Fecal microbiota case-control study in PDAC patients, Germany
A case-control study of 76 fecal samples from Germany, comparing treatment-naïve pancreatic cancer (other_cancer) patients with healthy controls to screen for microbiota linked to pancreatic ductal adenocarcinoma. machine-written summary
76 samples · 152 runs · DE · Adult · 2022 · 5.84 Gbp / sample · cohort A faecal microbiota signature with high specificit
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 380 sample values (collection date, country, latitude, location region, longitude) |
| ✓ Abstract / description | 107 sample values (health condition detail, subject id) |
| ○ Full text | read; no usable statement or table · PMC11915875 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 376 sample values (age, antibiotic exposure, bmi, health condition, health condition detail, sex) · 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 71 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 | 76 | 100% | ||||
| country | 76 | 100% | 76 | |||
| health_condition | 76 | 100% | 76 | |||
| subject_id | 76 | 100% | 76 | |||
| age_at_collection_days | 76 | 100% | 76 | |||
| collection_date | 76 | 100% | 76 | |||
| detailed_location | 76 | 100% | ||||
| health_condition_detail | 76 | 100% | 45 | 31 | ||
| latitude | 76 | 100% | 76 | |||
| location_region | 76 | 100% | 76 | |||
| longitude | 76 | 100% | 76 | |||
| sex | 76 | 100% | 76 | |||
| antibiotic_exposure | 52 | 68% | 52 | |||
| bmi | 51 | 67% | 51 |
- Association of tumor microbiome with survival in resected early-stage PDAC. 2025 PMID 40013793 PMC11915875 own_data
- A faecal microbiota signature with high specificity for pancreatic cancer. 2022 PMID 35260444 PMC9185815 unsure
- Highly accurate diagnosis of pancreatic cancer by integrative modeling using gut microbiome and exposome data. 2024 PMID 38450156 PMC10915599 unsure
- The microbial composition of pancreatic ductal adenocarcinoma: a systematic review of 16S rRNA gene sequencing. 2024 PMID 38874485 PMC11487005 unsure
- Strain transmission links human microbiomes along the oral-gut axis and across cohabiting individuals. 2026 PMID 42312244 PMC13269251 unsure
Archive description
Pancreatic ductal adenocarcinoma (PDAC), the most frequent form of pancreatic cancer, poses an increasing disease burden worldwide. Recent evidence suggests a role for the microbiome in PDAC etiology and progression. We analysed the fecal microbiota in a prospectively recruited German population of treatment-naïve PDAC patients and healthy controls using shotgun metagenomic sequencing.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- body site study.title · “robust and specific fecal microbiota-based screening for”
- body site study.description · “We analysed the fecal microbiota in a”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA13321860 | age_at_collection_days | 23741.25 | R2 | 0.75 | external.cmd source | age: 65; age_unit: (empty); age_group: Elderly |
| SAMEA13321860 | antibiotic_exposure | no | R2 | 0.75 | external.cmd source | antibiotics_current_use: No |
| SAMEA13321860 | bmi | 27.0 | R2 | 0.75 | external.cmd source | bmi: 27 |
| SAMEA13321860 | collection_date | 2014/2020 | R1 | 0.90 | biosample.attribute:collection_date | 2014/2020 |
| SAMEA13321860 | country | DE | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Germany |
| SAMEA13321860 | health_condition | other_cancer | R2 | 0.75 | external.cmd source | disease: Pancreatic Ductal Adenocarcinoma |
| SAMEA13321860 | health_condition_detail | Pancreatic Ductal Adenocarcinoma | R2 | 0.75 | external.cmd source | disease: Pancreatic Ductal Adenocarcinoma |
| SAMEA13321861 | health_condition_detail | mixed_case_control: PDAC patients vs healthy controls | R4 | 0.40 | study.description | treatment-naïve PDAC patients and healthy controls |
| SAMEA13321860 | latitude | 49.5999 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 49.599941 11.0063 |
| SAMEA13321860 | location_region | Bavaria | R1 | 0.60 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 49.599941 11.0063 |
| SAMEA13321860 | longitude | 11.0063 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 49.599941 11.0063 |
| SAMEA13321860 | sex | female | R2 | 0.75 | external.cmd source | sex: Female |
| SAMEA13321860 | subject_id | SAMEA13321860 | R4 | 0.60 | design.one_sample_per_subject:description | prospectively recruited German population of treatment-naïve PDAC patients and healthy controls |
Sequencing
152 runs over 76 samples · mean 2.95 Gbp per run (median 2.14 Gbp, total 448.30 Gbp; 152 runs with a base count) · layout PAIRED 76, SINGLE 76 · platform ILLUMINA 152 · models Illumina HiSeq 4000 (152) · 47% of runs with a Sandpiper profile · first public 2022-03-11 – 2022-06-24
Authors (94)
Kartal E first · Schmidt TSB · Molina-Montes E · Rodríguez-Perales S · Wirbel J · Maistrenko OM · Akanni WA · Alashkar Alhamwe B · Alves RJ · Carrato A · Erasmus HP · Estudillo L · Finkelmeier F · Fullam A · Glazek AM · Gómez-Rubio P · Hercog R · Jung F · Kandels S · Kersting S · Langheinrich M · Márquez M · Molero X · Orakov A · Van Rossum T · Torres-Ruiz R · Telzerow A · Zych K · MAGIC Study investigators · PanGenEU Study investigators · Benes V · Zeller G · Trebicka J · Real FX · Malats N · Bork P last · Zhang Y first · Zhang H · Liu B · Ning K last · Merali N first · Chouari T · Sweeney C · Halle-Smith J · Jessel MD · Wang B · O' Brien J · Suyama S · Jiménez JI · Roberts KJ · Velliou E · Sivakumar S · Rockall TA · Demirkan A · Pedicord V · Deng D · Giovannetti E · Annels NE · Frampton AE last · Tarracchini C first · Lugli GA · Mancabelli L · van Sinderen D · Turroni F · Ventura M · Milani C last · Meng Y first · Wang C · Usyk M · Kwak S · Peng C · Hu KS · Oberstein PE · Krogsgaard M · Li H · Hayes RB · Ahn J last · Heidrich V first · Fackelmann G · Ricci L · Spadazzi R · Baldanzi G · Punčochář M · Catassi G · Marchi P · Modesto M · Piccinno G · Porcari S · Rondinella D · Asnicar F · Valles-Colomer M · Mattarelli P · Ianiro G · Segata N last
Downloads
PRJEB42013.csv.gz (3.7 KB) · parquet (75.6 KB) — all 76 samples, every field with route and confidence · PRJEB42013_determinations.csv.gz (10.9 KB) — 863 evidence rows