Gut microbiome in mixed-cancer cohort vs healthy controls, USA
1,651 gut microbiome samples from a US case-control cohort (Mayo Clinic Cancer Microbiome) across Minnesota, Arizona, and Florida, comparing cancer patients (mostly other/colorectal cancer) to healthy controls to identify cancer-associated microbial signatures. machine-written summary
1,651 samples · 1,651 runs · US · Age unknown · 2025 · 3.14 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 21,757 sample values (age, antibiotic exposure, bmi, collection date, country, health condition, health condition detail, latitude) |
| ✓ Abstract / description | 3,302 sample values (location site, subject id) |
| – 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 |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Genera, mean relative abundance over 1,621 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 | 1,643 | 100% | ||||
| country | 1,651 | 100% | 1,651 | |||
| health_condition | 1,651 | 100% | 1,651 | |||
| subject_id | 1,651 | 100% | 1,651 | |||
| antibiotic_exposure | 1,651 | 100% | 1,651 | |||
| collection_date | 1,651 | 100% | 1,651 | |||
| detailed_location | 1,651 | 100% | ||||
| health_condition_detail | 1,651 | 100% | 1,651 | |||
| latitude | 1,651 | 100% | 1,651 | |||
| location_site | 1,651 | 100% | 1,651 | |||
| longitude | 1,651 | 100% | 1,651 | |||
| sex | 1,651 | 100% | 1,651 | |||
| age_at_collection_days | 1,643 | 100% | 1,643 | |||
| bmi | 1,602 | 97% | 1,602 | |||
| lifestyle | 1,356 | 82% | 1,356 | |||
| lifestyle_detail | 1,356 | 82% | 1,356 | |||
| stool_consistency_bristol | 1,328 | 80% | 1,328 | |||
| location_region | 1,231 | 75% | 1,231 | |||
| medication | 33 | 2% | 33 |
- Microbiome signatures linked to cancer and treatment adverse events in a real-world cohort. 2026 PMID 42810338 own_data
Archive description
The gut microbiome has emerged as a key contributor to cancer biology, yet human studies linking the microbiome to cancer are limited by focus on individual cancers, and inadequate adjustment for cancer-specific clinical features. Here we present findings from a real-world mixed-cancer cohort (Mayo Clinic Cancer Microbiome), comprising 1,364 cancer patients and 287 healthy controls. Using a rigorous framework to account for non-specific microbiome associations with cancer, comorbidities, and clinical variables, we identified 341 cancer-associated species across five cancer classes that represent the most plausible contributors to cancer pathogenesis. Within cancer classes, we found reduced secondary bile acid pathway levels in early-onset breast cancer and elevated Veillonella parvula and stool lactate in early-onset colorectal cancer. Additionally, high levels of Anaerostipes hadrus encoding dihydropyrimidine dehydrogenase were protective against 5-fluorouracil-induced diarrhea. These findings demonstrate the strength of our cohort and provide a foundational resource for discovery of cancer-specific microbiome signatures and predictive biomarkers.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult and elderly by sonnet_x2 with confidence 0.72. Assay shotgun_dna.
- host run.scientific_name · “human gut metagenome”
- body site run.scientific_name · “human gut metagenome”
- life stage sample.attr.host_age · “67 (n=876/1651)”
- life stage sample.attr.host_age · “66 (n=683/1651)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN47319728 | age_at_collection_days | 16436.2 | R1 | 0.85 | sample.attr.host_age | 45 |
| SAMN47319728 | antibiotic_exposure | no | R1 | 0.90 | biosample_attr | No |
| SAMN47319728 | bmi | 21.91 | R1 | 0.90 | sample.attr.host_body_mass_index | 21.91 |
| SAMN47319728 | collection_date | 2016/2017 | R1 | 0.90 | biosample.attribute:collection_date | 2016/2017 |
| SAMN47319728 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: RST |
| SAMN47319728 | health_condition | healthy_control | R1 | 0.90 | biosample_attr | Healthy control |
| SAMN47319728 | health_condition_detail | Healthy control | R1 | 0.90 | sample.attr.host_disease | Healthy control |
| SAMN47319728 | latitude | 44.0227 | R1 | 0.90 | biosample.attribute:lat_lon | 44.0227 N 92.4668 W |
| SAMN47320015 | lifestyle | urban_industrialized | R1 | 0.85 | biosample.attribute:urban | urban |
| SAMN47320015 | lifestyle_detail | urban | R1 | 0.85 | biosample.attribute:urban | urban |
| SAMN47319728 | location_region | Minnesota | R1 | 0.60 | biosample.attribute:lat_lon | 44.0227 N 92.4668 W |
| SAMN47320015 | location_region | Florida | R1 | 0.75 | biosample.attribute:geo_loc_name | USA: FLA |
| SAMN47319728 | location_site | Mayo Clinic | R4 | 0.40 | ena.study_description | Mayo Clinic Cancer Microbiome |
| SAMN47319728 | longitude | -92.4668 | R1 | 0.90 | biosample.attribute:lat_lon | 44.0227 N 92.4668 W |
| SAMN47320016 | medication | ppi | R1 | 0.90 | biosample.attribute:ppi_last_month | Yes |
| SAMN47319728 | sex | female | R1 | 0.90 | sample.attr.host_sex | female |
| SAMN47320015 | stool_consistency_bristol | 3 | R1 | 0.90 | biosample.attribute:bristol_score | 3 |
| SAMN47319728 | subject_id | SAMN47319728 | R4 | 0.60 | design.one_sample_per_subject:abstract | comprising 1,364 cancer patients and 287 healthy controls |
Sequencing
1,651 runs over 1,651 samples · mean 3.24 Gbp per run (median 3.14 Gbp, total 5,345.47 Gbp; 1,651 runs with a base count) · layout PAIRED 1,651 · platform ILLUMINA 1,651 · models Illumina NovaSeq 6000 (1,651) · 98% of runs with a Sandpiper profile · first public 2025-11-16 – 2025-11-23
Authors (0)
No author record.
Downloads
PRJNA1235197.csv.gz (75.9 KB) · parquet (163.1 KB) — all 1,651 samples, every field with route and confidence · PRJNA1235197_determinations.csv.gz (229.3 KB) — 25,059 evidence rows