Gut microbiota in dietary intervention study, Japan
45 gut microbiome samples from adults in Tokyo (Shinjuku) and Osaka (Settsu), Japan, collected as part of a dietary intervention study examining factors affecting energy balance via digestion and absorption rate. machine-written summary
45 samples · 45 runs · JP · Adult · 2025 · 7.75 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 555 sample values (age, collection date, country, diet, diet detail, intervention, intervention detail, latitude) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 165 sample values (antibiotic exposure, diet, diet detail, health condition, health condition detail) · PMC12150606 |
| ○ 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
Controlled / prescribed diet or feeding regimen design single_arm_before_after · Controlled diet study examining digestion/absorption and energy balance
“dietary intervention study UMIN000047018” — bioproject.description (study level; per-sample arms are in the intervention column below)
longitudinal
15 of 15 people sampled more than once (45 samples; median 3, up to 3 per person) · follow-up median 2 mo (max 3 mo) · median interval between samples 31 d (time from collection months (month precision)). Schedule stated by the source: “feces collected during each 8-day condition (OF, CON, UF), days 5-8, crossover with ≥3 week washout” (time origin: intervention_start).
Each row is one person (15 shown); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 45 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 | 45 | 100% | ||||
| country | 45 | 100% | 45 | |||
| health_condition | 45 | 100% | 45 | |||
| subject_id | 45 | 100% | 45 | |||
| age_at_collection_days | 45 | 100% | 45 | |||
| antibiotic_exposure | 45 | 100% | 45 | |||
| collection_date | 45 | 100% | 45 | |||
| detailed_location | 45 | 100% | ||||
| diet | 45 | 100% | 30 | 15 | ||
| diet_detail | 45 | 100% | 30 | 15 | ||
| health_condition_detail | 45 | 100% | 45 | |||
| intervention | 45 | 100% | 45 | |||
| intervention_detail | 45 | 100% | 45 | |||
| latitude | 45 | 100% | 45 | |||
| location_locality | 45 | 100% | 45 | |||
| location_region | 45 | 100% | 45 | |||
| longitude | 45 | 100% | 45 | |||
| sex | 45 | 100% | 45 |
- Effect of short-term dietary intervention on fecal serotonin, gut microbiome-derived tryptophanase, and energy absorption in a randomized crossover trial: an exploratory analysis. 2025 PMID 40488306 PMC12150606 own_data
Archive description
Shotgun metagenomic sequence of gut microbiota of dietary intervention study UMIN000047018: a study on the factors affecting the variation of energy balance focusing on the digestion and absorption rate.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.70. Assay shotgun_dna.
- host run.scientific_name · “human gut metagenome”
- body site study.title · “Gut microbiota of dietary intervention study”
- life stage sample.attr.host_age · “20-24 (n=45/45)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMD00797372 | age_at_collection_days | 7933.0 | R1 | 0.85 | sample.attr.host_age | 20-24 |
| SAMD00797372 | antibiotic_exposure | no | R3 | 0.70 | paper.body.methods | the participants did not have digestion/absorption-related illnesses or use antibiotics |
| SAMD00797372 | collection_date | 2022-03 | R1 | 0.90 | biosample.attribute:collection_date | 2022-03 |
| SAMD00797372 | country | JP | R1 | 0.90 | sample.attr.geo_loc_name | Japan:Tokyo, Shinjuku |
| SAMD00797372 | diet | therapeutic_or_study_diet | R1 | 0.90 | biosample.attribute:host_diet | Overfeeding |
| SAMD00797382 | diet | therapeutic_or_study_diet | R3 | 0.70 | paper.body.methods | All diets had similar macronutrient profiles (15% protein, 30% fat, and 55% carbohydrate) |
| SAMD00797372 | diet_detail | Overfeeding | R1 | 0.90 | biosample.attribute:host_diet | Overfeeding |
| SAMD00797382 | diet_detail | controlled study diet varying only in energy intake | R3 | 0.70 | paper.body.methods | All diets had similar macronutrient profiles (15% protein, 30% fat, and 55% carbohydrate) |
| SAMD00797372 | health_condition | healthy_control | R3 | 0.70 | paper.body.methods | Fifteen healthy males and females aged ≥20 years were included in this study |
| SAMD00797372 | health_condition_detail | healthy males and females | R3 | 0.70 | paper.body.methods | Fifteen healthy males and females aged ≥20 years were included in this study |
| SAMD00797372 | intervention | diet_intervention | R1 | 0.90 | biosample.attribute:host_diet | host_diet: Overfeeding |
| SAMD00797372 | intervention_detail | overfeeding (caloric excess) diet arm | R1 | 0.90 | biosample.attribute:host_diet | host_diet: Overfeeding |
| SAMD00797372 | latitude | 35.6900 | R1 | 0.90 | biosample.attribute:lat_lon | 35.69 N 139.70 E |
| SAMD00797372 | location_locality | Shinjuku | R1 | 0.85 | biosample.attribute:geo_loc_name | Japan:Tokyo, Shinjuku |
| SAMD00797372 | location_region | Tokyo | R1 | 0.85 | biosample.attribute:geo_loc_name | Japan:Tokyo, Shinjuku |
| SAMD00797372 | longitude | 139.7000 | R1 | 0.90 | biosample.attribute:lat_lon | 35.69 N 139.70 E |
| SAMD00797372 | sex | male | R1 | 0.90 | sample.attr.host_sex | male |
| SAMD00797372 | subject_id | PN015289 | R1 | 0.85 | sample.attr.host_subject_id | PN015289 |
Sequencing
45 runs over 45 samples · mean 6.45 Gbp per run (median 7.75 Gbp, total 290.37 Gbp; 45 runs with a base count) · layout PAIRED 45 · platform ILLUMINA 45 · models Illumina NovaSeq 6000 (45) · 100% of runs with a Sandpiper profile · first public 2025-06-18
Authors (0)
No author record.
Downloads
PRJDB18359.csv.gz (2.5 KB) · parquet (73.8 KB) — all 45 samples, every field with route and confidence · PRJDB18359_determinations.csv.gz (5.9 KB) — 720 evidence rows