Gut microbiome of healthy Japanese adults, cross-sectional
Cross-sectional study of 1268 gut microbiome samples from healthy Japanese individuals, mainly from Hokkaido, with additional samples from Tokyo, Nagasaki, Kyoto, and Miyazaki. machine-written summary
1,268 samples · 1,268 runs · JP · Age unknown · 2024 · 7.92 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 5,745 sample values (collection date, country, latitude, location region, longitude) |
| – Abstract / description | no abstract or project description |
| – Full text | no open-access full text linked |
| – Supplementary tables | no supplementary tables available (or none open access) |
| ✓ External resources | 2,536 sample values (health condition, health condition detail) · from GMrepo v3 |
| – User contribution | nothing uploaded yet · share metadata |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Genera, mean relative abundance over 1,128 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 | 1,268 | 100% | 1,268 | |||
| health_condition | 1,268 | 100% | 1,268 | |||
| subject_id | 0 | 0% | ||||
| detailed_location | 1,268 | 100% | ||||
| health_condition_detail | 1,268 | 100% | 1,268 | |||
| latitude | 1,268 | 100% | 1,268 | |||
| location_region | 1,268 | 100% | 1,268 | |||
| longitude | 1,268 | 100% | 1,268 | |||
| collection_date | 673 | 53% | 673 |
Archive description
Gut microbiome of healthy Japanese
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.host_tax_id · “9606”
- body site study.title · “Gut microbiome of healthy Japanese”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN39971309 | collection_date | 2019-06-23 | R1 | 0.90 | biosample.attribute:collection_date | 2019-06-23 |
| SAMN39971309 | country | JP | R1 | 0.90 | sample.attr.geo_loc_name | Japan: Hokkaido |
| SAMN39971309 | health_condition | healthy_control | R2 | 0.75 | external.gmrepo source | phenotype: Health |
| SAMN39971309 | health_condition_detail | Health | R2 | 0.75 | external.gmrepo source | phenotype: Health |
| SAMN39971309 | latitude | 43.2842 | R1 | 0.90 | biosample.attribute:lat_lon | 43.28418022 N 142.63752112 E |
| SAMN39971309 | location_region | Hokkaido | R1 | 0.85 | biosample.attribute:geo_loc_name | Japan: Hokkaido |
| SAMN39971309 | longitude | 142.6375 | R1 | 0.90 | biosample.attribute:lat_lon | 43.28418022 N 142.63752112 E |
Sequencing
1,268 runs over 1,268 samples · mean 7.88 Gbp per run (median 7.92 Gbp, total 9,994.59 Gbp; 1,268 runs with a base count) · layout PAIRED 1,268 · platform ILLUMINA 1,268 · models Illumina NovaSeq 6000 (1,268) · 89% of runs with a Sandpiper profile · first public 2024-03-23
Authors (0)
No author record.
Help complete this project
2 of the 4 core fields are below 50% coverage: age_category, subject_id. Share metadata
Downloads
PRJNA1077400.csv.gz (29.8 KB) · parquet (115.3 KB) — all 1,268 samples, every field with route and confidence · PRJNA1077400_determinations.csv.gz (47.8 KB) — 8,281 evidence rows