Gut bacterial and fungal dysbiosis in tuberculosis patients/Experiment 1
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
- Healthy controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Tuberculosis (TB) patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Smear/culture-confirmed pulmonary tuberculosis.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 20
- Group 1 sample size Number of subjects in the case (exposed) group
- 33
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- None within 1 month prior
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)?
- 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
- 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: Figure 1e and 2e
Description: 1e) Identified the differentially abundant taxa between the TB patients and HC (LDA > 4, P < 0.05). The taxa enriched in the HC were characterized by a positive LDA score (red), and the TB-enriched taxa were indicated with a negative LDA score (blue). 2e) The LEfSe analysis identified the differentially abundant taxa between the TB patients and HC (LDA > 4, P < 0.05).
Abundance in Group 1: increased abundance in Tuberculosis (TB) patients
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotella | ||
| Saccharomyces | ||
| Bacteroides |
Revision editor(s): Nuerteye
Signature 2
Source: Figure 1e and 2e
Description: 1e) Identified the differentially abundant taxa between the TB patients and HC (LDA > 4, P < 0.05). The taxa enriched in the HC were characterized by a positive LDA score (red), and the TB-enriched taxa were indicated with a negative LDA score (blue). 2e) The LEfSe analysis identified the differentially abundant taxa between the TB patients and HC (LDA > 4, P < 0.05).
Abundance in Group 1: decreased abundance in Tuberculosis (TB) patients
Revision editor(s): Nuerteye
