Longitudinal gut microbiome in Danish youth obesity cohort
619 fecal samples from 5-19-year-old children and adolescents in Denmark, drawn from a hospital-based obesity clinic cohort and a population-based cohort, studied longitudinally. machine-written summary
619 samples · 1,238 runs · DK · Child · 2024 · 7.21 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,857 sample values (country, subject id, timepoint) |
| ✓ Abstract / description | 619 sample values (location locality) |
| – Full text | no open-access full text linked |
| – Supplementary tables | no supplementary tables available (or none open access) |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet · share metadata |
| – Human verified | not yet checked by a person · I checked this project — verify it |
intervention — arms not resolved
design observational_with_procedure
longitudinal — not resolved
200 of 419 people sampled more than once (400 samples; median 2, up to 2 per person). Schedule stated by the source: “Baseline sample before treatment initiation, with follow-up sample(s) at subsequent clinic contacts; up to 2 samples per subject.” (time origin: treatment start).
Genera, mean relative abundance over 592 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 | 0 | 0% | ||||
| country | 619 | 100% | 619 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 619 | 100% | 619 | |||
| detailed_location | 619 | 100% | ||||
| location_locality | 619 | 100% | 619 | |||
| timepoint_label | 619 | 100% | 619 |
Archive description
We collected fecal samples from 5-19-year-olds children and adolescents from a hospital-based obesity clinic cohort and from a population-based cohort. The hospital-based obesity clinic cohort consists of children and adolescents enrolled in multifaceted obesity management from January 2008 onwards at the hospital-based obesity clinic. These patients were received via referrals from their general practitioners, pediatric departments, or community-based doctors. In the hospital-based obesity clinic cohort, the longitudinal data collection began just prior to the initiation of treatment and continued with the subsequent contacts in the clinic in a systematic, family-based, person-centered, chronic care setting.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of child and adolescent 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.title · “Metagenomics of the gut microbiome in the”
- body site study.description · “We collected fecal samples from 5-19-year-olds”
- life stage external_curation.infant_catalog · “infant triage reason_code age_child_over_36m”
- life stage study.description · “samples from 5-19-year-olds children and adolescents from”
- life stage study.description · “5-19-year-olds children and adolescents from a hospital-based”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA116086105 | country | DK | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Denmark |
| SAMEA116086105 | location_locality | Holbaek | R4 | 0.40 | ena.study_title | Holbaek cohort |
| SAMEA116086105 | subject_id | CLDZM | R1 | 0.70 | sample.name_rule:alias | alias: HOLBAEK_CLDZM-BL |
| SAMEA116086105 | timepoint_label | baseline | R1 | 0.70 | sample.name_rule:alias | alias: HOLBAEK_CLDZM-BL |
Sequencing
1,238 runs over 619 samples · mean 3.71 Gbp per run (median 1.30 Gbp, total 4,594.43 Gbp; 1,238 runs with a base count) · layout PAIRED 619, SINGLE 619 · platform ILLUMINA 1,238 · models Illumina HiSeq 4000 (632), NextSeq 2000 (606) · 73% of runs with a Sandpiper profile · first public 2024-11-12
Authors (0)
No author record.
Help complete this project
2 of the 4 core fields are below 50% coverage: age_category, health_condition. Share metadata
Downloads
PRJEB81697.csv.gz (18.8 KB) · parquet (94.5 KB) — all 619 samples, every field with route and confidence · PRJEB81697_determinations.csv.gz (25.7 KB) — 2,476 evidence rows