Gut microbiome in colorectal cancer survivors, US
Cross-sectional pilot study of 28 stool samples from colorectal cancer survivors at the University of California, San Francisco (2019–2020), examining associations between ACS lifestyle guideline adherence (diet, activity, alcohol) and gut microbiome composition. machine-written summary
28 samples · 28 runs · US · Adult · 2022 · 8.50 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 224 sample values (collection date, country, health condition, health condition detail, latitude, location region, longitude, subject id) |
| ✓ Abstract / description | 28 sample values (location site) |
| ✓ Full text | 28 sample values (location locality) · PMC10550847 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| – 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 26 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 | 28 | 100% | ||||
| country | 28 | 100% | 28 | |||
| health_condition | 28 | 100% | 28 | |||
| subject_id | 28 | 100% | 28 | |||
| collection_date | 28 | 100% | 28 | |||
| detailed_location | 28 | 100% | ||||
| health_condition_detail | 28 | 100% | 28 | |||
| latitude | 28 | 100% | 28 | |||
| location_locality | 28 | 100% | 28 | |||
| location_region | 28 | 100% | 28 | |||
| location_site | 28 | 100% | 28 | |||
| longitude | 28 | 100% | 28 |
- Variety of Fruit and Vegetables and Alcohol Intake are Associated with Gut Microbial Species and Gene Abundance in Colorectal Cancer Survivors. 2023 PMID 37474105 PMC10550847 own_data
Archive description
The goal of the LOGIC study is to examine associations between health behaviors and variations in the gut microbiome among gastrointestinal cancer survivors.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.60. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.title · “microbiome study”
- life stage study.title · “Gastrointestinal Cancer”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN32096118 | collection_date | 2019 | R1 | 0.90 | biosample.attribute:collection_date | 2019 |
| SAMN32096118 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA |
| SAMN32096118 | health_condition | colorectal_cancer | R1 | 0.85 | biosample.attribute:gastrointest_disord | Colorectal cancer |
| SAMN32096118 | health_condition_detail | Colorectal cancer | R1 | 0.90 | sample.attr.gastrointest_disord | Colorectal cancer |
| SAMN32096118 | latitude | 36.7783 | R1 | 0.90 | biosample.attribute:lat_lon | 36.7783 N 119.4179 W |
| SAMN32096118 | location_locality | San Francisco | R3 | 0.70 | paper.fulltext.abstract | University of California, San Francisco from 2019 to 2020 |
| SAMN32096118 | location_region | California | R1 | 0.60 | biosample.attribute:lat_lon | 36.7783 N 119.4179 W |
| SAMN32096118 | location_site | University of California, San Francisco | R4 | 0.45 | paper.abstract | collected from 28 CRC survivors at the University of California, San Francisco |
| SAMN32096118 | longitude | -119.4179 | R1 | 0.90 | biosample.attribute:lat_lon | 36.7783 N 119.4179 W |
| SAMN32096118 | subject_id | LOGICS-8350003 | R1 | 0.85 | sample.attr.host_subject_id | LOGICS-8350003 |
Sequencing
28 runs over 28 samples · mean 8.59 Gbp per run (median 8.50 Gbp, total 240.60 Gbp; 28 runs with a base count) · layout PAIRED 28 · platform ILLUMINA 28 · models Illumina NovaSeq 6000 (28) · 93% of runs with a Sandpiper profile · first public 2022-12-10
Authors (16)
Kyaw TS first · Upadhyay V · Tolstykh I · Van Loon K · Laffan A · Stanfield D · Gempis D · Kenfield SA · Chan JM · Piawah S · Atreya CE · Ng K · Venook A · Kidder W · Turnbaugh PJ · Van Blarigan EL last
Downloads
PRJNA909793.csv.gz (1.8 KB) · parquet (71.8 KB) — all 28 samples, every field with route and confidence · PRJNA909793_determinations.csv.gz (2.5 KB) — 280 evidence rows