Insights into the Unique Lung Microbiota Profile of Pulmonary Tuberculosis Patients Using Metagenomic Next-Generation Sequencing
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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
The lung microbiota profile in pulmonary tuberculosis (TB) patients and the effects of anti-TB treatment on the profile need to be determined thoroughly and comprehensively. This study primarily aimed to determine the lung microbiota profile associated with pulmonary TB and characterize the longitudinal changes during anti-TB treatment. A total of 53 participants, comprising 8 healthy individuals, 12 untreated pulmonary TB patients, 15 treated pulmonary TB patients, 11 cured pulmonary TB patients, and 7 lung cancer patients, were recruited in the present study. Bronchioalveolar lavage fluid (BALF) samples were collected from the above participants, and throat swabs were taken from healthy individuals. Microbiomes in the samples were examined using metagenomic next-generation sequencing (mNGS). Differences in microbiota profiles were determined through a comparison of the indicated groups. Our findings indicated that the BALF samples displayed decreased richness and diversity of the microbiota compared to those of the throat swab samples, and these two kinds of samples exhibited obvious separation on principal-coordinate analysis (PCoA) plots. Untreated pulmonary TB patients displayed a unique lung microbiota signature distinct from that of healthy individuals and lung cancer patients. Our data first demonstrated that anti-TB treatment with first-line drugs increases alpha diversity and significantly affects the beta diversity of the lung microbiota, while it also induces antibiotic resistance genes (ARGs).
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
- Throat Gula,Throat,throat
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Mycobacterium tuberculosis Bacillus tuberculosis,Bacterium tuberculosis,Mycobacterium tuberculosis typus humanus,Mycobacterium tuberculosis var. hominis,Mycobacterium tuberculosis,mycobacterium tuberculosis
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy Control Group (HCG)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Untreated TB Group (UTG)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group consists of patients who have Untreated Pulmonary Tuberculosis and are not taking any antibiotics.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 8
- Group 1 sample size Number of subjects in the case (exposed) group
- 12
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
- LEfSe
- 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)?
- No
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 4.0
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Richness Number of species
- decreased
Signature 1
Source: Fig 3C
Description: Differentially enriched taxa identified by linear discriminant analysis effect size (LEfSe) among the three groups.
Abundance in Group 1: increased abundance in Untreated TB Group (UTG)
| NCBI | Quality Control | Links |
|---|---|---|
| Pasteurella multocida | ||
| Staphylococcus aureus | ||
| Ralstonia solanacearum |
Signature 2
Source: Fig 3C
Description: Differentially enriched taxa identified by linear discriminant analysis effect size (LEfSe) among the three groups.
Abundance in Group 1: decreased abundance in Untreated TB Group (UTG)
| NCBI | Quality Control | Links |
|---|---|---|
| Ralstonia pickettii | ||
| Staphylococcus haemolyticus |
Revision editor(s): Victoria
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Lung Cancer Group (LCG)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Untreated TB Group (LCG)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 7
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
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Richness Number of species
- decreased
Signature 1
Source: Fig 3C
Description: Differentially enriched taxa identified by linear discriminant analysis effect size (LEfSe) among the three groups.
Abundance in Group 1: increased abundance in Untreated TB Group (LCG)
| NCBI | Quality Control | Links |
|---|---|---|
| Pasteurella multocida | ||
| Staphylococcus aureus | ||
| Ralstonia solanacearum |
Signature 2
Source: Fig 3C
Description: Differentially enriched taxa identified by linear discriminant analysis effect size (LEfSe) among the three groups.
Abundance in Group 1: decreased abundance in Untreated TB Group (LCG)
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotella intermedia | ||
| Streptomyces sp. ICC4 |
Revision editor(s): Victoria
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Cured TB Group (CTG)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Untreated TB Group (UTG)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 11
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
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Richness Number of species
- decreased
