Whole-grain diet crossover study, healthy adults, Copenhagen
185 gut metagenome samples from a whole-grain diet intervention study in Copenhagen, Denmark, mostly healthy controls, using a crossover design to assess effects on the gut microbiome and insulin sensitivity. machine-written summary
185 samples · 185 runs · DK · Age unknown · 2017 · 7.25 Gbp / sample · cohort Data integration for prediction of weight loss in
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 925 sample values (collection date, country, location locality, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC10408196, PMC13039869, PMC7674420 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 340 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 |
intervention — arms not resolved
Controlled / prescribed diet or feeding regimen design crossover · population cardiometabolic_other · Whole-grain rich diet cross-over feeding study
“Whole-Grain rich diet cross-over study” — study.title (study level; per-sample arms are in the intervention column below)
longitudinal
48 of 51 people sampled more than once (182 samples; median 4, up to 4 per person) · follow-up median 5 mo (max 9 mo) · median interval between samples 2 mo (time from collection months (month precision)).
Each row is one person (36 shown of 48); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 162 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 | 185 | 100% | 185 | |||
| health_condition | 170 | 92% | 170 | |||
| subject_id | 185 | 100% | 185 | |||
| collection_date | 185 | 100% | 185 | |||
| detailed_location | 185 | 100% | ||||
| location_locality | 185 | 100% | 185 | |||
| timepoint_label | 185 | 100% | 185 | |||
| health_condition_detail | 170 | 92% | 170 |
- Data integration for prediction of weight loss in randomized controlled dietary trials. 2020 PMID 33208769 PMC7674420 unsure
- Identification of robust and generalizable biomarkers for microbiome-based stratification in lifestyle interventions. 2023 PMID 37553697 PMC10408196 unsure
- pH regulates gut bacterial tryptophan metabolism. 2026 PMID 41730870 PMC13039869 unsure
Archive description
To investigate whether a wholegrain diet alters the gut microbiome and insulin sensitivity, as well as biomarkers of metabolic health and gut functionality.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.65. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site run.scientific_name · “human gut metagenome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN07414234 | collection_date | 2012-10 | R1 | 0.90 | biosample.attribute:collection_date | 2012-10 |
| SAMN07414234 | country | DK | R1 | 0.90 | sample.attr.geo_loc_name | Denmark: Copenhagen |
| SAMN07414234 | health_condition | healthy_control | R2 | 0.75 | external.gmrepo source | phenotype: Health |
| SAMN07414234 | health_condition_detail | Health | R2 | 0.75 | external.gmrepo source | phenotype: Health |
| SAMN07414234 | location_locality | Copenhagen | R1 | 0.85 | biosample.attribute:geo_loc_name | Denmark: Copenhagen |
| SAMN07414234 | subject_id | 5333 | R1 | 0.85 | sample.attr.individual | 5333 |
| SAMN07414234 | timepoint_label | 1 | R1 | 0.70 | sample.name_rule:alias | 5333_1 |
Sequencing
185 runs over 185 samples · mean 7.86 Gbp per run (median 7.25 Gbp, total 1,454.99 Gbp; 185 runs with a base count) · layout PAIRED 185 · platform ILLUMINA 185 · models Illumina HiSeq 2000 (185) · 88% of runs with a Sandpiper profile · first public 2017-07-27
Authors (42)
Nielsen RL first · Helenius M · Garcia SL · Roager HM · Aytan-Aktug D · Hansen LBS · Lind MV · Vogt JK · Dalgaard MD · Bahl MI · Jensen CB · Muktupavela R · Warinner C · Aaskov V · Gøbel R · Kristensen M · Frøkiær H · Sparholt MH · Christensen AF · Vestergaard H · Hansen T · Kristiansen K · Brix S · Petersen TN · Lauritzen L · Licht TR · Pedersen O · Gupta R last · Chen J first · Siliceo SL · Ni Y · Nielsen HB · Xu A · Panagiotou G last · Brinck JE first · Laursen MF · Pedersen M · Carey MR · Procházková N · Jørgensen MS · Mortensen MS · Sinha AK last
Downloads
PRJNA395744.csv.gz (5.5 KB) · parquet (76.8 KB) — all 185 samples, every field with route and confidence · PRJNA395744_determinations.csv.gz (9.4 KB) — 1,265 evidence rows