Effect of amoxicillin on the gut microbiome of children with severe acute malnutrition in Madarounfa, Niger: a retrospective metagenomic analysis of a placebo-controlled trial
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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
- Niger
- 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
- Treatment Treatment,treatment
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Amoxicillin Week 0
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Amoxicillin Week 1
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Children with severe acute malnutrition who received amoxicillin for one week and had their fecal samples collected at the end of treatment (Week 1).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 35
- Group 1 sample size Number of subjects in the case (exposed) group
- 39
Lab analysis
- Sequencing type
- WMS
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
- 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
- Mann-Whitney (Wilcoxon)
- 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
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Richness Number of species
- decreased
Signature 1
Source: Figure 3E
Description: Significant taxonomic changes at the genus level with Benjamini-Hochberg-corrected q-values.
Abundance in Group 1: increased abundance in Amoxicillin Week 1
| NCBI | Quality Control | Links |
|---|---|---|
| Escherichia sp. |
Revision editor(s): Anne-mariesharp
Signature 2
Source: Figure 3A, B, C
Description: Significant taxonomic changes at the genus level with Benjamini-Hochberg-corrected q-values.
Abundance in Group 1: decreased abundance in Amoxicillin Week 1
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium sp. | ||
| Holdemanella sp. | ||
| Lactobacillus sp. |
Revision editor(s): Anne-mariesharp
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Placebo Week 1
- Group 0 sample size Number of subjects in the control (unexposed) group
- 33
Lab analysis
Statistical Analysis
- Matched on Factors on which subjects have been matched on in a case-control study
- age
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure 3E
Description: Significant taxonomic changes at the genus level with Benjamini-Hochberg-corrected q-values.
Abundance in Group 1: increased abundance in Amoxicillin Week 1
| NCBI | Quality Control | Links |
|---|---|---|
| Escherichia sp. |
Revision editor(s): Anne-mariesharp
Signature 2
Source: Figure 3A, B
Description: Significant taxonomic changes at the genus level with Benjamini-Hochberg-corrected q-values.
Abundance in Group 1: decreased abundance in Amoxicillin Week 1
| NCBI | Quality Control | Links |
|---|---|---|
| Holdemanella sp. | ||
| Lactobacillus sp. |
Revision editor(s): Anne-mariesharp
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Placebo Week 0
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Placebo Week 1
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Children with severe acute malnutrition who received Placebo for one week and had their fecal samples collected at week 1
- Group 0 sample size Number of subjects in the control (unexposed) group
- 32
- Group 1 sample size Number of subjects in the case (exposed) group
- 33
Lab analysis
Statistical Analysis
- Matched on Factors on which subjects have been matched on in a case-control study
- Not specified
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure 3D
Description: Significant taxonomic changes at the genus level with Benjamini-Hochberg-corrected q-values.
Abundance in Group 1: decreased abundance in Placebo Week 1
| NCBI | Quality Control | Links |
|---|---|---|
| Klebsiella sp. |
Revision editor(s): Anne-mariesharp
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Placebo Week 1
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Amoxicillin Week 1
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Children with severe acute malnutrition who received amoxicillin for one week and had their fecal samples collected at the end of treatment (Week 1).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 33
- Group 1 sample size Number of subjects in the case (exposed) group
- 39
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- arcsine square-root
- Statistical test
- MaAsLin2
- Matched on Factors on which subjects have been matched on in a case-control study
- age
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure 3F, Appendix 3 (tab 3)
Description: Coefficients (effect size) and 95% confidence intervals for significant taxonomic enrichment and depletion
Abundance in Group 1: increased abundance in Amoxicillin Week 1
| NCBI | Quality Control | Links |
|---|---|---|
| Escherichia sp. |
Revision editor(s): Anne-mariesharp
Signature 2
Source: Figure 3F, Appendix 3 (tab 3)
Description: Coefficients (effect size) and 95% confidence intervals for significant taxonomic enrichment and depletion
Abundance in Group 1: decreased abundance in Amoxicillin Week 1
| NCBI | Quality Control | Links |
|---|---|---|
| Dorea sp. | ||
| Holdemanella sp. | ||
| Lactobacillus sp. | ||
| Streptococcus sp. |
Revision editor(s): Anne-mariesharp
Experiment 5
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Amoxicillin Week 0
- Group 0 sample size Number of subjects in the control (unexposed) group
- 35
Lab analysis
Statistical Analysis
- Matched on Factors on which subjects have been matched on in a case-control study
- Not specified
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Richness Number of species
- decreased
Signature 1
Source: Figure 3F, Appendix 3 (tab 3)
Description: Coefficients (effect size) and 95% confidence intervals for significant taxonomic enrichment and depletion
Abundance in Group 1: increased abundance in Amoxicillin Week 1
| NCBI | Quality Control | Links |
|---|---|---|
| Escherichia sp. | ||
| Klebsiella sp. |
Revision editor(s): Anne-mariesharp
Signature 2
Source: Figure 3F, Appendix 3 (tab 3)
Description: Coefficients (effect size) and 95% confidence intervals for significant taxonomic enrichment and depletion
Abundance in Group 1: decreased abundance in Amoxicillin Week 1
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium sp. | ||
| Holdemanella sp. | ||
| Lactobacillus sp. |
Revision editor(s): Anne-mariesharp
Experiment 6
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Placebo-treated children (Week 104)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Amoxicillin-treated children (Week 104)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Children with severe acute malnutrition who received amoxicillin for one week, and had their fecal samples collected at the 2-year follow-up (Week 104).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 13
- Group 1 sample size Number of subjects in the case (exposed) group
- 22
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 5C, Appendix 3 (tab 10)
Description: Coefficients (effect size) and 95% CI for taxa significantly different between amoxicillin-treated and placebo-treated children
Abundance in Group 1: increased abundance in Amoxicillin-treated children (Week 104)
Revision editor(s): Anne-mariesharp
Signature 2
Source: Figure 5C, Appendix 3 (tab 10)
Description: Coefficients (effect size) and 95% CI for taxa significantly different between amoxicillin-treated and placebo-treated children
Abundance in Group 1: decreased abundance in Amoxicillin-treated children (Week 104)
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium bifidum | ||
| Bifidobacterium longum |
Revision editor(s): Anne-mariesharp
Experiment 7
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- non-SAM (Severe Acute Malnutrition) Week 104
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- SAM (Severe Acute Malnutrition) Placebo at Week 104
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Children with severe acute malnutrition who received placebo for one week, and had their fecal samples collected at the 2-year follow-up (Week 104).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 6
- Group 1 sample size Number of subjects in the case (exposed) group
- 13
Lab analysis
Statistical Analysis
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, Confounders controlled for: "anthropometry" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.anthropometry
Signature 1
Source: Supplementary Figure 5, Appendix 3 (tab15)
Description: Coefficient of significantly increased species between placebo-treated and non-SAM children
Abundance in Group 1: increased abundance in SAM (Severe Acute Malnutrition) Placebo at Week 104
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium bifidum | ||
| Bifidobacterium breve | ||
| Bifidobacterium longum |
Revision editor(s): Anne-mariesharp
Signature 2
Source: Supplementary Figure 5, Appendix 3 (tab15)
Description: Coefficient of significantly increased species between placebo-treated and non-SAM children
Abundance in Group 1: decreased abundance in SAM (Severe Acute Malnutrition) Placebo at Week 104
| NCBI | Quality Control | Links |
|---|---|---|
| Faecalibacterium prausnitzii | ||
| Prevotella sp. 885 | ||
| Segatella copri | ||
| Prevotella sp. AM42-24 |
Revision editor(s): Anne-mariesharp
