Gut/oral metagenomics in pancreatic cancer
560 fecal and salivary samples from pancreatic cancer (PDAC) patients and controls in Japan, Spain, and Germany, analyzed in a case-control study of gut and oral microbiome signatures. machine-written summary
560 samples · 560 runs · JP · Adult · 2022 · 1.16 Gbp / sample · cohort Multi-biome analysis identifies distinct gut micro
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 2,240 sample values (health condition, health condition detail, sex, subject id) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC11060577, PMC11293218, PMC11603027, PMC12340149, PMC13269251 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 556 sample values (antibiotic exposure, country) · from curatedMetagenomicData 3 (cMD 3) |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Genera, mean relative abundance over 504 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 | 560 | 100% | ||||
| country | 278 | 50% | 278 | |||
| health_condition | 560 | 100% | 560 | |||
| subject_id | 560 | 100% | 560 | |||
| health_condition_detail | 560 | 100% | 560 | |||
| sex | 560 | 100% | 560 | |||
| antibiotic_exposure | 278 | 50% | 278 |
- Metagenomic Identification of Microbial Signatures Predicting Pancreatic Cancer From a Multinational Study. 2022 PMID 35398347 own_data
- Oral microbiome-driven virulence factors: A novel approach to pancreatic cancer diagnosis. 2023 PMID 38153528 PMC11293218 own_data
- Leveraging genomic signatures of oral microbiome-associated antibiotic resistance genes for diagnosing pancreatic cancer. 2024 PMID 38687802 PMC11060577 own_data
- Genderized Gut and Oral Microbiome Shifts: Uncovering Sex-Specific Dysbiosis in Pancreatic Cancer 2024 own_data
- Multi-biome analysis identifies distinct gut microbial signatures and their crosstalk in ulcerative colitis and Crohn's disease. 2024 PMID 39604394 PMC11603027 unsure
2 more
- Giant extrachromosomal element "Inocle" potentially expands the adaptive capacity of the human oral microbiome. 2025 PMID 40790024 PMC12340149
- Strain transmission links human microbiomes along the oral-gut axis and across cohabiting individuals. 2026 PMID 42312244 PMC13269251
Archive description
Metagenomics of the fecal and salivary microbiome of pancreatic cancer patients
How this project entered the registry
Classified as human gut / stool / oral cavity shotgun DNA metagenome of adult and elderly by sonnet_x2 with confidence 0.62. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.title · “fecal and salivary microbiome”
- body site run.scientific_name · “human oral metagenome”
- life stage study.title · “pancreatic cancer patients”
- life stage sample.attr.host_age · “>70 (n=332/560)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN27925172 | antibiotic_exposure | no | R2 | 0.75 | external.cmd source | antibiotics_current_use: No |
| SAMN27925172 | country | JP | R2 | 0.75 | external.cmd source | country: Japan |
| SAMN27925172 | health_condition | healthy_control | R1 | 0.80 | biosample_attr | Control |
| SAMN27925172 | health_condition_detail | Control | R1 | 0.90 | sample.attr.host_disease | Control |
| SAMN27925172 | sex | male | R1 | 0.90 | sample.attr.host_sex | male |
| SAMN27925172 | subject_id | CTRL_feces_001 | R1 | 0.85 | sample.attr.host_subject_id | CTRL_feces_001 |
Sequencing
560 runs over 560 samples · mean 1.19 Gbp per run (median 1.16 Gbp, total 667.26 Gbp; 560 runs with a base count) · layout PAIRED 560 · platform ILLUMINA 560 · models Illumina HiSeq 4000 (560) · 90% of runs with a Sandpiper profile · first public 2022-05-21
Authors (73)
Nagata N first · Nishijima S · Kojima Y · Hisada Y · Imbe K · Miyoshi-Akiyama T · Suda W · Kimura M · Aoki R · Sekine K · Ohsugi M · Miki K · Osawa T · Ueki K · Oka S · Mizokami M · Kartal E · Schmidt TSB · Molina-Montes E · Estudillo L · Malats N · Trebicka J · Kersting S · Langheinrich M · Bork P · Uemura N · Itoi T · Kawai T last · Zeng X first · Ren D · Liu R · Zhang Q · Yan X · Yuan X last · Shen X first · Zhu X · Liu H · Yuan R · Guo Q · Zhao P last · Tarracchini C first · Lugli GA · Mancabelli L · van Sinderen D · Turroni F · Ventura M · Milani C last · Kiguchi Y first · Hamamoto N · Kashima Y · Runtuwene LR · Ishizaka A · Kuze Y · Enokida T · Tanaka N · Tahara M · Kageyama SI · Fujisawa T · Yamashita R · Kanai A · Tuda JSB · Mizutani T · Suzuki Y last · Khan ZA first · Ghorbani M · Heffinger L · Damdimopoulos A · Moro CF · Björnstedt M · Löhr J · Heuchel R · Chen MS · Sarhan D last
Downloads
PRJNA832909.csv.gz (14.4 KB) · parquet (92.6 KB) — all 560 samples, every field with route and confidence · PRJNA832909_determinations.csv.gz (17.9 KB) — 2,796 evidence rows