Assessment of lower respiratory tract microbiota associated with pulmonary tuberculosis in children
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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
- China
- 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 Expectoration,Sputum,sputum
- 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
- non severe group TB (DC group)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Active pulmonary tuberculosis (severe TB)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- children with active pulmonary TB (bacteriologically confirmed or clinically diagnosed)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 70
- Group 1 sample size Number of subjects in the case (exposed) group
- 15
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- not received antibiotics for a minimum of 3 months before the study.
Lab analysis
- Sequencing type
- 16S
- 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
- 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
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Source: Figure 2C
Description: Comparisons of respiratory microbiota in severe TB and non‐severe TB groups. (A) Relative abundance of the top 10 respiratory microbiota at the phylum level. Relative abundance of the top 10 respiratory microbiota at the genus level. Linear discriminant analysis (LDA) score histogram
Abundance in Group 1: increased abundance in Active pulmonary tuberculosis (severe TB)
Revision editor(s): Nuerteye
Signature 2
Source: Figure 2C
Description: Comparisons of respiratory microbiota in severe TB and non‐severe TB groups. (A) Relative abundance of the top 10 respiratory microbiota at the phylum level. Relative abundance of the top 10 respiratory microbiota at the genus level. Linear discriminant analysis (LDA) score histogram
Abundance in Group 1: decreased abundance in Active pulmonary tuberculosis (severe TB)
| NCBI | Quality Control | Links |
|---|---|---|
| Lachnospiraceae UCG 001Lachnospiraceae UCG 001 | ||
| Moraxella lincolniiMoraxella lincolnii | ||
| Agrobacterium radiobacterAgrobacterium radiobacter | ||
| Burkholderiales |
Revision editor(s): Nuerteye
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- clinical diagnosis (negative)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- bacteriologically confirmed TB (positive)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 34
- Group 1 sample size Number of subjects in the case (exposed) group
- 51
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
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Source: Figure 3D
Description: Association of respiratory microbiota with bacteriologically confirmed TB. (D) Identification of species with significant differences in abundance between the two groups using LEfSe (LDA effect size) analysis.
Abundance in Group 1: increased abundance in bacteriologically confirmed TB (positive)
| NCBI | Quality Control | Links |
|---|---|---|
| XanthomonadalesXanthomonadales | ||
| PaenibacillalesPaenibacillales | ||
| Paenibacillaceae | ||
| Paenibacillus |
Revision editor(s): Nuerteye
Signature 2
Source: Figure 3D
Description: Association of respiratory microbiota with bacteriologically confirmed TB. (D) Identification of species with significant differences in abundance between the two groups using LEfSe (LDA effect size) analysis.
Abundance in Group 1: decreased abundance in bacteriologically confirmed TB (positive)
Revision editor(s): Nuerteye
