Gut metagenomes in colorectal cancer case-control study, USA
22 gut metagenome samples from adults and elderly adults in Rochester, Minnesota, USA, comparing colorectal cancer patients (11) with age- and sex-matched healthy controls (11) in a case-control design. machine-written summary
22 samples · 66 runs · US · Adult · 2017 · 102.71 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 209 sample values (age, antibiotic exposure, bmi, country, health condition, health condition detail, latitude, location locality) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC10477861, PMC12844167, PMC13034871, PMC13205780, PMC6191348, PMC8857837, PMC9784093 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 22 sample values (health condition, health condition detail) · from GMrepo v3 |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Genera, mean relative abundance over 22 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 | 22 | 100% | ||||
| country | 22 | 100% | 22 | |||
| health_condition | 22 | 100% | 11 | 11 | ||
| subject_id | 0 | 0% | ||||
| age_at_collection_days | 22 | 100% | 22 | |||
| bmi | 22 | 100% | 22 | |||
| detailed_location | 22 | 100% | ||||
| health_condition_detail | 22 | 100% | 11 | 11 | ||
| latitude | 22 | 100% | 22 | |||
| location_locality | 22 | 100% | 22 | |||
| location_region | 22 | 100% | 22 | |||
| longitude | 22 | 100% | 22 | |||
| sex | 22 | 100% | 22 | |||
| antibiotic_exposure | 11 | 50% | 11 |
- Synthesis of multi-omic data and community metabolic models reveals insights into the role of hydrogen sulfide in colon cancer. 2018 PMID 29704665 PMC6191348 own_data
- FOXQ1-mediated SIRT1 upregulation enhances stemness and radio-resistance of colorectal cancer cells and restores intestinal microbiota function by promoting β-catenin nuclear translocation. 2022 PMID 35183223 PMC8857837 own_data
- Efficient Mining of Anticancer Peptides from Gut Metagenome. 2023 PMID 37382183 PMC10477861 own_data
- MetaPepticon: automated prediction of anticancer peptides from microbial genomes and metagenomes. 2026 PMID 41918857 PMC13034871 own_data
- Metagenomic analysis of the interaction between the gut microbiota and colorectal cancer: a paired-sample study based on the GMrepo database. 2022 PMID 36564826 PMC9784093 unsure
2 more
- Co-Metabolic Network Reveals the Metabolic Mechanism of Host-Microbiota Interplay in Colorectal Cancer. 2026 PMID 41590671 PMC12844167
- Identifying Cytokine Motif-Containing, Immunomodulatory Bacterial Proteins in Human Gut Microbiome. 2026 PMID 41869887 PMC13205780
Archive description
We sequenced the gut metagenomes of patients with colorectal cancer, together age- and sex-matched controls. Our goal is to analyze their taxonomic and functional profiles, as well as reconstruct bacterial and archaeal genomes of interest, related to the microbial metabolic toxicity that may be driving colorectal cancer progression.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult and elderly 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 · “Gut metagenomes of patients”
- body site study.description · “We sequenced the gut metagenomes of patients”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- life stage sample.attr.host_age · “78 (n=12/22)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN07452475 | age_at_collection_days | 18262.5 | R1 | 0.70 | sample.attr.host_age | 50 |
| SAMN07452475 | antibiotic_exposure | no | R1 | 0.90 | biosample_attr | no |
| SAMN07452475 | bmi | 30.1 | R1 | 0.90 | sample.attr.host_body_mass_index | 30.1 |
| SAMN07452475 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA:Minnesota, Rochester |
| SAMN07452475 | health_condition | colorectal_cancer | R1 | 0.90 | biosample_attr | colorectal cancer |
| SAMN07452486 | health_condition | healthy_control | R2 | 0.75 | external.gmrepo source | phenotype: Health |
| SAMN07452475 | health_condition_detail | colorectal cancer | R1 | 0.90 | sample.attr.host_disease | colorectal cancer |
| SAMN07452486 | health_condition_detail | Health | R2 | 0.75 | external.gmrepo source | phenotype: Health |
| SAMN07452475 | latitude | 44.0234 | R1 | 0.90 | biosample.attribute:lat_lon | 44.0234 N 92.46295 W |
| SAMN07452475 | location_locality | Rochester | R1 | 0.85 | biosample.attribute:geo_loc_name | USA:Minnesota, Rochester |
| SAMN07452475 | location_region | Minnesota | R1 | 0.85 | biosample.attribute:geo_loc_name | USA:Minnesota, Rochester |
| SAMN07452475 | longitude | -92.4630 | R1 | 0.90 | biosample.attribute:lat_lon | 44.0234 N 92.46295 W |
| SAMN07452475 | sex | male | R1 | 0.90 | sample.attr.host_sex | male |
Sequencing
66 runs over 22 samples · mean 34.19 Gbp per run (median 37.25 Gbp, total 2,256.29 Gbp; 66 runs with a base count) · layout PAIRED 66 · platform ILLUMINA 66 · models Illumina HiSeq 2500 (66) · 88% of runs with a Sandpiper profile · first public 2017-08-07
Authors (73)
Hale VL first · Jeraldo P · Mundy M · Yao J · Keeney G · Scott N · Cheek EH · Davidson J · Greene M · Martinez C · Lehman J · Pettry C · Reed E · Lyke K · White BA · Diener C · Resendis-Antonio O · Gransee J · Dutta T · Petterson XM · Boardman L · Larson D · Nelson H · Chia N last · Ormaasen I first · Rudi K · Diep DB · Snipen L last · Ma Y first · Liu X · Zhang X · Yu Y · Li Y · Song M · Wang J last · Argentini C first · Lugli GA · Tarracchini C · Fontana F · Mancabelli L · Viappiani A · Anzalone R · Angelini L · Alessandri G · Longhi G · Bianchi MG · Taurino G · Bussolati O · Milani C · van Sinderen D · Turroni F · Ventura M last · Wang HW first · Li W · Ma QJ · Zhang HY · Quan Y · Zhu Q last · Wang Z first · Guo S · Li J · Huang Q · Ning J · Xia B · Lv X · Gao Z · Liu L · Erözden AA first · Tavşanlı N · Demirel G · Sanli NO · Çalışkan M · Arıkan M last
Downloads
PRJNA397219.csv.gz (1.8 KB) · parquet (71.5 KB) — all 22 samples, every field with route and confidence · PRJNA397219_determinations.csv.gz (2.6 KB) — 231 evidence rows