Alterations in the intestinal microbiota associated with active tuberculosis and latent tuberculosis infection/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
- Active TB
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Clinical and microbiologically confirmed pulmonary TB, treatment-naïve.
- 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
- 19
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 2 months
Lab analysis
- Sequencing type
- PCR
- 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
- Linear Discriminant Analysis
- 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
- 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 5A and B
Description: (A) Column diagram of LDA analysis of fecal microbiome in the three groups (HC, LTBI and ATB) (P < 0.05; LDA score >4.0). (B) Pairwise LDA effect size (LEfSe) analysis table of fecal microbiome. The phyla and subsequent taxonomic levels are sorted alphabetically, and the corresponding LDA score for each pairwise analysis is indicated in the column (P < 0.05; LDA score >4.0)
Abundance in Group 1: increased abundance in Active TB
| NCBI | Quality Control | Links |
|---|---|---|
| Enterobacteriaceae | ||
| EnterobacterialesEnterobacteriales | ||
| Gammaproteobacteria | ||
| ProteobacteriaProteobacteria | ||
| ErysipelatoclostridiumErysipelatoclostridium |
Revision editor(s): Nuerteye
Signature 2
Source: Figure 5A and B
Description: (A) Column diagram of LDA analysis of fecal microbiome in the three groups (HC, LTBI and ATB) (P < 0.05; LDA score >4.0). (B) Pairwise LDA effect size (LEfSe) analysis table of fecal microbiome. The phyla and subsequent taxonomic levels are sorted alphabetically, and the corresponding LDA score for each pairwise analysis is indicated in the column (P < 0.05; LDA score >4.0).
Abundance in Group 1: decreased abundance in Active TB
Revision editor(s): Nuerteye
