Pediatric gut microbiome in NAFLD, case-control
124 fecal samples from children with liver disease (n=87) and healthy controls (n=37), studying the intestinal microbiome's relationship to NAFLD/NASH development and severity; case-control design. machine-written summary
124 samples · 124 runs · Child · 2019 · 3.70 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 458 sample values (health condition, health condition detail, sex, subject id) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC12101585 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 37 sample values (health condition) · from GMrepo v3 |
| – 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 1 sample (e.g. liver_disease vs healthy_control) — withheld.
The sources disagree on 1 sample. 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 (1)
| sample | field | value | other value | handling |
|---|---|---|---|---|
| SAMN12623430 | health condition | liver_disease (sequence archive) | healthy_control (GMrepo) | withheld: neither value published |
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 124 | 100% | ||||
| country | 0 | 0% | ||||
| health_condition | 123 | 99% | 86 | 37 | ||
| subject_id | 124 | 100% | 124 | |||
| health_condition_detail | 124 | 100% | 124 | |||
| sex | 124 | 100% | 124 |
- Meta-analysis of shotgun sequencing of gut microbiota in obese children with MASLD or MASH. 2025 PMID 40396204 PMC12101585 unsure
Archive description
Nonalcoholic fatty liver disease (NAFLD) is the most common cause of chronic liver disease in children in the United States. NAFLD is associated with obesity and metabolic syndrome however, there is limited understanding of the development and progression of NAFLD. There is evidence of abnormalities of bacterial colonization, and intestinal bacterial product-induced inflammation associated with NAFLD and disease progression. The goal of this study was to characterize the intestinal microbiome in pediatric participants with NAFLD and in both obese and normal weight controls to determine the relationship between alterations in the intestinal microbiome, inflammation, and the development of NAFLD. We hypothesized that alterations in the intestinal microbiome are associated with increased systemic inflammation and the development and severity of NAFLD.
How this project entered the registry
Classified as human gut / stool / blood / tissue / internal fluids shotgun DNA metagenome of child by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage reason_code age_child_over_36m”
- body site study.description · “bacterial colonization, and intestinal bacterial product-induced inflammation”
- body site external_curation.infant_catalog · “body_site_call stool”
- body site study.description · “Nonalcoholic fatty liver disease (NAFLD) is”
- life stage external_curation.infant_catalog · “infant triage reason_code age_child_over_36m”
- life stage study.description · “liver disease in children in the United”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN12623248 | health_condition | liver_disease | R1 | 0.90 | biosample_attr | Non-alcoholic Fatty Liver Disease |
| SAMN12623250 | health_condition | healthy_control | R2 | 0.75 | external.gmrepo source | phenotype: Health |
| SAMN12623248 | health_condition_detail | Non-alcoholic Fatty Liver Disease | R1 | 0.90 | sample.attr.study_disease | Non-alcoholic Fatty Liver Disease |
| SAMN12623248 | sex | male | R1 | 0.90 | sample.attr.sex | male |
| SAMN12623248 | subject_id | 2992965 | R1 | 0.85 | sample.attr.gap_subject_id | 2992965 |
Sequencing
124 runs over 124 samples · mean 3.73 Gbp per run (median 3.70 Gbp, total 462.58 Gbp; 124 runs with a base count) · layout PAIRED 124 · platform ILLUMINA 124 · models Illumina HiSeq 2000 (124) · 0% of runs with a Sandpiper profile · first public 2019-11-02
Authors (8)
Zöggeler T first · Kavallar AM · Pollio AR · Aldrian D · Decristoforo C · Scholl-Bürgi S · Müller T · Vogel GF last
Downloads
PRJNA546034.csv.gz (4.2 KB) · parquet (74.6 KB) — all 124 samples, every field with route and confidence · PRJNA546034_determinations.csv.gz (3.7 KB) — 495 evidence rows