Microbiome diversity in the sputum of patients with pulmonary tuberculosis/Experiment 1
From BugSigDB
Subjects
- Location of subjects
- India
- 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
- Healthy controls (asymptomatic, TB negative)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Tuberculosis patients (PTB)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Confirmed active pulmonary TB by sputum smear, culture, and RT‑PCR; no antibiotic use prior to sampling; HIV‑negative.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 16
- Group 1 sample size Number of subjects in the case (exposed) group
- 23
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- None had taken antibiotics before sputum sampling (confirmed by clinical records).
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V6-V7
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Ion Torrent
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)
- T-Test
- 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
- Matched on Factors on which subjects have been matched on in a case-control study
- age, sex
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- ethnic group, HIV infection, antibiotic exposure, geographic area
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- unchanged
- 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
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- decreased
- Richness Number of species
- decreased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Source: Fig. 2; Fig. 3; Table 2
Description: Phyla-level relative abundance of microbial composition in TB and normal patients groups. Genera-level relative abundance of microbial composition in TB and normal patients groups.
Abundance in Group 1: increased abundance in Tuberculosis patients (PTB)
Revision editor(s): Nuerteye
Signature 2
Source: Fig. 2; Fig. 3; Table 2
Description: Phyla-level relative abundance of microbial composition in TB and normal patients groups. Genera-level relative abundance of microbial composition in TB and normal patients groups.
Abundance in Group 1: decreased abundance in Tuberculosis patients (PTB)
| NCBI | Quality Control | Links |
|---|---|---|
| FusobacteriaFusobacteria | ||
| ProteobacteriaProteobacteria |
Revision editor(s): Nuerteye
