Sputum microbiota profiles of patients with rifampicin-resistant tuberculosis during the intensive-phase treatment/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
- Sputum Expectoration,Sputum,sputum
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Tuberculosis active tuberculosis,Kochs disease,TB,tuberculosis,tuberculosis disease,Tuberculosis
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- rifampicin-resistant tuberculosis (RR-TB) patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Smear/Xpert-confirmed rifampicin‑resistant pulmonary tuberculosis.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 14
- Group 1 sample size Number of subjects in the case (exposed) group
- 14
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V1-V3
- 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
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 4
- Matched on Factors on which subjects have been matched on in a case-control study
- age, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on 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 4A–B
Description: (A) Significantly different taxa in terms of relative abundance (LDA score ≥ 4); (B) Cladogram highlighting significantly different taxa (LDA score ≥ 4)
Abundance in Group 1: increased abundance in rifampicin-resistant tuberculosis (RR-TB) patients
Revision editor(s): Nuerteye
Signature 2
Source: Figure 4A–B
Description: (A) Significantly different taxa in terms of relative abundance (LDA score ≥ 4); (B) Cladogram highlighting significantly different taxa (LDA score ≥ 4)
Abundance in Group 1: decreased abundance in rifampicin-resistant tuberculosis (RR-TB) patients
| NCBI | Quality Control | Links |
|---|---|---|
| Fusobacterium | ||
| Fusobacteriaceae | ||
| Fusobacteriia | ||
| FusobacteriaFusobacteria | ||
| ParaprevotellaceaeParaprevotellaceae | ||
| Prevotella |
Revision editor(s): Nuerteye
