Gut microbiota and prostate cancer PRS, Japan (cross-sectional)
Cross-sectional shotgun metagenomic study of 166 gut microbiota samples from Japan, examining links between polygenic risk score for prostate cancer and gut microbial taxa/pathways, including androgen-producing (SSTD-related) gene potential. machine-written summary
166 samples · 166 runs · JP · Age unknown · 2024 · 11.94 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 498 sample values (collection date, country, health condition) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC12876203 |
| ✓ Supplementary tables | 166 sample values (health condition detail) |
| – 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 147 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 | 166 | 100% | 166 | |||
| health_condition | 166 | 100% | 166 | |||
| subject_id | 0 | 0% | ||||
| collection_date | 166 | 100% | 166 | |||
| health_condition_detail | 166 | 100% | 166 |
- SSTDhunter: a curated gene database for investigating androgen producing potential in microbiota species. 2026 PMID 41660426 PMC12876203 unsure
Archive description
Shotgun sequencing for metagenomic analysis was employed to comprehensively identify taxa and pathways in the gut microbiota.
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 run.scientific_name · “human gut metagenome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMD00797768 | collection_date | 2018-12-18 | R1 | 0.90 | biosample.attribute:collection_date | 2018-12-18 |
| SAMD00797768 | country | JP | R1 | 0.90 | sample.attr.geo_loc_name | Japan |
| SAMD00797768 | health_condition | healthy_control | R1 | 0.70 | sample.name_rule:sample_name | SG_HC_OU_00001 |
| SAMD00797768 | health_condition_detail | Healthy | R2 | 0.85 | paper.supp.Table4.xlsx[Table S4!Group] | Group: Healthy |
Sequencing
166 runs over 166 samples · mean 10.43 Gbp per run (median 11.94 Gbp, total 1,731.58 Gbp; 166 runs with a base count) · layout PAIRED 166 · platform ILLUMINA 166 · models Illumina NovaSeq 6000 (166) · 89% of runs with a Sandpiper profile · first public 2024-07-09
Authors (11)
Wang S first · Yang Y · Lei L · Wan R · Su Z · Liu Y · Tang H · Hu G · Li C · Meng J · Yang K last
Help complete this project
2 of the 4 core fields are below 50% coverage: age_category, subject_id. Share metadata
Downloads
PRJDB18316.csv.gz (5.3 KB) · parquet (76.1 KB) — all 166 samples, every field with route and confidence · PRJDB18316_determinations.csv.gz (5.6 KB) — 664 evidence rows