Diagnosis and insight into the unique lung microbiota of pediatric pulmonary tuberculosis patients by bronchoalveolar lavage using metagenomic next-generation sequencing/Experiment 1
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
- pediatric pneumonia patients (NTB group)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- pediatric pulmonary tuberculosis (PTB group)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- showing positive TB culturing, TB-PCR, or mNGS result
- Group 0 sample size Number of subjects in the control (unexposed) group
- 21
- Group 1 sample size Number of subjects in the case (exposed) group
- 43
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
Signature 1
Source: Figures 3F, G; Supplementary Table 2
Description: LEfSe analysis was performed to identify differentially abundant taxa, which are highlighted on the phylogenetic tree in cladogram format (F) and for which the linear discriminant analysis scores are shown (G)
Abundance in Group 1: increased abundance in pediatric pulmonary tuberculosis (PTB group)
Revision editor(s): Nuerteye
Signature 2
Source: Figures 3F, G; Supplementary Table 2
Description: LEfSe analysis was performed to identify differentially abundant taxa, which are highlighted on the phylogenetic tree in cladogram format (F) and for which the linear discriminant analysis scores are shown (G)
Abundance in Group 1: decreased abundance in pediatric pulmonary tuberculosis (PTB group)
Revision editor(s): Nuerteye
