Microbiome Alteration in Lung Tissues of Tuberculosis Patients Revealed by Metagenomic Next-Generation Sequencing and Immune-Related Transcriptional Profile Identified by Transcriptome 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
- patients with Non-tuberculosis
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- patients with tuberculosis
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mtb-positive in the bacteriological examination, including sputum smear or sputum culture, mNGS, acid-fast staining, T-spot, adenosine deaminase, PCR, and interferon-gamma release assay; clinical manifestations such as constitutional symptoms and imaging manifestations; improvement following initiation of anti-TB therapy.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 25
- Group 1 sample size Number of subjects in the case (exposed) group
- 110
Lab analysis
- Sequencing type
- WMS
- 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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
Signature 1
Source: Figure 2C
Description: Microbial distribution in lung tissues of TB and NonTB patients. LEfSe analyses were performed to determine the microbial features with significant differences in the relative abundance.
Abundance in Group 1: increased abundance in patients with tuberculosis
Revision editor(s): Nuerteye
Signature 2
Source: Figure 2C
Description: Microbial distribution in lung tissues of TB and NonTB patients. LEfSe analyses were performed to determine the microbial features with significant differences in the relative abundance.
Abundance in Group 1: decreased abundance in patients with tuberculosis
Revision editor(s): Nuerteye
