Altered intestinal microbiota and fecal metabolites in patients with latent and active pulmonary tuberculosis/Experiment 2
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
- 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
- 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
- latent tuberculosis patients (LTBI)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- pulmonary tuberculosis (PTB)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- confirmed pulmonary tuberculosis patients
- Group 0 sample size Number of subjects in the control (unexposed) group
- 13
- Group 1 sample size Number of subjects in the case (exposed) group
- 13
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- No prior antibiotics treatment
Lab analysis
- Sequencing type
- 16S
- 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
- 3
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- decreased
- 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
- Richness Number of species
- decreased
Signature 1
Source: Fig. 3C and D
Description: Identification of differential microbial biomarkers. (A, B and C) Evolutionary branching plots showing the most divergent taxa identified by LEfSe. (B, D and F) Bar graphs showing LDA values for LEfSe analysis of bacterial abundance.
Abundance in Group 1: increased abundance in pulmonary tuberculosis (PTB)
| NCBI | Quality Control | Links |
|---|---|---|
| Erysipelotrichaceae | ||
| Erysipelotrichales | ||
| Erysipelotrichia | ||
| Alloprevotella | ||
| Desulfovibrio sp. |
Revision editor(s): Nuerteye
Signature 2
Source: Fig. 3C and D
Description: Identification of differential microbial biomarkers. (A, B and C) Evolutionary branching plots showing the most divergent taxa identified by LEfSe. (B, D and F) Bar graphs showing LDA values for LEfSe analysis of bacterial abundance.
Abundance in Group 1: decreased abundance in pulmonary tuberculosis (PTB)
| NCBI | Quality Control | Links |
|---|---|---|
| Fusobacteriales | ||
| Fusobacteriia | ||
| Lachnospiraceae | ||
| unclassified Lachnospiraceae | ||
| FusobacteriaFusobacteria |
Revision editor(s): Nuerteye
