Comprehensive Analysis of Pathogen Diversity and Diagnostic Biomarkers in Patients with Suspected Pulmonary Tuberculosis Through Metagenomic Next-Generation Sequencing/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
- Non‑Tuberculosis
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Tuberculosis (TB)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Clinical (microbiological) confirmation of pulmonary tuberculosis.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 111
- Group 1 sample size Number of subjects in the case (exposed) group
- 87
Lab analysis
- Sequencing type
- PCR
- 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
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Signature 1
Source: Figure 3A
Description: Microbial species with differential abundance between TB and Non-TB groups identified through LEfSe analysis with the thresholds of log10 LDA score≥2 and P value<0.05.
Abundance in Group 1: increased abundance in Tuberculosis (TB)
| NCBI | Quality Control | Links |
|---|---|---|
| Streptococcus infantis | ||
| Campylobacter curvus | ||
| Microbacterium tuberculosisMicrobacterium tuberculosis | ||
| Microbacterium tuberculosis complexMicrobacterium tuberculosis complex |
Revision editor(s): Nuerteye
Signature 2
Source: Figure 3A
Description: Microbial species with differential abundance between TB and Non-TB groups identified through LEfSe analysis with the thresholds of log10 LDA score≥2 and P value<0.05.
Abundance in Group 1: decreased abundance in Tuberculosis (TB)
| NCBI | Quality Control | Links |
|---|---|---|
| Corynebacterium striatum | ||
| Staphylococcus epidermidis | ||
| Ralstonia mannitolilytica | ||
| Mycoplasma hominisMycoplasma hominis |
Revision editor(s): Nuerteye
