Comparative analysis of the lung microbiota in patients with respiratory infections, tuberculosis, and lung cancer: A preliminary study
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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
- Lung Pulmo,Lung,lung
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Pulmonary tuberculosis , Lung cancer lung TB,lung tuberculosis,pulmonary TB,pulmonary tuberculosis,Tuberculosis, Pulmonary,Pulmonary tuberculosis,alveolar cell carcinoma,cancer of lung,lung cancer,lung cancer, protection against,lung neoplasm,malignant lung neoplasm,malignant lung tumor,malignant neoplasm of lung,malignant neoplasm of the lung,malignant tumor of lung,malignant tumor of the lung,Nonsmall cell lung cancer,Lung cancer
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Lung cancer
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Tuberculosis patients (PTB)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Confirmed pulmonary tuberculosis
- 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
- 21
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- No antibiotics in the previous 1 month
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-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
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Source: Figure 3
Description: Taxonomic differences of the lung microbiota among patients with primary pulmonary tuberculosis (PTB), newly diagnosed lung cancer (LC), and community-acquired pneumonia (CAP). LEfSe identified the most differentially abundant taxa between the two groups
Abundance in Group 1: increased abundance in Tuberculosis patients (PTB)
| NCBI | Quality Control | Links |
|---|---|---|
| Selenomonas | ||
| Mycobacteriaceae | ||
| Mycobacterium |
Revision editor(s): Nuerteye
Signature 2
Source: Figure 3
Description: Taxonomic differences of the lung microbiota among patients with primary pulmonary tuberculosis (PTB), newly diagnosed lung cancer (LC), and community-acquired pneumonia (CAP). LEfSe identified the most differentially abundant taxa between the two groups
Abundance in Group 1: decreased abundance in Tuberculosis patients (PTB)
| NCBI | Quality Control | Links |
|---|---|---|
| MarseillaMarseilla | ||
| Sphingobium |
Revision editor(s): Nuerteye
Experiment 2
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Pulmonary tuberculosis , Pneumonia lung TB,lung tuberculosis,pulmonary TB,pulmonary tuberculosis,Tuberculosis, Pulmonary,Pulmonary tuberculosis,acute pneumonia,chest infection due to pneumonia,pneumonia,Pneumonia (disorder),Pneumonia (disorder) [Ambiguous],Pneumonia due to other specified organism,Pneumonia due to other specified organisms,Pneumonia due to other specified organisms (disorder),Pneumonia NOS,Pneumonia NOS (disorder),pneumonia with infectious disease,Pneumonitis,Pneumonitis (disorder),Pneumonia
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- community-acquired pneumonia (CAP)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Pulmonary tuberculosis
- Group 0 sample size Number of subjects in the control (unexposed) group
- 49
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- antibiotics in the previous 1 month
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Source: Figure 3
Description: Taxonomic differences of the lung microbiota among patients with primary pulmonary tuberculosis (PTB), newly diagnosed lung cancer (LC), and community-acquired pneumonia (CAP). LEfSe identified the most differentially abundant taxa between the two groups.
Abundance in Group 1: increased abundance in Pulmonary tuberculosis
Revision editor(s): Nuerteye
Signature 2
Source: Figure 3
Description: Taxonomic differences of the lung microbiota among patients with primary pulmonary tuberculosis (PTB), newly diagnosed lung cancer (LC), and community-acquired pneumonia (CAP). LEfSe identified the most differentially abundant taxa between the two groups.
Abundance in Group 1: decreased abundance in Pulmonary tuberculosis
| NCBI | Quality Control | Links |
|---|---|---|
| Parvimonas | ||
| Peptoniphilaceae | ||
| Deinococcus_ThermusDeinococcus_Thermus | ||
| Deinococcaceae | ||
| Deinococcales | ||
| Deinococcus | ||
| Deinococci | ||
| Mediterranea | ||
| Selenomonadaceae |
Revision editor(s): Nuerteye
Experiment 3
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Lung cancer , Pneumonia alveolar cell carcinoma,cancer of lung,lung cancer,lung cancer, protection against,lung neoplasm,malignant lung neoplasm,malignant lung tumor,malignant neoplasm of lung,malignant neoplasm of the lung,malignant tumor of lung,malignant tumor of the lung,Nonsmall cell lung cancer,Lung cancer,acute pneumonia,chest infection due to pneumonia,pneumonia,Pneumonia (disorder),Pneumonia (disorder) [Ambiguous],Pneumonia due to other specified organism,Pneumonia due to other specified organisms,Pneumonia due to other specified organisms (disorder),Pneumonia NOS,Pneumonia NOS (disorder),pneumonia with infectious disease,Pneumonitis,Pneumonitis (disorder),Pneumonia
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Lung cancer
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- patients with newly diagnosed lung cancer.
- Group 1 sample size Number of subjects in the case (exposed) group
- 8
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- No antibiotics, antitumor drugs in the previous 1 month.
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
Signature 1
Source: Figure 3
Description: Taxonomic differences of the lung microbiota among patients with primary pulmonary tuberculosis (PTB), newly diagnosed lung cancer (LC), and community-acquired pneumonia (CAP). LEfSe identified the most differentially abundant taxa between the two groups.
Abundance in Group 1: increased abundance in Lung cancer
Revision editor(s): Nuerteye
Signature 2
Source: Figure 3
Description: Taxonomic differences of the lung microbiota among patients with primary pulmonary tuberculosis (PTB), newly diagnosed lung cancer (LC), and community-acquired pneumonia (CAP). LEfSe identified the most differentially abundant taxa between the two groups.
Abundance in Group 1: decreased abundance in Lung cancer
| NCBI | Quality Control | Links |
|---|---|---|
| Lautropia | ||
| Phenylobacterium |
Revision editor(s): Nuerteye
