Characteristic gut microbiota and metabolic changes in patients with pulmonary tuberculosis/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
- PTB patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Clinically and/or bacteriologically confirmed active PTB, T-SPOT.TB positive, pre-treatment
- Group 0 sample size Number of subjects in the control (unexposed) group
- 52
- Group 1 sample size Number of subjects in the case (exposed) group
- 83
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- No antibiotics or pre/probiotics within 1 month prior to sampling; all PTB patients were treatment-naïve.
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
- Ion Torrent
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- LEfSe
- Mann-Whitney (Wilcoxon)
- 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
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- HIV infection
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 2D
Description: LDA, linear discriminant analysis. The circular cladogram was derived from the LEfSe analysis and showed the relationship between the most differentially abundant taxa in the patients with PTB (green) and the HCs (red). HCs, healthy controls; LEfSe, linear discriminant analysis effect size; PTB, pulmonary tuberculosis.
Abundance in Group 1: increased abundance in PTB patients
NCBI | Quality Control | Links |
---|---|---|
Bacteroidales | ||
Prevotellaceae | ||
Bacteroides vulgatusBacteroides vulgatus |
Revision editor(s): Nuerteye
Signature 2
Source: Figure 2D
Description: LDA, linear discriminant analysis. The circular cladogram was derived from the LEfSe analysis and showed the relationship between the most differentially abundant taxa in the patients with PTB (green) and the HCs (red). HCs, healthy controls; LEfSe, linear discriminant analysis effect size; PTB, pulmonary tuberculosis.
Abundance in Group 1: decreased abundance in PTB patients
NCBI | Quality Control | Links |
---|---|---|
Blautia wexlerae | ||
Lachnospiraceae | ||
ClostridialesClostridiales | ||
FirmicutesFirmicutes | ||
RuminococcaceaeRuminococcaceae | ||
ActinobacteriaActinobacteria | ||
Bifidobacteriales |
Revision editor(s): Nuerteye