Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy/Experiment 29
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
- VANM(uninfected mice receiving vanomycin, ampicillin, neomycin, and metronidazole)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- RZ (R-Rifampin, Z-Pyrazinamide)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- RZ (R-Rifampin, Z-Pyrazinamide) refers to the Rifampin and Pyrazinamide treatment given to uninfected and 4week Mtb-infected mice.
- 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
- increased
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Needs review
Source: Additional file 12: Figure S12
Description: Differentially abundant taxa between the VANM group and RZ treatment group.
Abundance in Group 1: increased abundance in RZ (R-Rifampin, Z-Pyrazinamide)
| NCBI | Quality Control | Links |
|---|---|---|
| Eubacterium | ||
| Erysipelotrichaceae | ||
| Thomasclavelia | ||
| Anaeroplasma | ||
| Anaerostipes | ||
| Blautia | ||
| Akkermansia | ||
| Alistipes | ||
| Tannerella | ||
| Bacteroides |
Revision editor(s): KateRasheed
Signature 2
Needs review
Source: Additional file 12: Figure S12
Description: Differentially abundant taxa between the VANM group and RZ treatment group.
Abundance in Group 1: decreased abundance in RZ (R-Rifampin, Z-Pyrazinamide)
| NCBI | Quality Control | Links |
|---|---|---|
| Parabacteroides | ||
| Brenneria | ||
| Ruminiclostridium | ||
| Eubacteriales Family XIII. Incertae Sedis | ||
| Lactobacillus |
Revision editor(s): KateRasheed
