Metagenome in obese youth with/without NAFLD, New Haven, CT
36 fecal samples from adolescents and children with obesity in New Haven, CT, comparing microbiomes of those with and without nonalcoholic fatty liver disease (NAFLD) in a case-control design. machine-written summary
36 samples · 36 runs · US · Age unknown · 2022 · 3.68 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 354 sample values (age, collection date, country, health condition, health condition detail, latitude, location locality, location region) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 72 sample values (location site, subject id) · PMC10797006, PMC11264842, PMC12101585, PMC12866134, PMC7458486, PMC9315112 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 6 sample values (health condition, health condition detail) · from BugSigDB |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Genera, mean relative abundance over 32 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 | 36 | 100% | ||||
| country | 36 | 100% | 36 | |||
| health_condition | 36 | 100% | 33 | 3 | ||
| subject_id | 36 | 100% | 36 | |||
| age_at_collection_days | 36 | 100% | 36 | |||
| collection_date | 36 | 100% | 36 | |||
| detailed_location | 36 | 100% | ||||
| health_condition_detail | 36 | 100% | 33 | 3 | ||
| latitude | 36 | 100% | 36 | |||
| location_locality | 36 | 100% | 36 | |||
| location_region | 36 | 100% | 36 | |||
| location_site | 36 | 100% | 36 | |||
| longitude | 36 | 100% | 36 | |||
| sex | 36 | 100% | 36 |
- Effect of Gut Microbiota and PNPLA3 rs738409 Variant on Nonalcoholic Fatty Liver Disease (NAFLD) in Obese Youth. 2020 PMID 32561908 PMC7458486 own_data
- Insights from shotgun metagenomics into bacterial species and metabolic pathways associated with NAFLD in obese youth. 2022 PMID 35344283 PMC9315112 own_data
- The role of gut microbiota in the occurrence and progression of non-alcoholic fatty liver disease. 2023 PMID 38249477 PMC10797006 unsure
- Adolescent gut microbiome imbalance and its association with immune response in inflammatory bowel diseases and obesity. 2024 PMID 39030520 PMC11264842 unsure
- Meta-analysis of shotgun sequencing of gut microbiota in obese children with MASLD or MASH. 2025 PMID 40396204 PMC12101585 unsure
1 more
- Integrative multi-omics reveals microbial genomic variants driving altered host-microbe interactions in autism spectrum disorder. 2026 PMID 41421350 PMC12866134
Archive description
Evaluation of fecal microbiota associated with obesity.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of child and adolescent by sonnet_x2 with confidence 0.72. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- host run.scientific_name · “human gut metagenome”
- body site study.title · “feces metagenome Metagenome”
- life stage sample.attr.host_age · “10 (n=17/36)”
- life stage sample.attr.host_age · “13.2 (n=14/36)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN05590469 | age_at_collection_days | 3067.0 | R1 | 0.85 | sample.attr.host_age | 8.4 |
| SAMN05590469 | collection_date | 2012-11-09 | R1 | 0.90 | biosample.attribute:collection_date | 2012-11-09 |
| SAMN05590469 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: New Haven, CT |
| SAMN05590469 | health_condition | obesity | R1 | 0.85 | biosample.attribute:nafld | Absent |
| SAMN05590489 | health_condition | obesity | R2 | 0.60 | external.bugsigdb source | Obese youths without/with NAFLD |
| SAMN05590469 | health_condition_detail | nafld: no | R1 | 0.85 | sample.attr.nafld | Absent |
| SAMN05590489 | health_condition_detail | Non-alcoholic fatty liver disease | R2 | 0.60 | external.bugsigdb source | Condition: Non-alcoholic fatty liver disease |
| SAMN05590469 | latitude | 41.3083 | R1 | 0.90 | biosample.attribute:lat_lon | 41.3083 N 72.9279 W |
| SAMN05590469 | location_locality | New Haven | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: New Haven, CT |
| SAMN05590469 | location_region | Connecticut | R1 | 0.75 | biosample.attribute:geo_loc_name | USA: New Haven, CT |
| SAMN05590469 | location_site | Yale Pediatric Obesity Clinic | R3 | 0.70 | paper.fulltext.methods | recruited from the Yale Pediatric Obesity Clinic |
| SAMN05590469 | longitude | -72.9279 | R1 | 0.90 | biosample.attribute:lat_lon | 41.3083 N 72.9279 W |
| SAMN05590469 | sex | female | R1 | 0.90 | sample.attr.host_sex | female |
| SAMN05590469 | subject_id | SAMN05590469 | R3 | 0.75 | design.one_sample_per_subject:fulltext | A stool sample from each subject was also collected. |
Sequencing
36 runs over 36 samples · mean 3.82 Gbp per run (median 3.68 Gbp, total 137.60 Gbp; 36 runs with a base count) · layout PAIRED 36 · platform ILLUMINA 36 · models Illumina HiSeq 2500 (36) · 89% of runs with a Sandpiper profile · first public 2022-09-03
Authors (47)
Testerman T first · Li Z · Galuppo B · Graf J · Santoro N last · Mai H first · Yang X · Xie Y · Zhou J · Wang Q · Wei Y · Yang Y · Lu D · Ye L · Cui P · Liang H · Huang J last · Joo M first · Nam S last · Zöggeler T first · Kavallar AM · Pollio AR · Aldrian D · Decristoforo C · Scholl-Bürgi S · Müller T · Vogel GF last · Chen W first · Wang X · Zhu R · Gao W · Tao L · Yang R · Wei Q · Zhang Y · Gong Y · Zhong H · Huang L · Zhu X · Zhang L · Wan L · Yang G · Li Y · Jiao N · Wang J · Qin H · Zhu L last
Downloads
PRJNA328258.csv.gz (2.5 KB) · parquet (73.2 KB) — all 36 samples, every field with route and confidence · PRJNA328258_determinations.csv.gz (4.5 KB) — 432 evidence rows