Gut metagenome in Japanese colonoscopy patients, cross-sectional
50 fecal metagenome samples from Japanese patients who underwent colonoscopy at National Cancer Research Center, including healthy individuals and those with gastrectomy; cross-sectional design. machine-written summary
50 samples · 50 runs · JP · Age unknown · 2019 · 6.61 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 210 sample values (collection date, country, latitude, location region, longitude) |
| ✓ Abstract / description | 100 sample values (health condition detail, location site) |
| ○ Full text | read; no usable statement or table · PMC11402979, PMC7398469 |
| – 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 |
Genera, mean relative abundance over 42 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 | 50 | 100% | 50 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 0 | 0% | ||||
| collection_date | 50 | 100% | 50 | |||
| detailed_location | 50 | 100% | ||||
| health_condition_detail | 50 | 100% | 50 | |||
| latitude | 50 | 100% | 50 | |||
| location_site | 50 | 100% | 50 | |||
| longitude | 50 | 100% | 50 | |||
| location_region | 10 | 20% | 10 |
- An expanded database and analytical toolkit for identifying bacterial virulence factors and their associations with chronic diseases. 2024 PMID 39278950 PMC11402979 cites_accession
- Influence of gastrectomy for gastric cancer treatment on faecal microbiome and metabolome profiles. 2020 PMID 31953253 PMC7398469 own_data
Archive description
Total microbial community DNA was isolated from the fecal samples of Japanese patients who underwent colonoscopy at National Cancer Research Center. The study population contains health, gastrectomy.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.68. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.description · “fecal samples of Japanese patients”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMD00136647 | collection_date | 2014 | R1 | 0.90 | biosample.attribute:collection_date | 2014 |
| SAMD00136647 | country | JP | R1 | 0.90 | sample.attr.geo_loc_name | Japan |
| SAMD00136647 | health_condition_detail | mixed_case_control: healthy subjects and gastrectomy patients | R4 | 0.40 | study.description | health, gastrectomy |
| SAMD00136647 | latitude | 35.6600 | R1 | 0.90 | biosample.attribute:lat_lon | 35.66 N 139.76 E |
| SAMD00136649 | location_region | Tokyo | R1 | 0.60 | biosample.attribute:lat_lon | 35.66 N 139.78 E |
| SAMD00136647 | location_site | National Cancer Research Center | R4 | 0.45 | ena.study_description | colonoscopy at National Cancer Research Center |
| SAMD00136647 | longitude | 139.7600 | R1 | 0.90 | biosample.attribute:lat_lon | 35.66 N 139.76 E |
Sequencing
50 runs over 50 samples · mean 6.78 Gbp per run (median 6.61 Gbp, total 339.06 Gbp; 50 runs with a base count) · layout PAIRED 50 · platform ILLUMINA 50 · models Illumina HiSeq 2500 (50) · 84% of runs with a Sandpiper profile · first public 2019-12-09
Authors (0)
No author record.
Help complete this project
3 of the 4 core fields are below 50% coverage: age_category, health_condition, subject_id. Share metadata
Downloads
PRJDB7378.csv.gz (2.2 KB) · parquet (71.8 KB) — all 50 samples, every field with route and confidence · PRJDB7378_determinations.csv.gz (2.4 KB) — 310 evidence rows