Comparative analysis of the lung microbiota in patients with respiratory infections, tuberculosis, and lung cancer: A preliminary study/Experiment 2
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 , 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 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
- 49
- 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)
- 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
- 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
