Airway microbiome signature accurately discriminates Mycobacterium tuberculosis infection status/Experiment 1
From BugSigDB
Subjects
- Location of subjects
- Uganda
- 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‑Tuberculosis (M.tb-uninfected)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Active tuberculosis patients (PTB)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Active tuberculosis defined by GeneXpert
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
- Matched on Factors on which subjects have been matched on in a case-control study
- age, sex, smoking status
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- decreased
- 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: Figure 4C
Description: Bar plots showing linear discriminant analysis (LDA) effect size scores of OTUs in active TB versus LTBI and M.tb-uninfected groups.
Abundance in Group 1: increased abundance in Active tuberculosis patients (PTB)
| NCBI | Quality Control | Links |
|---|---|---|
| ActinobacteriaActinobacteria | ||
| Brevibacillus | ||
| Microbacterium | ||
| Streptomyces | ||
| Beijerinckiaceae | ||
| Mycobacterium tuberculosis |
Revision editor(s): Nuerteye
Signature 2
Source: Figure 4C
Description: Bar plots showing linear discriminant analysis (LDA) effect size scores of OTUs in active TB versus LTBI and M.tb-uninfected groups.
Abundance in Group 1: decreased abundance in Active tuberculosis patients (PTB)
Revision editor(s): Nuerteye
