Stool/oropharyngeal metagenomes, UTI, ciprofloxacin
295 stool and oropharyngeal swab samples from Switzerland, Poland, and Belgium, from uncomplicated UTI patients treated with ciprofloxacin (short vs long duration) and untreated controls; 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 | 2,616 sample values (antibiotic exposure, collection date, country, health condition, health condition detail, intervention, latitude, location region) |
| ○ 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 |
| – Human verified | not yet checked by a person · I checked this project — verify it |
longitudinal
50 of 50 people sampled more than once (295 samples; median 6, up to 6 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 262 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 | 295 | 100% | 295 | |||
| subject_id | 295 | 100% | 295 | |||
| collection_date | 295 | 100% | 295 | |||
| health_condition_detail | 295 | 100% | 295 | |||
| latitude | 295 | 100% | 295 | |||
| longitude | 295 | 100% | 295 | |||
| timepoint_label | 295 | 100% | 295 | |||
| detailed_location | 88 | 30% | ||||
| location_region | 88 | 30% | 88 | |||
| antibiotic_exposure | 84 | 28% | 84 | |||
| intervention | 84 | 28% | 84 |
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 shotgun DNA metagenome of age unknown by opus_adjudicated with confidence 0.75. Assay shotgun_dna.
- host study.description · “patients presenting with uncomplicated UTI to primary care”
- body site study.title · “Stool and oropharyngeal swabs metagenome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA115290045 | antibiotic_exposure | no | R1 | 0.70 | sample.name_rule:alias | SATURN_001_untreated_Stool1 |
| SAMEA115290045 | collection_date | 2011-01-17 | R1 | 0.90 | biosample.attribute:collection_date | 2011-01-17 |
| SAMEA115290045 | country | CH | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Switzerland |
| SAMEA115290045 | health_condition | healthy_control | R1 | 0.70 | sample.name_rule:alias | SATURN_001_untreated_Stool1 |
| SAMEA115290045 | health_condition_detail | Control subjects not undergoing antibiotic treatment (description: 'Control subjects not undergoing antibiotic treatment were also included') | R1 | 0.70 | sample.name_rule:alias | SATURN_001_untreated_Stool1 |
| SAMEA115290045 | intervention | no_intervention | R1 | 0.70 | sample.name_rule:alias | SATURN_001_untreated_Stool1 |
| SAMEA115290045 | latitude | 46.2000 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 46.2 6.1 |
| SAMEA115290084 | location_region | Lodz Voivodeship | R1 | 0.60 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 51.75 19.46 |
| SAMEA115290045 | longitude | 6.1000 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 46.2 6.1 |
| SAMEA115290045 | subject_id | 001 | R1 | 0.70 | sample.name_rule:alias | SATURN_001_untreated_Stool1 |
| SAMEA115290045 | timepoint_label | 1 | R1 | 0.70 | sample.name_rule:alias | SATURN_001_untreated_Stool1 |
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) · 89% of runs with a Sandpiper profile · first public 2024-06-20
Authors (0)
No author record.
Downloads
PRJEB72433.csv.gz (8.7 KB) · parquet (82.6 KB) — all 295 samples, every field with route and confidence · PRJEB72433_determinations.csv.gz (23.8 KB) — 2,616 evidence rows