Oral & fecal microbiomes in pancreatic cancer & pancreatitis
244 samples from Spanish adults and elderly, comparing microbiota in treatment-naïve pancreatic ductal adenocarcinoma patients, chronic pancreatitis patients, and healthy controls using metagenomic and 16S sequencing. machine-written summary
244 samples · 522 runs · ES · Adult · 2022 · 1.84 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 | 1,227 sample values (collection date, country, latitude, location region, longitude, subject id) |
| ✓ Abstract / description | 200 sample values (health condition detail) |
| ○ Full text | read; no usable statement or table · PMC10915599, PMC11487005, PMC13269251, PMC9185815 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 528 sample values (age, antibiotic exposure, 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 |
longitudinal — not resolved
96 of 148 people sampled more than once (192 samples; median 2, up to 2 per person).
Genera, mean relative abundance over 96 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 | 244 | 100% | ||||
| country | 244 | 100% | 244 | |||
| health_condition | 77 | 32% | 77 | |||
| subject_id | 244 | 100% | 244 | |||
| collection_date | 244 | 100% | 244 | |||
| health_condition_detail | 244 | 100% | 44 | 200 | ||
| latitude | 244 | 100% | 244 | |||
| longitude | 244 | 100% | 244 | |||
| age_at_collection_days | 136 | 56% | 136 | |||
| sex | 136 | 56% | 136 | |||
| antibiotic_exposure | 135 | 55% | 135 | |||
| detailed_location | 7 | 3% | ||||
| location_region | 7 | 3% | 7 |
- 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 and salivary microbiota in a prospectively recruited population of treatment-naïve PDAC patients, chronic pancreatitis patients and healthy controls using shotgun metagenomic and 16S rRNA amplicon sequencing.
How this project entered the registry
Classified as human gut / stool / oral cavity 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 · “The oral and fecal microbiome in chronic”
- body site study.description · “We analysed the fecal and salivary microbiota”
- body site study.title · “The oral and fecal microbiome”
- body site study.description · “the fecal and salivary 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 |
|---|---|---|---|---|---|---|
| SAMEA13445370 | age_at_collection_days | 24471.75 | R2 | 0.75 | external.cmd source | age: 67; age_unit: (empty); age_group: Elderly |
| SAMEA13445370 | antibiotic_exposure | no | R2 | 0.75 | external.cmd source | antibiotics_current_use: No |
| SAMEA13445370 | collection_date | 2015/2018 | R1 | 0.90 | biosample.attribute:collection_date | 2015/2018 |
| SAMEA13445370 | country | ES | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Spain |
| SAMEA13445370 | health_condition | other_disease | R2 | 0.75 | external.cmd source | disease: Chronic Pancreatitis |
| SAMEA13445370 | health_condition_detail | Chronic Pancreatitis | R2 | 0.75 | external.cmd source | disease: Chronic Pancreatitis |
| SAMEA13445375 | health_condition_detail | mixed_case_control: treatment-naïve PDAC patients vs chronic pancreatitis patients vs healthy controls | R4 | 0.50 | study.description | PDAC patients, chronic pancreatitis patients and healthy controls |
| SAMEA13445370 | latitude | 41.3900 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 41.39 2.15 |
| SAMEA13445370 | location_region | Catalonia | R1 | 0.60 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 41.39 2.15 |
| SAMEA13445370 | longitude | 2.1500 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 41.39 2.15 |
| SAMEA13445370 | sex | male | R2 | 0.75 | external.cmd source | sex: Male |
| SAMEA13445370 | subject_id | 3103311 | R1 | 0.70 | sample.name_rule:alias | MMPC-3103311-ST-0 |
Sequencing
522 runs over 244 samples · mean 2.77 Gbp per run (median 0.55 Gbp, total 1,447.62 Gbp; 522 runs with a base count) · layout PAIRED 261, SINGLE 261 · platform ILLUMINA 522 · models Illumina HiSeq 4000 (522) · 22% of runs with a Sandpiper profile · first public 2022-03-18 – 2022-06-24
Authors (76)
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 · 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
PRJEB38625.csv.gz (8.4 KB) · parquet (81.5 KB) — all 244 samples, every field with route and confidence · PRJEB38625_determinations.csv.gz (20.5 KB) — 1,955 evidence rows