Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy/Experiment 5
From BugSigDB
Needs review
Subjects
- Location of subjects
- United States of America
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Mus musculus
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Response to anti-tuberculosis drug Response to anti-tuberculosis drug,response to anti-tuberculosis drug
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Naive
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- TB +HRZ group - 4months HR(W20)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- TB +HRZ group - 4months into HR therapy(W20) refers to the group of mice infected with Mycobacterium tuberculosis (H37Rv) by aerosol inhalation, that are four months into HR therapy. This is also referred to as the termination of HR therapy
- Group 0 sample size Number of subjects in the control (unexposed) group
- 3
- Group 1 sample size Number of subjects in the case (exposed) group
- 4
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V4
- 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)?
- No
- 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
- decreased
Signature 1
Needs review
Source: Additional file 4: Figure S4
Description: Differentially abundant bacterial taxa between the naive and TB + HRZ groups at 4months into anti-tuberculosis HR therapy(end of therapy).
Abundance in Group 1: increased abundance in TB +HRZ group - 4months HR(W20)
Revision editor(s): KateRasheed
Signature 2
Needs review
Source: Additional file 4: Figure S4
Description: Differentially abundant bacterial taxa between the naive and TB + HRZ groups at 4months into anti-tuberculosis HR therapy(end of therapy).
Abundance in Group 1: decreased abundance in TB +HRZ group - 4months HR(W20)
Revision editor(s): KateRasheed
