Microbiome recovery in adult females with uncomplicated urinary tract infections in a randomised phase 2A trial of the novel antibiotic gepotidacin (GSK140944)
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Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Experiment 1
Subjects
- Location of subjects
- United States of America
- Host species Species from which microbiome was sampled (if applicable)
- 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
- 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)
- 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
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- End of dosing (this is relative to the gepotidacin dosing regimen).
- 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).
- relative abundances
- 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
Source: Supplementary Data File S1, Figure 3
Description: Relative abundances of assigned bacterial taxa.
Abundance in Group 1: increased abundance in Day 5
Revision editor(s): Atrayees
Signature 2
Source: Supplementary Data File S1, Figure 3
Description: Relative abundances of assigned bacterial taxa.
Abundance in Group 1: decreased abundance in Day 5
| NCBI | Quality Control | Links |
|---|---|---|
| Tyzzerella | ||
| Parabacteroides | ||
| Enterococcus | ||
| Dialister | ||
| Fusobacterium | ||
| Veillonella |
Revision editor(s): Atrayees
Experiment 2
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Follow-up
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Day 28 ± 3 days (this is relative to the gepotidacin dosing regimen).
Lab analysis
Statistical Analysis
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
Source: Supplementary Data File S1, Figure 3
Description: Relative abundances of assigned bacterial taxa.
Abundance in Group 1: increased abundance in Follow-up
Revision editor(s): Atrayees
Signature 2
Source: Supplementary Data File S1, Figure 3
Description: Relative abundances of assigned bacterial taxa.
Abundance in Group 1: decreased abundance in Follow-up
| NCBI | Quality Control | Links |
|---|---|---|
| Collinsella | ||
| Parabacteroides | ||
| Fusicatenibacter | ||
| Treponema | ||
| Oscillibacter | ||
| Bacteroides | ||
| Lactobacillus | ||
| Gardnerella | ||
| Granulicatella | ||
| Rikenellaceae | ||
| Rothia |
Revision editor(s): Atrayees
Experiment 3
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Saliva Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Day 5
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- End of dosing (this is relative to the gepotidacin dosing regimen).
Lab analysis
Statistical Analysis
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
Source: Supplementary Data File S1, Figure 3
Description: Relative abundances of assigned bacterial taxa.
Abundance in Group 1: increased abundance in Day 5
| NCBI | Quality Control | Links |
|---|---|---|
| Aerococcus | ||
| Shuttleworthia | ||
| Acidaminococcus | ||
| Faecalibacterium | ||
| Megasphaera | ||
| Ruminococcus |
Revision editor(s): Atrayees
Signature 2
Source: Supplementary Data File S1, Figure 3
Description: Relative abundances of assigned bacterial taxa.
Abundance in Group 1: decreased abundance in Day 5
Revision editor(s): Atrayees
Experiment 4
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Follow-up
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Day 28 ± 3 days (this is relative to the gepotidacin dosing regimen).
Lab analysis
Statistical Analysis
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
Source: Supplementary Data File S1, Figure 3
Description: Relative abundances of assigned bacterial taxa.
Abundance in Group 1: increased abundance in Follow-up
| NCBI | Quality Control | Links |
|---|---|---|
| Acidaminococcus | ||
| Megasphaera | ||
| Subdoligranulum | ||
| Oscillospiraceae | ||
| Faecalibacterium |
Revision editor(s): Atrayees
Signature 2
Source: Supplementary Data File S1, Figure 3
Description: Relative abundances of assigned bacterial taxa.
Abundance in Group 1: decreased abundance in Follow-up
Revision editor(s): Atrayees
Experiment 5
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Vagina Distal oviductal region,Distal portion of oviduct,Vaginae,Vagina
Lab analysis
Statistical Analysis
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
Source: Supplementary Data File S1, Figure 3
Description: Relative abundances of assigned bacterial taxa.
Abundance in Group 1: decreased abundance in Follow-up
Revision editor(s): Atrayees
Signature 2
Source: Supplementary Data File S1, Figure 3
Description: Relative abundances of assigned bacterial taxa.
Abundance in Group 1: increased abundance in Follow-up
| NCBI | Quality Control | Links |
|---|---|---|
| Fretibacterium | ||
| Selenomonas | ||
| Parvimonas | ||
| Oscillibacter | ||
| Mitsuokella | ||
| Lachnospira | ||
| Pseudomonas | ||
| Treponema | ||
| Ruminiclostridium | ||
| Butyricicoccus | ||
| Eubacterium ventriosum | ||
| Bifidobacterium |
Revision editor(s): Atrayees
Experiment 6
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Day 5
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- End of dosing (this is relative to the gepotidacin dosing regimen).
Lab analysis
Statistical Analysis
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
Source: Supplementary Data File S1, Figure 3
Description: Relative abundances of assigned bacterial taxa.
Abundance in Group 1: increased abundance in Day 5
| NCBI | Quality Control | Links |
|---|---|---|
| Pseudomonas | ||
| Entamoebidae | ||
| Paraprevotella | ||
| Sutterella | ||
| Prevotella | ||
| Rothia | ||
| [Eubacterium] yurii |
Revision editor(s): Atrayees
Signature 2
Source: Supplementary Data File S1, Figure 3
Description: Relative abundances of assigned bacterial taxa.
Abundance in Group 1: decreased abundance in Day 5
Revision editor(s): Atrayees
