Patients infected with Mycobacterium africanum versus Mycobacterium tuberculosis possess distinct intestinal microbiota
-
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
- Mali
- 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
- Sputum , Feces Expectoration,Sputum,sputum,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
- Pulmonary tuberculosis lung TB,lung tuberculosis,pulmonary TB,pulmonary tuberculosis,Tuberculosis, Pulmonary,Pulmonary tuberculosis
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Mycobacterium africanum (MAF)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Mycobacterium tuberculosis (MTB)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- composed of newly infected active pulmonary tuberculosis patients defined by positive sputum culture
- Group 0 sample size Number of subjects in the control (unexposed) group
- 20
- Group 1 sample size Number of subjects in the case (exposed) group
- 21
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
- LEfSe
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Signature 1
Source: Figure 2A-C
Description: Alterations in the composition of the intestinal microbiome of MAF- and MTB-infected patients at the time of diagnosis. a. Relative abundances of the five most prominent phyla are compared between the three groups. b-c. LEfSe analyses were performed to identify differentially abundant families in the two infection groups, MAF and MTB, compared to the healthy participants (b) and between the two infection groups (c). Taxa are filtered for p < 0.05 and linear discriminant analysis (LDA) score > 2.
Abundance in Group 1: increased abundance in Mycobacterium tuberculosis (MTB)
Revision editor(s): Nuerteye
Signature 2
Source: Figure 2A-C
Description: Alterations in the composition of the intestinal microbiome of MAF- and MTB-infected patients at the time of diagnosis. a. Relative abundances of the five most prominent phyla are compared between the three groups. b-c. LEfSe analyses were performed to identify differentially abundant families in the two infection groups, MAF and MTB, compared to the healthy participants (b) and between the two infection groups (c). Taxa are filtered for p < 0.05 and linear discriminant analysis (LDA) score > 2.
Abundance in Group 1: decreased abundance in Mycobacterium tuberculosis (MTB)
| NCBI | Quality Control | Links |
|---|---|---|
| Coriobacteriaceae incertae sedis |
Revision editor(s): Nuerteye
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy controls
- Group 0 sample size Number of subjects in the control (unexposed) group
- 10
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- Not specified
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Source: Figure 2A-C
Description: Alterations in the composition of the intestinal microbiome of MAF- and MTB-infected patients at the time of diagnosis. a. Relative abundances of the five most prominent phyla are compared between the three groups. b-c. LEfSe analyses were performed to identify differentially abundant families in the two infection groups, MAF and MTB, compared to the healthy participants (b) and between the two infection groups (c). Taxa are filtered for p < 0.05 and linear discriminant analysis (LDA) score > 2.
Abundance in Group 1: decreased abundance in Mycobacterium tuberculosis (MTB)
Revision editor(s): Nuerteye
Experiment 3
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Mycobacterium africanum (MAF)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- consist of active pulmonary tuberculosis patients defined by positive sputum culture who received anti tuberculosis treatment (ATT) two months after.
- Group 1 sample size Number of subjects in the case (exposed) group
- 20
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Source: Figure 2A-C
Description: Alterations in the composition of the intestinal microbiome of MAF- and MTB-infected patients at the time of diagnosis. a. Relative abundances of the five most prominent phyla are compared between the three groups. b-c. LEfSe analyses were performed to identify differentially abundant families in the two infection groups, MAF and MTB, compared to the healthy participants (b) and between the two infection groups (c). Taxa are filtered for p < 0.05 and linear discriminant analysis (LDA) score > 2.
Abundance in Group 1: increased abundance in Mycobacterium africanum (MAF)
| NCBI | Quality Control | Links |
|---|---|---|
| Enterobacteriaceae |
Revision editor(s): Nuerteye
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Mycobacterium africanum plus anti tuberculosis treatment (MAF+HRZE)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Mycobacterium tuberculosis plus anti tuberculosis treatment (MTB+HRZE)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- composed of newly infected active pulmonary tuberculosis patients defined by positive sputum culture who received anti tuberculosis treatment for the first two months.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 20
- Group 1 sample size Number of subjects in the case (exposed) group
- 21
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Figure 3C
Description: Perturbation in the intestinal microbiome composition due to HRZE treatment in both MAF and MTB infection. c. Pairwise LEfSe comparisons were performed between the three groups to identify differentially abundant families. Taxa are filtered for p <0.05 and LDA score > 2.
Abundance in Group 1: increased abundance in Mycobacterium tuberculosis plus anti tuberculosis treatment (MTB+HRZE)
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacteriaceae | ||
| Streptococcaceae | ||
| Coriobacteriaceae incertae sedis |
Revision editor(s): Nuerteye
Experiment 5
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Mycobacterium africanum plus anti tuberculosis treatment (MAF+HRZE)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- composed of newly infected active pulmonary tuberculosis patients defined by positive sputum culture who received HRZE treatment
- Group 0 sample size Number of subjects in the control (unexposed) group
- 10
- Group 1 sample size Number of subjects in the case (exposed) group
- 20
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Source: Figure 3C
Description: Perturbation in the intestinal microbiome composition due to HRZE treatment in both MAF and MTB infection. c. Pairwise LEfSe comparisons were performed between the three groups to identify differentially abundant families. Taxa are filtered for p <0.05 and LDA score > 2.
Abundance in Group 1: increased abundance in Mycobacterium africanum plus anti tuberculosis treatment (MAF+HRZE)
| NCBI | Quality Control | Links |
|---|---|---|
| Peptostreptococcaceae |
Revision editor(s): Nuerteye
Signature 2
Source: Figure 3C
Description: Perturbation in the intestinal microbiome composition due to HRZE treatment in both MAF and MTB infection. c. Pairwise LEfSe comparisons were performed between the three groups to identify differentially abundant families. Taxa are filtered for p <0.05 and LDA score > 2.
Abundance in Group 1: decreased abundance in Mycobacterium africanum plus anti tuberculosis treatment (MAF+HRZE)
Revision editor(s): Nuerteye
Experiment 6
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Mycobacterium tuberculosis plus anti tuberculosis treatment (MAF+HRZE))
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- consist of active pulmonary tuberculosis patients defined by positive sputum culture who received anti tuberculosis treatment (ATT) two months after.
- Group 1 sample size Number of subjects in the case (exposed) group
- 21
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Source: Figure 3C
Description: Perturbation in the intestinal microbiome composition due to HRZE treatment in both MAF and MTB infection. c. Pairwise LEfSe comparisons were performed between the three groups to identify differentially abundant families. Taxa are filtered for p <0.05 and LDA score > 2.
Abundance in Group 1: decreased abundance in Mycobacterium tuberculosis plus anti tuberculosis treatment (MAF+HRZE))
Revision editor(s): Nuerteye
