Fecal metagenomes in FAP patients vs healthy, Japan
180 fecal metagenome samples from Japanese colonoscopy patients at the National Cancer Research Center, comparing familial adenomatous polyposis patients and healthy subjects, in a case-control design. machine-written summary
250 samples · 250 runs · JP · Age unknown · 2025 · 6.41 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 745 sample values (collection date, country, health condition, health condition detail, subject id) |
| ✓ Abstract / description | 493 sample values (health condition detail, location site) |
| – Full text | no open-access full text linked |
| – 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 |
longitudinal
38 of 148 people sampled more than once (140 samples; median 3, up to 10 per person) · follow-up median 3.0 y (max 6.1 y) · median interval between samples 11 mo (time from collection dates).
Each row is one person (36 shown of 38); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 163 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 | 250 | 100% | 250 | |||
| health_condition | 7 | 3% | 7 | |||
| subject_id | 250 | 100% | 250 | |||
| detailed_location | 250 | 100% | ||||
| health_condition_detail | 250 | 100% | 7 | 243 | ||
| location_site | 250 | 100% | 250 | |||
| collection_date | 231 | 92% | 231 |
- Dynamics of the gut microbiome in FAP patients undergoing intensive endoscopic reduction of polyp burden. 2025 PMID 39089862 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 patients with familial adenomatous polyposis, and healthy subjects.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.80. Assay shotgun_dna.
- host study.description · “fecal samples of Japanese patients”
- body site study.title · “metagenomic data from human fecal samples”
- body site run.scientific_name · “human gut metagenome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMD00632792 | collection_date | 2014-02-27 | R1 | 0.90 | biosample.attribute:collection_date | 2014-02-27 |
| SAMD00632792 | country | JP | R1 | 0.90 | sample.attr.geo_loc_name | Japan |
| SAMD00632937 | health_condition | healthy_control | R1 | 0.70 | biosample.attribute:collection_date | collection_date: missing: control sample |
| SAMD00632937 | health_condition_detail | control sample (healthy subject) | R1 | 0.70 | biosample.attribute:collection_date | collection_date: missing: control sample |
| SAMD00632792 | health_condition_detail | mixed_case_control: FAP patients vs healthy controls. | R4 | 0.40 | study.description | familial adenomatous polyposis, and healthy subjects |
| SAMD00632792 | location_site | National Cancer Research Center | R4 | 0.45 | ena.study_description | colonoscopy at National Cancer Research Center |
| SAMD00632792 | subject_id | 10002 | R1 | 0.70 | sample.name_rule:sample_name | 10002_1 |
| SAMD00632793 | subject_id | 10002 | R1 | 0.85 | biosample.attribute:sample_name | sample_name: 10002_2 |
Sequencing
250 runs over 250 samples · mean 6.30 Gbp per run (median 6.41 Gbp, total 1,574.93 Gbp; 250 runs with a base count) · layout PAIRED 250 · platform ILLUMINA 250 · models Illumina HiSeq 2500 (250) · 91% of runs with a Sandpiper profile · first public 2025-01-03
Authors (0)
No author record.
Help complete this project
2 of the 4 core fields are below 50% coverage: age_category, health_condition. Share metadata
Downloads
PRJDB16260.csv.gz (8.7 KB) · parquet (81.9 KB) — all 250 samples, every field with route and confidence · PRJDB16260_determinations.csv.gz (11.5 KB) — 1,238 evidence rows