Metagenomic analysis of the lung microbiome in pulmonary tuberculosis - a pilot study/Experiment 1
From BugSigDB
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 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 tuberculosis (MTB−)
- 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
- Mycobacterium tuberculosis (MTB) detected by smear, culture, PCR, or GeneXpert.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 30
- Group 1 sample size Number of subjects in the case (exposed) group
- 30
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
- Mann-Whitney (Wilcoxon)
- 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)?
- Yes
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on 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: Figure 2
Description: Average relative taxon abundance comparisons between the MTB+ and MTB- groups at the genus level.
Abundance in Group 1: increased abundance in Mycobacterium tuberculosis (MTB+)
| NCBI | Quality Control | Links |
|---|---|---|
| Mycobacterium tuberculosis |
Revision editor(s): Nuerteye
Signature 2
Source: Figure 2
Description: Average relative taxon abundance comparisons between the MTB+ and MTB- groups at the genus level.
Abundance in Group 1: decreased abundance in Mycobacterium tuberculosis (MTB+)
| NCBI | Quality Control | Links |
|---|---|---|
| Streptococcus | ||
| Prevotella | ||
| Neisseria | ||
| Selenomonas | ||
| Bifidobacterium |
Revision editor(s): Nuerteye
