Gut microbiome in capecitabine-treated CRC patients (Netherlands)
159 longitudinal stool samples from adult colorectal cancer patients in the Netherlands treated with capecitabine, collected at baseline, mid-treatment, and post-treatment to study gut microbiota and drug toxicity. machine-written summary
159 samples · 159 runs · NL · Adult · 2025 · 8.85 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,272 sample values (collection date, country, intervention, latitude, location region, longitude, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 477 sample values (antibiotic exposure, health condition, health condition detail) · PMC12153289 |
| ✓ Supplementary tables | 8 sample values (bmi, 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 |
intervention · arms resolved
53 people have samples in more than one arm.
Non-antibiotic pharmaceutical given as the study intervention (metformin design single_arm_before_after · population colorectal_cancer · Capecitabine chemotherapy, longitudinal stool sampling baseline/cycle3/post-treatment
“stool from capecitabine-treated colorectal cancer patients” — bioproject.description (study level; per-sample arms are in the intervention column below)
longitudinal — not resolved
53 of 57 people sampled more than once (155 samples; median 3, up to 3 per person). Schedule stated by the source: “stool at baseline (t1), during cycle 3 (t2), and post-treatment (t3)” (time origin: baseline).
Genera, mean relative abundance over 156 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 | 159 | 100% | ||||
| country | 159 | 100% | 159 | |||
| health_condition | 159 | 100% | 159 | |||
| subject_id | 159 | 100% | 159 | |||
| antibiotic_exposure | 159 | 100% | 159 | |||
| collection_date | 159 | 100% | 159 | |||
| detailed_location | 159 | 100% | ||||
| health_condition_detail | 159 | 100% | 159 | |||
| intervention | 159 | 100% | 159 | |||
| latitude | 159 | 100% | 159 | |||
| location_region | 159 | 100% | 159 | |||
| longitude | 159 | 100% | 159 | |||
| timepoint_label | 159 | 100% | 159 | |||
| bmi | 4 | 3% | 4 | |||
| sex | 4 | 3% | 4 |
- Microbial vitamin biosynthesis links gut microbiota dynamics to chemotherapy toxicity. 2025 PMID 40391895 PMC12153289 own_data
Archive description
Metagenomic sequencing of stool from capecitabine-treated colorectal cancer patients, collected at baseline (t1), during cycle 3 (t2), and post-treatment (t3).
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.80. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.description · “stool from capecitabine-treated colorectal cancer patients”
- life stage study.title · “colorectal cancer patients”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN44209749 | antibiotic_exposure | no | R3 | 0.70 | paper.fulltext.methods | antibiotic use within 3 months of enrollment |
| SAMN44209758 | bmi | 24.16 | R2 | 0.75 | paper.supp.mbio.00930-25-s0002.xlsx[TableS1!BMI] | 24.1632653 |
| SAMN44209749 | collection_date | 2024 | R1 | 0.90 | biosample.attribute:collection_date | 2024 |
| SAMN44209749 | country | NL | R1 | 0.90 | sample.attr.geo_loc_name | Netherlands |
| SAMN44209749 | health_condition | colorectal_cancer | R3 | 0.70 | paper.fulltext.methods | metastatic or unresectable CRC with planned CAP treatment |
| SAMN44209749 | health_condition_detail | metastatic or unresectable colorectal cancer treated with capecitabine | R3 | 0.70 | paper.fulltext.methods | metastatic or unresectable CRC with planned CAP treatment |
| SAMN44209749 | intervention | no_intervention | R1 | 0.70 | sample.name_rule:alias | T1 |
| SAMN44209749 | latitude | 50.8470 | R1 | 0.90 | biosample.attribute:lat_lon | 50.8470 N 5.6880 E |
| SAMN44209749 | location_region | Limburg | R1 | 0.60 | biosample.attribute:lat_lon | 50.8470 N 5.6880 E |
| SAMN44209749 | longitude | 5.6880 | R1 | 0.90 | biosample.attribute:lat_lon | 50.8470 N 5.6880 E |
| SAMN44209758 | sex | female | R2 | 0.75 | paper.supp.mbio.00930-25-s0002.xlsx[TableS1!Sex] | Female |
| SAMN44209749 | subject_id | P01 | R1 | 0.70 | sample.name_rule:alias | P01 |
| SAMN44209749 | timepoint_label | baseline (t1) | R1 | 0.70 | sample.name_rule:alias | T1 |
Sequencing
159 runs over 159 samples · mean 11.50 Gbp per run (median 8.85 Gbp, total 1,829.27 Gbp; 159 runs with a base count) · layout PAIRED 159 · platform ILLUMINA 159 · models Illumina NovaSeq 6000 (159) · 98% of runs with a Sandpiper profile · first public 2025-04-19
Authors (22)
Hillege LE first · Trepka KR · Guthrie BGH · Fu X · Aarnoutse R · Paymar MR · Olson C · Zhang C · Ortega E · Ramirez L · de Vos-Geelen J · Valkenburg-van Iersel L · van Hellemond IEG · Baars A · Vestjens JHMJ · Penders J · Deutschbauer A · Atreya CE · Kidder WA · Smidt ML · Ziemons J · Turnbaugh PJ last
Downloads
PRJNA1171107.csv.gz (5.1 KB) · parquet (77.2 KB) — all 159 samples, every field with route and confidence · PRJNA1171107_determinations.csv.gz (11.8 KB) — 1,757 evidence rows