Ciprofloxacin impact on gut resistome in healthy adults
12 stool samples from two healthy adult male volunteers in Germany, collected before, during and after a 6-day course of oral ciprofloxacin, to study effects on intestinal antibiotic resistance genes. machine-written summary
12 samples · 12 runs · DE · Adult · 2015 · 6.62 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 112 sample values (antibiotic exposure, collection date, country, intervention, latitude, location region, longitude, sex) |
| ✓ Abstract / description | 4 sample values (antibiotic exposure) |
| ○ Full text | read; no usable statement or table · PMC4649198, PMC8288446 |
| ○ 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 design single_arm_before_after · population healthy_control · Ciprofloxacin 500 mg orally twice daily for 6 days
“treated with ciprofloxacin for 6 days” — bioproject.description (study level; per-sample arms are in the intervention column below)
longitudinal
2 of 2 people sampled more than once (12 samples; median 6, up to 6 per person) · follow-up median 31 d (max 31 d) · median interval between samples 31 d (time from collection months (month precision)). Schedule stated by the source: “Stool collected before treatment (baseline), on days 1, 3, 6 of ciprofloxacin treatment, and 2 and 28 days after treatment ended.” (time origin: intervention start); stated follow-up 28 d.
Each row is one person (2 shown); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 8 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 | 12 | 100% | ||||
| country | 12 | 100% | 12 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 12 | 100% | 12 | |||
| antibiotic_exposure | 12 | 100% | 8 | 4 | ||
| collection_date | 12 | 100% | 12 | |||
| detailed_location | 12 | 100% | ||||
| latitude | 12 | 100% | 12 | |||
| location_region | 12 | 100% | 12 | |||
| longitude | 12 | 100% | 12 | |||
| sex | 12 | 100% | 12 | |||
| timepoint_label | 12 | 100% | 12 | |||
| intervention | 8 | 67% | 8 |
- Antibiotic Selection Pressure Determination through Sequence-Based Metagenomics. 2015 PMID 26369961 PMC4649198 own_data
- Dispersal strategies shape persistence and evolution of human gut bacteria. 2021 PMID 34111423 PMC8288446 unsure
Archive description
Two healthy male volunteers (S1 and S2) were treated with ciprofloxacin for 6 days (500 mg orally twice daily). Stool samples from both participants were collected before treatment (baseline), on day 1, 3 and 6 of treatment as well as 2 and 28 days after treatment. Metagenomic shotgun sequencing was performed with all samples.
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_unknown_no_evidence”
- body site study.title · “pertubation on the intestinal resistome and microbiota”
- body site study.description · “orally twice daily). Stool samples from both”
- life stage study.title · “in two healthy volunteers”
- life stage study.description · “Two healthy male volunteers (S1 and S2)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA3506758 | antibiotic_exposure | no | R1 | 0.85 | biosample.attribute:description | baseline stool sample |
| SAMEA3506762 | antibiotic_exposure | yes | R4 | 0.50 | study.description | treated with ciprofloxacin for 6 days |
| SAMEA3506758 | collection_date | 2013-12 | R1 | 0.90 | biosample.attribute:collection_date | 2013-12 |
| SAMEA3506758 | country | DE | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Germany |
| SAMEA3506758 | intervention | no_intervention | R1 | 0.85 | biosample.attribute:description | baseline stool sample |
| SAMEA3506758 | latitude | 48.5369 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 48.5369 9.0536 |
| SAMEA3506758 | location_region | Baden-Wuerttemberg | R1 | 0.60 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 48.5369 9.0536 |
| SAMEA3506758 | longitude | 9.0536 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 48.5369 9.0536 |
| SAMEA3506758 | sex | male | R1 | 0.90 | sample.attr.host_sex | male |
| SAMEA3506758 | subject_id | TUE-S1 | R1 | 0.70 | sample.name_rule:alias | TUE-S1_1 |
| SAMEA3506758 | timepoint_label | baseline stool sample | R1 | 0.85 | biosample.attribute:description | baseline stool sample |
Sequencing
12 runs over 12 samples · mean 6.89 Gbp per run (median 6.62 Gbp, total 82.71 Gbp; 12 runs with a base count) · layout PAIRED 12 · platform ILLUMINA 12 · models Illumina HiSeq 2000 (12) · 67% of runs with a Sandpiper profile · first public 2015-09-07
Authors (17)
Willmann M first · El-Hadidi M · Huson DH · Schütz M · Weidenmaier C · Autenrieth IB · Peter S last · Hildebrand F first · Gossmann TI · Frioux C · Özkurt E · Myers PN · Ferretti P · Kuhn M · Bahram M · Nielsen HB · Bork P last
Downloads
PRJEB10391.csv.gz (1.3 KB) · parquet (70.9 KB) — all 12 samples, every field with route and confidence · PRJEB10391_determinations.csv.gz (1.7 KB) — 116 evidence rows