Gut microbiome in colon cancer surgery patients, Switzerland
88 longitudinal rectal/intraluminal samples from 27 adult colorectal cancer patients in Switzerland, comparing standard antibiotic prophylaxis versus carbapenems before and after elective colon surgery. machine-written summary
88 samples · 88 runs · CH · Adult · 2022 · 89.5 Mbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 610 sample values (collection date, country, latitude, location region, longitude, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 440 sample values (antibiotic exposure, health condition, health condition detail, location locality, location site) · PMC8729125 |
| ○ 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 |
intervention — arms not resolved
Antibiotic given as the study intervention (incl. eradication therapy Surgical procedure studied before/after (bariatric surgery design observational_with_procedure · population colorectal_cancer · Elective colon cancer surgery; antibiotic prophylaxis (cefuroxime/metronidazole vs carbapenems)
“before and after elective oncologic colon surgery” — abstract:34983654 (study level; per-sample arms are in the intervention column below)
longitudinal
28 of 28 people sampled more than once (85 samples; median 3, up to 4 per person) · follow-up median 3 d (max 12 d) · median interval between samples 3 d (time from collection dates). Schedule stated by the source: “Rectal sample before surgery, intraoperative intraluminal stool sample, and rectal/stoma sample 3 days after surgery.”; stated follow-up 3 d.
Each row is one person (27 shown of 28); dots are samples at days since that person's first sample.
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 88 | 100% | ||||
| country | 88 | 100% | 88 | |||
| health_condition | 88 | 100% | 88 | |||
| subject_id | 85 | 97% | 85 | |||
| antibiotic_exposure | 88 | 100% | 88 | |||
| collection_date | 88 | 100% | 88 | |||
| detailed_location | 88 | 100% | ||||
| health_condition_detail | 88 | 100% | 88 | |||
| latitude | 88 | 100% | 88 | |||
| location_locality | 88 | 100% | 88 | |||
| location_region | 88 | 100% | 88 | |||
| location_site | 88 | 100% | 88 | |||
| longitude | 88 | 100% | 88 | |||
| timepoint_label | 85 | 97% | 85 |
- Changes in the gut bacterial communities in colon cancer surgery patients: an observational study. 2022 PMID 34983654 PMC8729125 own_data
Archive description
Between March and September, 2019 we included 27 adult patients who were scheduled to undergo elective colorectal cancer surgery. We performed a prospective descriptive observational study whose primary aim was to evaluate changes in the gut microbiome before and after surgery, and to evaluate the effect of different prophylaxis regimens (standard prophylaxis with cefuroxime and metronidazole versus carbapenems for ESBL-E carriers). We obtained rectal sample before and 3 days after surgery, and an intraoperative intraluminal stool sample. We performed metataxonomics analysis based on sequencing of the bacterial 16S rRNA gene marker.We observed large and significant increases in the genus Enterococcus between both the preoperative and intraoperative samples and the post-operative sample, mainly driven by Enterococcus faecalis. There were significant differences in the postoperative microbiome between patients who received standard prophylaxis and carbapenems, specifically in the family Erysipelotrichaceae. Preoperative haemoglobin and prealbumin levels were associated to post-operative differences in gut microbiome.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- body site study.title · “Changes in the gut microbiome in colon”
- body site study.description · “to undergo elective colorectal cancer surgery. We”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- life stage study.description · “we included 27 adult patients who were”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA8547893 | antibiotic_exposure | no | R3 | 0.70 | paper.fulltext.methods | antibiotic within 30 days preceding the colon surgery |
| SAMEA8547893 | collection_date | 2019-03-27 | R1 | 0.90 | biosample.attribute:collection_date | 2019-03-27 |
| SAMEA8547893 | country | CH | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Switzerland |
| SAMEA8547893 | health_condition | colorectal_cancer | R3 | 0.70 | paper.fulltext.methods | undergo elective colon surgery for oncological reasons |
| SAMEA8547893 | health_condition_detail | elective colon surgery for oncological reasons | R3 | 0.70 | paper.fulltext.methods | undergo elective colon surgery for oncological reasons |
| SAMEA8547893 | latitude | 46.1934 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 46.19336429 6.149056901 |
| SAMEA8547893 | location_locality | Geneva | R3 | 0.70 | paper.fulltext.methods | elective colon surgery at Geneva University Hospitals, Switzerland |
| SAMEA8547893 | location_region | Geneva | R1 | 0.60 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 46.19336429 6.149056901 |
| SAMEA8547893 | location_site | Geneva University Hospitals | R3 | 0.70 | paper.fulltext.methods | elective colon surgery at Geneva University Hospitals, Switzerland |
| SAMEA8547893 | longitude | 6.1491 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 46.19336429 6.149056901 |
| SAMEA8547893 | subject_id | 1 | R1 | 0.70 | sample.name_rule:alias | alias: Ca_1A |
| SAMEA8547893 | timepoint_label | A | R1 | 0.70 | sample.name_rule:alias | alias: Ca_1A |
Sequencing
88 runs over 88 samples · mean 88.6 Mbp per run (median 89.5 Mbp, total 7.79 Gbp; 88 runs with a base count) · layout PAIRED 88 · platform ILLUMINA 88 · models Illumina MiSeq (88) · 0% of runs with a Sandpiper profile · first public 2022-01-05
Authors (11)
Abbas M first · Gaïa N · Buchs NC · Delaune V · Girard M · Andrey DO · Meyer J · Schrenzel J · Ris F · Harbarth S · Lazarevic V last
Downloads
PRJEB44214.csv.gz (3.4 KB) · parquet (75.0 KB) — all 88 samples, every field with route and confidence · PRJEB44214_determinations.csv.gz (8.0 KB) — 1,050 evidence rows