Peripheral blood microbiome signature and Mycobacterium tuberculosis-derived rsRNA as diagnostic biomarkers for tuberculosis in human/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
- Blood Portion of blood,Vertebrate blood,Whole blood,Blood,blood
- 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 pulmonary tuberculosis
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Culture-confirmed pulmonary tuberculosis (PTB)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 62
- Group 1 sample size Number of subjects in the case (exposed) group
- 73
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- No prebiotics, or antibiotics one month before the enrollment.
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
- RT-qPCR
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
- 2
- 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
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
Signature 1
Source: Figure 1A and B
Description: (A) Significantly differential taxa in terms of relative abundance (LDA score of ≥ 2) between TB and healthy control groups. (B) Significantly different taxa in the cladogram according to a LDA score of ≥ 2 (each circle represents phylogenetic levels from phylum to genus [inside to outside], and each diameter is proportional to the taxon’s abundance).
Abundance in Group 1: increased abundance in Active pulmonary tuberculosis
Revision editor(s): Nuerteye
Signature 2
Source: Figure 1A and B
Description: (A) Significantly differential taxa in terms of relative abundance (LDA score of ≥ 2) between TB and healthy control groups. (B) Significantly different taxa in the cladogram according to a LDA score of ≥ 2 (each circle represents phylogenetic levels from phylum to genus [inside to outside], and each diameter is proportional to the taxon’s abundance).
Abundance in Group 1: decreased abundance in Active pulmonary tuberculosis
Revision editor(s): Nuerteye
