attribute:lat_lon | 39.9473 N 75.1958 W |
| SAMN36736951 | subject_id | Vibriolambda7 | R1 | 0.85 | sample.attr.subject_id | Vibriolambda7 |
Sequencing
307 runs over 307 samples · mean 2.96 Gbp per run (median 3.05 Gbp, total 907.48 Gbp; 307 runs with a base count) · layout PAIRED 307 · platform ILLUMINA 307 · models Illumina HiSeq 2500 (307) · 85% of runs with a Sandpiper profile · first public 2023-07-29
Authors (0)
No author record.
Downloads
PRJNA999593.csv.gz (8.6 KB) · parquet (82.7 KB) — all 307 samples, every field with route and confidence · PRJNA999593_determinations.csv.gz (14.9 KB) — 2,093 evidence rows