CRC patients, antibiotic prophylaxis for surgery, Hiroshima Japan
59 oral and stool samples from colorectal cancer patients in Hiroshima, Japan, collected before and after antibiotic prophylaxis for colon cancer surgery, to assess effects on oral and gut microbiomes and resistomes. machine-written summary
59 samples · 59 runs · JP · Elderly · 2025 · 6.74 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 606 sample values (age, antibiotic exposure, collection date, country, intervention, latitude, location region, longitude) |
| ✓ Abstract / description | 118 sample values (health condition, health condition detail) |
| – Full text | no open-access full text linked |
| – Supplementary tables | no supplementary tables available (or none open access) |
| – 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 not resolved
Antibiotic given as the study intervention (incl. eradication therapy Surgical procedure studied before/after (bariatric surgery design single_arm_before_after · population colorectal_cancer · Antibiotic prophylaxis before/after colon cancer surgery
“before and after administration of antibiotic prophylaxis” — study.title (study level; per-sample arms are in the intervention column below)
longitudinal
8 of 8 people sampled more than once (28 samples; median 4, up to 4 per person) · follow-up median 28 d (max 28 d) · median interval between samples 7 d (time from timepoint labels). Schedule stated by the source: “baseline, 1, 7, 28 (same subject ID sampled at each)” (time origin: surgery).
Each row is one person (8 shown); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 28 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 | 59 | 100% | ||||
| country | 59 | 100% | 59 | |||
| health_condition | 59 | 100% | 59 | |||
| subject_id | 59 | 100% | 59 | |||
| age_at_collection_days | 59 | 100% | 59 | |||
| antibiotic_exposure | 59 | 100% | 59 | |||
| collection_date | 59 | 100% | 59 | |||
| detailed_location | 59 | 100% | ||||
| health_condition_detail | 59 | 100% | 59 | |||
| latitude | 59 | 100% | 59 | |||
| location_region | 59 | 100% | 59 | |||
| longitude | 59 | 100% | 59 | |||
| sex | 59 | 100% | 59 | |||
| timepoint_label | 59 | 100% | 59 | |||
| intervention | 16 | 27% | 16 |
- Impact of antimicrobial prophylaxis in colorectal cancer surgery on the gut and oral microbiome and resistome: A prospective observational cohort study. 2026 PMID 41455576 own_data
Archive description
This project includes the metagenome data of oral and stool samples which were collected from colon cancer patients to assess the effects of antibiotic prophylaxis during colon cancer surgery on the oral and gut microbiomes and resistomes of patients.
How this project entered the registry
Classified as human oral cavity / gut / stool shotgun DNA metagenome of elderly and adult by opus_adjudicated with confidence 0.70. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- host study.title · “colorectal cancer patients”
- body site run.scientific_name · “human oral metagenome”
- body site run.scientific_name · “human feces metagenome”
- life stage sample.attr.host_age · “71 (n=44/59)”
- life stage sample.attr.host_age · “63 (n=15/59)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMD00889219 | age_at_collection_days | 22980.8 | R1 | 0.85 | sample.attr.host_age | 63 |
| SAMD00889219 | antibiotic_exposure | no | R1 | 0.85 | biosample.attribute:chem_administration | chem_administration: before antibiotic administration |
| SAMD00889219 | collection_date | 2023 | R1 | 0.90 | biosample.attribute:collection_date | 2023 |
| SAMD00889219 | country | JP | R1 | 0.90 | sample.attr.geo_loc_name | Japan:Hiroshima |
| SAMD00889219 | health_condition | colorectal_cancer | R4 | 0.50 | paper.abstract | Among the eight patients with colorectal cancer |
| SAMD00889219 | health_condition_detail | colorectal cancer | R4 | 0.50 | paper.abstract | Among the eight patients with colorectal cancer |
| SAMD00889219 | intervention | no_intervention | R1 | 0.85 | biosample.attribute:chem_administration | chem_administration: before antibiotic administration |
| SAMD00889219 | latitude | 34.3800 | R1 | 0.90 | biosample.attribute:lat_lon | 34.38 N 132.48 E |
| SAMD00889219 | location_region | Hiroshima | R1 | 0.85 | biosample.attribute:geo_loc_name | Japan:Hiroshima |
| SAMD00889219 | longitude | 132.4800 | R1 | 0.90 | biosample.attribute:lat_lon | 34.38 N 132.48 E |
| SAMD00889219 | sex | female | R1 | 0.90 | sample.attr.host_sex | female |
| SAMD00889219 | subject_id | HKCMZ2 | R1 | 0.70 | sample.name_rule:sample_name | HKCMZ2_o_baseline |
| SAMD00889219 | timepoint_label | baseline | R1 | 0.85 | biosample.attribute:chem_administration | chem_administration: before antibiotic administration |
Sequencing
59 runs over 59 samples · mean 6.80 Gbp per run (median 6.74 Gbp, total 401.38 Gbp; 59 runs with a base count) · layout PAIRED 59 · platform ILLUMINA 59 · models Illumina NovaSeq X (59) · 100% of runs with a Sandpiper profile · first public 2025-05-04
Authors (0)
No author record.
Downloads
PRJDB20343.csv.gz (2.7 KB) · parquet (73.1 KB) — all 59 samples, every field with route and confidence · PRJDB20343_determinations.csv.gz (5.5 KB) — 724 evidence rows