Gut microbiome in colon polyps vs polyp-free adults, USA
Case-control study of 252 fecal and colon mucosa samples from adults in California, USA, comparing gut microbiome composition among tubular adenoma, serrated polyp, and polyp-free individuals. machine-written summary
251 samples · 252 runs · US · Adult · 2021 · 0.32 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,506 sample values (collection date, country, latitude, location region, longitude, subject id) |
| ✓ Abstract / description | 27 sample values (health condition detail) |
| ✓ Full text | 251 sample values (antibiotic exposure) · PMC10464540, PMC13381771, PMC9424272 |
| ✓ Supplementary tables | 1,225 sample values (age, bmi, health condition, health condition detail, intervention, sex) |
| – 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 |
longitudinal — not resolved
Schedule stated by the source: “Colonoscopy-day mucosal/lavage sampling, with fecal sample collected 4-6 weeks post-colonoscopy from same participants” (time origin: colonoscopy); stated follow-up 42 d.
Genera, mean relative abundance over 197 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 | 251 | 100% | ||||
| country | 251 | 100% | 251 | |||
| health_condition | 224 | 89% | 224 | |||
| subject_id | 251 | 100% | 251 | |||
| antibiotic_exposure | 251 | 100% | 251 | |||
| collection_date | 251 | 100% | 251 | |||
| detailed_location | 251 | 100% | ||||
| health_condition_detail | 251 | 100% | 224 | 27 | ||
| latitude | 251 | 100% | 251 | |||
| location_region | 251 | 100% | 251 | |||
| longitude | 251 | 100% | 251 | |||
| sex | 218 | 87% | 218 | |||
| age_at_collection_days | 217 | 86% | 217 | |||
| bmi | 216 | 86% | 216 | |||
| intervention | 126 | 50% | 126 |
- Distinct colon mucosa microbiomes associated with tubular adenomas and serrated polyps. 2022 PMID 36038569 PMC9424272 own_data
- Multimodal metagenomic analysis reveals microbial single nucleotide variants as superior biomarkers for early detection of colorectal cancer. 2023 PMID 37635357 PMC10464540 unsure
- Instance-based transfer learning enables cross-cohort early detection of colorectal cancer. 2026 PMID 42106361 PMC13381771 unsure
Archive description
Colorectal cancer is one of the most common cancers in the world. Its development is heterogenous, with multiple mechanisms of carcinogenesis. Two distinct mechanisms include the adenoma-carcinoma sequence and the serrated pathway. The gut microbiome has been identified as a key player in the adenoma-carcinoma sequence, but its role in serrated carcinogenesis is unclear. Here, we investigated the gut microbiome associated with these two pathways using mucosal and fecal samples from human subjects during colonoscopy. Sample collection focused on healthy individuals and those with tubular adenomas, hyperplastic polyps, and sessile serrated polyps.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.70. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.title · “Fecal and colon mucosa sequencing”
- life stage study.description · “human subjects during colonoscopy”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN20163073 | age_at_collection_days | 23011.0 | R2 | 0.85 | paper.supp.41522_2022_328_MOESM5_ESM.zip::Source_Data_File/Figure5b.txt[!Age] | Age: 63 |
| SAMN20163071 | antibiotic_exposure | no | R3 | 0.70 | paper.fulltext.methods | had taken antibiotics within 6 weeks of colonoscopy |
| SAMN20163073 | bmi | 31.00 | R2 | 0.85 | paper.supp.41522_2022_328_MOESM5_ESM.zip::Source_Data_File/Figure5b.txt[!BMI] | BMI: 31 |
| SAMN20163071 | collection_date | 2017-12-15 | R1 | 0.90 | biosample.attribute:collection_date | 2017-12-15 |
| SAMN20163071 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: California |
| SAMN20163071 | health_condition | healthy_control | R2 | 0.85 | paper.supp.41522_2022_328_MOESM5_ESM.zip::Source_Data_File/Figure5b.txt[!MostMalignantPolypType] | MostMalignantPolypType: healthy |
| SAMN20163071 | health_condition_detail | healthy | R2 | 0.85 | paper.supp.41522_2022_328_MOESM5_ESM.zip::Source_Data_File/Figure5b.txt[!MostMalignantPolypType] | MostMalignantPolypType: healthy |
| SAMN20163160 | health_condition_detail | mixed_case_control: polyp-free individuals vs. tubular adenomas, hyperplastic polyps, sessile serrated polyps | R4 | 0.40 | study.description | healthy individuals and those with tubular adenomas, hyperplastic polyps, and sessile serrated |
| SAMN20163073 | intervention | bowel_preparation | R2 | 0.85 | paper.supp.41522_2022_328_MOESM5_ESM.zip::Source_Data_File/Figure5b.txt[!PrepType] | PrepType: PEG_w_lytes_(Golytely,_Trilyte,_etc) |
| SAMN20163071 | latitude | 33.4700 | R1 | 0.90 | biosample.attribute:lat_lon | 33.47 N 117.53 W |
| SAMN20163071 | location_region | California | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: California |
| SAMN20163071 | longitude | -117.5300 | R1 | 0.90 | biosample.attribute:lat_lon | 33.47 N 117.53 W |
| SAMN20163073 | sex | male | R2 | 0.85 | paper.supp.41522_2022_328_MOESM5_ESM.zip::Source_Data_File/Figure5b.txt[!Gender] | Gender: Male |
| SAMN20163071 | subject_id | 0054 | R1 | 0.85 | sample.attr.unique_id | 0054 |
Sequencing
252 runs over 251 samples · mean 0.31 Gbp per run (median 0.32 Gbp, total 79.02 Gbp; 252 runs with a base count) · layout PAIRED 252 · platform ILLUMINA 252 · models Illumina HiSeq 4000 (252) · 79% of runs with a Sandpiper profile · first public 2021-07-24
Authors (25)
Avelar-Barragan J first · DeDecker L · Lu ZN · Coppedge B · Karnes WE · Whiteson KL last · Gao W first · Gao X · Zhu L · Gao S · Sun R · Feng Z · Wu D · Liu Z · Zhu R · Jiao N last · Sun Y first · Wu S · Wu Z · Zhu W · Gao H · Xing J · Zhao J · Fan X · Su X last
Downloads
PRJNA745329.csv.gz (8.9 KB) · parquet (83.3 KB) — all 251 samples, every field with route and confidence · PRJNA745329_determinations.csv.gz (23.5 KB) — 3,009 evidence rows