Ciprofloxacin effects on gut/oral microbiome in UTI, case-control
295 stool and oropharyngeal samples from UTI patients treated with ciprofloxacin (short ≤7 days vs long >7 days courses) and untreated controls, collected in Geneva (Switzerland), Lodz (Poland), and Antwerp (Belgium); case-control design. machine-written summary
295 samples · 295 runs · CH, PL, BE · Age unknown · 2024 · 0.67 Gbp / sample
One study deposited as 2 BioProjects (590 catalog samples together): PRJEB72433 · PRJNA1074135 · show together
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 2,532 sample values (antibiotic exposure, collection date, country, intervention, latitude, location locality, location region, longitude) |
| ○ Abstract / description | read; no usable statement |
| – 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 · share metadata |
| – Human verified | not yet checked by a person · I checked this project — verify it |
intervention · arms resolved
design observational_with_procedure
longitudinal
50 of 50 people sampled more than once (150 samples; median 3, up to 3 per person) · follow-up median 36 d (max 2 mo) · median interval between samples 17 d (time from collection dates).
Each row is one person (36 shown of 50); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 138 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 | 0 | 0% | ||||
| country | 295 | 100% | 295 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 295 | 100% | 295 | |||
| collection_date | 295 | 100% | 295 | |||
| detailed_location | 295 | 100% | ||||
| intervention | 295 | 100% | 295 | |||
| latitude | 295 | 100% | 295 | |||
| longitude | 295 | 100% | 295 | |||
| timepoint_label | 295 | 100% | 295 | |||
| location_locality | 268 | 91% | 268 | |||
| location_region | 115 | 39% | 115 | |||
| antibiotic_exposure | 84 | 28% | 84 |
- Long-term effects of ciprofloxacin treatment on the gastrointestinal and oropharyngeal microbiome are more pronounced after longer antibiotic courses. 2024 PMID 38936492 own_data
Archive description
This study performed shotgun metagenomic sequencing on stool and oropharyngeal samples obtained from patients presenting with uncomplicated UTI to primary care and receiving ciprofloxacin treatment. Duration of treatment was different across the patients and categorized as short (less or equal to 7 days) or long ( more than 7 days). Control subjects not undergoing antibiotic treatment were also included.
How this project entered the registry
Classified as human gut / stool / oral cavity / nasal / nasopharyngeal shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.75. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site run.scientific_name · “gut metagenome”
- body site run.scientific_name · “human oral metagenome”
- body site sample.attr.isolation_source · “Oropharynx (n=145/295)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN39918592 | antibiotic_exposure | no | R1 | 0.70 | sample.name_rule:alias | SATURN_001_untreated_OP1 |
| SAMN39918592 | collection_date | 2011-01-17 | R1 | 0.90 | biosample.attribute:collection_date | 2011-01-17 |
| SAMN39918592 | country | CH | R1 | 0.90 | sample.attr.geo_loc_name | Switzerland: Geneva |
| SAMN39918592 | intervention | no_intervention | R1 | 0.70 | sample.name_rule:alias | alias: SATURN_001_untreated_OP1 |
| SAMN39918592 | latitude | 46.2000 | R1 | 0.90 | biosample.attribute:lat_lon | 46.20 N 6.10 E |
| SAMN39918592 | location_locality | Geneva | R1 | 0.85 | biosample.attribute:geo_loc_name | Switzerland: Geneva |
| SAMN39918658 | location_region | Antwerp | R1 | 0.85 | biosample.attribute:geo_loc_name | Belgium: Antwerp |
| SAMN39918670 | location_region | Lodz Voivodeship | R1 | 0.60 | biosample.attribute:lat_lon | 51.75 N 19.46 E |
| SAMN39918592 | longitude | 6.1000 | R1 | 0.90 | biosample.attribute:lat_lon | 46.20 N 6.10 E |
| SAMN39918592 | subject_id | 001 | R1 | 0.70 | sample.name_rule:alias | alias: SATURN_001_untreated_OP1 |
| SAMN39918592 | timepoint_label | 1 | R1 | 0.70 | sample.name_rule:alias | SATURN_001_untreated_OP1 |
Sequencing
295 runs over 295 samples · mean 0.67 Gbp per run (median 0.67 Gbp, total 198.40 Gbp; 295 runs with a base count) · layout PAIRED 295 · platform ILLUMINA 295 · models Illumina MiSeq (295) · 87% of runs with a Sandpiper profile · first public 2024-06-21
Authors (0)
No author record.
Help complete this project
2 of the 4 core fields are below 50% coverage: age_category, health_condition. Share metadata
Downloads
PRJNA1074135.csv.gz (9.0 KB) · parquet (81.9 KB) — all 295 samples, every field with route and confidence · PRJNA1074135_determinations.csv.gz (21.6 KB) — 2,532 evidence rows