Isocaloric high- vs low-protein diet RCT, Netherlands/France
430 gut metagenome samples from participants in a multi-center randomized controlled trial comparing isocaloric high-protein (n=79) versus low-protein (n=73) diets over 12 weeks, from the Netherlands and France. machine-written summary
430 samples · 430 runs · NL, FR · Age unknown · 2024 · 6.19 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 2,988 sample values (country, diet, diet detail, intervention, intervention detail, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 2,150 sample values (antibiotic exposure, health condition, health condition detail, medication, medication detail) · PMC10432813 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
intervention · arms resolved
134 people have samples in more than one arm.
Controlled / prescribed diet or feeding regimen design randomized_controlled_trial · High-protein vs low-protein isocaloric diet, 12 weeks
“randomized to follow either a HP” — bioproject.description (study level; per-sample arms are in the intervention column below)
longitudinal
148 of 153 people sampled more than once (418 samples; median 3, up to 3 per person) · follow-up median 3 mo (max 3 mo) · median interval between samples 42 d (time from timepoint labels). Schedule stated by the source: “Study visits at week 0 (baseline), week 6, and week 12 (end of intervention); sample titles encode visit as V1/V2/V3” (time origin: intervention start (randomization/baseline, week 0)); stated follow-up 3 mo.
Each row is one person (36 shown of 148); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 389 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 | 430 | 100% | 430 | |||
| health_condition | 430 | 100% | 430 | |||
| subject_id | 423 | 98% | 423 | |||
| antibiotic_exposure | 430 | 100% | 430 | |||
| health_condition_detail | 430 | 100% | 430 | |||
| intervention | 430 | 100% | 430 | |||
| medication | 430 | 100% | 430 | |||
| medication_detail | 430 | 100% | 430 | |||
| timepoint_label | 430 | 100% | 430 | |||
| diet | 425 | 99% | 425 | |||
| diet_detail | 425 | 99% | 425 | |||
| intervention_detail | 425 | 99% | 425 |
- Protein supplementation changes gut microbial diversity and derived metabolites in subjects with type 2 diabetes. 2023 PMID 37599833 PMC10432813 own_data
Archive description
shotgun metagenomics data from participants in a multi-center, randomized controlled isocaloric protein intervention with 152 participants that were randomized to follow either a HP (n=79) or LP (n=73) diet for 12 weeks.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.75. Assay shotgun_dna.
- host run.scientific_name · “human gut metagenome”
- body site run.scientific_name · “human gut metagenome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA114212908 | antibiotic_exposure | no | R3 | 0.70 | paper.fulltext.methods_results | Exclusion criteria were: use of insulin therapy, antibiotic usage within the last three months |
| SAMEA114212908 | country | FR | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | France |
| SAMEA114212908 | diet | therapeutic_or_study_diet | R1 | 0.90 | biosample.attribute:special_diet | Low protein diet 0 Weeks |
| SAMEA114212908 | diet_detail | Low protein diet 0 Weeks | R1 | 0.90 | biosample.attribute:special_diet | Low protein diet 0 Weeks |
| SAMEA114212908 | health_condition | type2_diabetes | R3 | 0.70 | paper.fulltext.methods_results | This study recruited non-insulin dependent individuals with T2D. |
| SAMEA114212908 | health_condition_detail | non-insulin dependent individuals with T2D, defined by the American Diabetes Association, on stable metformin ≥3 months | R3 | 0.70 | paper.fulltext.methods_results | This study recruited non-insulin dependent individuals with T2D. |
| SAMEA114212908 | intervention | no_intervention | R1 | 0.80 | biosample.attribute:special diet | special diet: Low protein diet 0 Weeks |
| SAMEA114212940 | intervention | no_intervention | R1 | 0.85 | biosample.attribute:special_diet | NA 0 Weeks |
| SAMEA114212908 | intervention_detail | baseline before low-protein diet (0 weeks) | R1 | 0.80 | biosample.attribute:special diet | special diet: Low protein diet 0 Weeks |
| SAMEA114212908 | medication | metformin | R3 | 0.70 | paper.fulltext.methods_results | All subjects were on stable metformin therapy and a subset also used other diabetes lowering drugs |
| SAMEA114212908 | medication_detail | stable use of metformin for ≥3 months, first-line antidiabetic drug | R3 | 0.70 | paper.fulltext.methods_results | All subjects were on stable metformin therapy and a subset also used other diabetes lowering drugs |
| SAMEA114212908 | subject_id | D010 | R1 | 0.70 | sample.name_rule:alias | D010_V1 |
| SAMEA114212908 | timepoint_label | week 0 | R1 | 0.85 | biosample.attribute:special_diet | Low protein diet 0 Weeks |
Sequencing
430 runs over 430 samples · mean 6.27 Gbp per run (median 6.19 Gbp, total 2,698.13 Gbp; 430 runs with a base count) · layout PAIRED 430 · platform ILLUMINA 430 · models Illumina NovaSeq 6000 (430) · 90% of runs with a Sandpiper profile · first public 2024-10-07
Authors (0)
No author record.
Downloads
PRJEB56830.csv.gz (12.3 KB) · parquet (87.7 KB) — all 430 samples, every field with route and confidence · PRJEB56830_determinations.csv.gz (39.9 KB) — 5,138 evidence rows