Microbiome changes in healthy volunteers treated with GSK1322322, a novel antibiotic targeting bacterial peptide deformylase
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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. 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
- Antimicrobial agent antibiotic,antibiotics,Antibiotika,Antibiotikum,antibiotique,antimicrobial,antimicrobial agents,microbicide,microbicides,Antimicrobial agent,antimicrobial agent
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- received oral-i.v.-administered GSK1322322 (prestudy)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- received oral-i.v.-administered GSK1322322 (end-of-study)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- received oral-i.v.-administered GSK1322322
- Group 0 sample size Number of subjects in the control (unexposed) group
- 38
- Group 1 sample size Number of subjects in the case (exposed) group
- 38
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
- Statistical test
- ANOVA
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
Source: Table 2
Description: Significantly changed gut bacterial operational taxonomic units in subjects receiving oral-i.v.-administered GSK1322322 in prestudy versus end-of-study comparisons
Abundance in Group 1: increased abundance in received oral-i.v.-administered GSK1322322 (end-of-study)
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium | ||
| Bifidobacterium adolescentis | ||
| Bifidobacterium pseudolongum | ||
| Enterobacteriaceae | ||
| Lachnospiraceae | ||
| Sutterella |
Revision editor(s): Mmarin
Signature 2
Source: Table 2
Description: Significantly changed gut bacterial operational taxonomic units in subjects receiving oral-i.v.-administered GSK1322322 in prestudy versus end-of-study comparisons
Abundance in Group 1: decreased abundance in received oral-i.v.-administered GSK1322322 (end-of-study)
Signature 3
Source: Figure 5
Description: Phylogenetic tree of peptide deformylase amino acid sequences for species of gastrointestinal (GI) microbiota detected in this study and bacterial pathogens with available MIC data for GSK1322322. Bacterial pathogens were classified as low susceptible (red) or high susceptible (green) according to an MIC cutoff of ≥ 8.0 μg/ml (see Materials and Methods). GI bacteria were classified by changes in oral-i.v. end-of-study compared to prestudy samples as having a statistically significant increase (blue) or decrease (orange) in the relative abundances, or as no change (black). The phylogenetic tree was reconstructed using the neighbor-joining method with the JTT option in the software MEGA6. Support for nodes in 1,000 bootstrap replicates is indicated by increased sizes as well as weighting to the red color spectrum of the circles at the nodes.
Abundance in Group 1: increased abundance in received oral-i.v.-administered GSK1322322 (end-of-study)
Signature 4
Source: Figure 5
Description: Phylogenetic tree of peptide deformylase amino acid sequences for species of gastrointestinal (GI) microbiota detected in this study and bacterial pathogens with available MIC data for GSK1322322. Bacterial pathogens were classified as low susceptible (red) or high susceptible (green) according to an MIC cutoff of ≥ 8.0 μg/ml (see Materials and Methods). GI bacteria were classified by changes in oral-i.v. end-of-study compared to prestudy samples as having a statistically significant increase (blue) or decrease (orange) in the relative abundances, or as no change (black). The phylogenetic tree was reconstructed using the neighbor-joining method with the JTT option in the software MEGA6. Support for nodes in 1,000 bootstrap replicates is indicated by increased sizes as well as weighting to the red color spectrum of the circles at the nodes.
Abundance in Group 1: decreased abundance in received oral-i.v.-administered GSK1322322 (end-of-study)
Revision editor(s): Mmarin
Experiment 2
Subjects
Lab analysis
Statistical Analysis
- Statistical test
- cluster analysis Statistical test: "cluster analysis" is not in the list (ANCOM, ANOSIM, ANOVA, Beta Binomial Regression, Chi-Square, Cox Proportional-Hazards Regression, Dunn's test, DESeq2, edgeR, Fisher's Exact Test, ...) of allowed values.
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Not specified
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
Source: Figure 5
Description: Phylogenetic tree of peptide deformylase amino acid sequences for species of gastrointestinal (GI) microbiota detected in this study and bacterial pathogens with available MIC data for GSK1322322. Bacterial pathogens were classified as low susceptible (red) or high susceptible (green) according to an MIC cutoff of ≥ 8.0 μg/ml (see Materials and Methods). GI bacteria were classified by changes in oral-i.v. end-of-study compared to prestudy samples as having a statistically significant increase (blue) or decrease (orange) in the relative abundances, or as no change (black). The phylogenetic tree was reconstructed using the neighbor-joining method with the JTT option in the software MEGA6. Support for nodes in 1,000 bootstrap replicates is indicated by increased sizes as well as weighting to the red color spectrum of the circles at the nodes.
Abundance in Group 1: increased abundance in received oral-i.v.-administered GSK1322322 (end-of-study)
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium adolescentis | ||
| Bifidobacterium dentium | ||
| Bifidobacterium sp. | ||
| Enterobacteriaceae bacterium | ||
| Sutterella parvirubra | ||
| Sutterella wadsworthensis |
Revision editor(s): Mmarin
Signature 2
Source: Figure 5
Description: Phylogenetic tree of peptide deformylase amino acid sequences for species of gastrointestinal (GI) microbiota detected in this study and bacterial pathogens with available MIC data for GSK1322322. Bacterial pathogens were classified as low susceptible (red) or high susceptible (green) according to an MIC cutoff of ≥ 8.0 μg/ml (see Materials and Methods). GI bacteria were classified by changes in oral-i.v. end-of-study compared to prestudy samples as having a statistically significant increase (blue) or decrease (orange) in the relative abundances, or as no change (black). The phylogenetic tree was reconstructed using the neighbor-joining method with the JTT option in the software MEGA6. Support for nodes in 1,000 bootstrap replicates is indicated by increased sizes as well as weighting to the red color spectrum of the circles at the nodes.
Abundance in Group 1: decreased abundance in received oral-i.v.-administered GSK1322322 (end-of-study)
Revision editor(s): Mmarin
