Fecal metagenomes in colorectal adenomas, TA vs SSA
971 stool samples from participants undergoing colonoscopy, profiled by shotgun metagenomics to study microbial signatures associated with premalignant tubular adenomas and sessile serrated adenomas, paired with diet and medication history; cross-sectional design. machine-written summary
971 samples · 971 runs · Age unknown · 2023 · 3.13 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ○ Sequence archive | records read; no usable sample values |
| ✓ Abstract / description | 1,942 sample values (health condition detail, subject id) |
| ✓ Full text | 1,942 sample values (collection date, location region) · PMC10477964, PMC11342677, PMC12121241 |
| ✓ Supplementary tables | 971 sample values (sex) |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet · share metadata |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Genera, mean relative abundance over 881 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 | 0 | 0% | ||||
| country | 0 | 0% | ||||
| health_condition | 0 | 0% | ||||
| subject_id | 971 | 100% | 971 | |||
| collection_date | 971 | 100% | 971 | |||
| detailed_location | 971 | 100% | ||||
| health_condition_detail | 971 | 100% | 971 | |||
| location_region | 971 | 100% | 971 | |||
| sex | 971 | 100% | 971 |
- Association of distinct microbial signatures with premalignant colorectal adenomas. 2023 PMID 37130517 PMC10477964 own_data
- Gut microbiome structure and function in asymptomatic diverticulosis. 2024 PMID 39180058 PMC11342677 own_data
- Characteristics of the gut virome in patients with premalignant colorectal adenoma. 2025 PMID 40437611 PMC12121241 own_data
Archive description
Colorectal cancers arise from pre-malignant lesions, which are either tubular adenomas (TAs) or sessile serrated adenomas (SSAs). Although the molecular genetics underlying these lesions are distinct, it is unknown whether they are also associated with distinct gut microbiomes. To study the microbiome associated with pre-malignant colon lesions, we profiled stool samples from 708 participants undergoing routine colonoscopy using shotgun sequencing and paired these data with curated dietary and medication history.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by opus_adjudicated with confidence 0.75. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- host study.description · “708 participants undergoing routine colonoscopy”
- body site study.description · “we profiled stool samples”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN36402227 | collection_date | 2018/2021 | R3 | 0.70 | paper.fulltext.methods | stool sample collected prior to the screening colonoscopy from 2018 to 2021 |
| SAMN36402227 | health_condition_detail | mixed_case_control: tubular adenomas (TA), sessile serrated adenomas (SSA), and healthy controls | R4 | 0.40 | paper.abstract | tubular adenomas (TAs) and sessile serrated adenomas (SSAs) |
| SAMN36402227 | location_region | Massachusetts | R3 | 0.70 | paper.fulltext.methods | Massachusetts General Hospital (MGH) |
| SAMN36402227 | sex | male | R2 | 0.85 | paper.supp.12967_2025_6404_MOESM1_ESM.zip::Table S1.xlsx[Table S1!Sex] | male |
| SAMN36402227 | subject_id | SAMN36402227 | R4 | 0.60 | design.one_sample_per_subject:abstract | we profiled stool samples from 971 participants undergoing colonoscopy |
Sequencing
971 runs over 971 samples · mean 3.57 Gbp per run (median 3.13 Gbp, total 3,467.55 Gbp; 971 runs with a base count) · layout PAIRED 971 · platform ILLUMINA 971 · models Illumina HiSeq 2500 (971) · 91% of runs with a Sandpiper profile · first public 2023-07-13
Authors (28)
Lee JWJ first · Plichta DR · Asher S · Delsignore M · Jeong T · McGoldrick J · Staller K · Khalili H · Xavier RJ · Chung DC last · Hua X first · Nakrour N · Zhang P first · Tuo X · Jiang J · Zhang Y · Zhao J · Deng C · Zhao G · Cheng Y · Song L · Yang Y · Guo R · Zhang H · Zhao H · Ma S · Li L · Shi H last
Help complete this project
3 of the 4 core fields are below 50% coverage: age_category, country, health_condition. Share metadata
Downloads
PRJNA784939.csv.gz (24.6 KB) · parquet (110.7 KB) — all 971 samples, every field with route and confidence · PRJNA784939_determinations.csv.gz (24.2 KB) — 4,855 evidence rows