Microbiome recovery in adult females with uncomplicated urinary tract infections in a randomised phase 2A trial of the novel antibiotic gepotidacin (GSK140944)/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Folakunmi on 2023-12-12
Subjects
- Location of subjects
- United States of America
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Urinary tract infection INFECTION, URINARY TRACT,TRACT, INFECTION OF URINARY,urinary tract infection,urinary tract infection (disease),Urinary tract infection
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Day 1 (pre-dose)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Day 5 (end of dosing or post-dose)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This represented the condition at the end of the 5-day regimen of gepotidacin treatment in the GIT microbiome
- Group 0 sample size Number of subjects in the control (unexposed) group
- 22
- Group 1 sample size Number of subjects in the case (exposed) group
- 22
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V4
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- raw counts
- Statistical test
- DESeq2
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.01
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2023-12-12
Source: Within results text(under "Changes in detected abundances of bacterial genera"line 8-14), Figure 3
Description: Relative abundances of assigned bacterial taxa.
Abundance in Group 1: increased abundance in Day 5 (end of dosing or post-dose)
Signature 2
Reviewed Marked as Reviewed by Folakunmi on 2023-12-12
Source: Within results text(under "Changes in detected abundances of bacterial genera"line 8-14), Figure 3
Description: Relative abundances of assigned bacterial taxa.
Abundance in Group 1: decreased abundance in Day 5 (end of dosing or post-dose)
| NCBI | Quality Control | Links |
|---|---|---|
| Dialister | ||
| Enterococcus | ||
| Fusobacterium | ||
| Parabacteroides | ||
| Prevotella sp. | ||
| Selenomonas | ||
| Treponema | ||
| Tyzzerella | ||
| Veillonella | ||
| unclassified Lachnospiraceae |
