Clinical metagenomics analysis of bacterial and fungal microbiota from sputum of patients suspected with tuberculosis infection based on nanopore sequencing/Experiment 1
Subjects
- Location of subjects
- Thailand
- 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
- Sputum Expectoration,Sputum,sputum
- 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
- Mycobacterium tuberculosis-negative (non-TB)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Mycobacterium tuberculosis-positive
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mycobacterium tuberculosis confirmed by standard tests (culture, Xpert, etc.)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 41
- Group 1 sample size Number of subjects in the case (exposed) group
- 56
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V1-V9
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Nanopore
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
- 4
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Source: Figure 2B; 4B; S2
Description: Differential abundance analysis was performed using Linear Discriminant Analysis Effect Size (LEfSe) on MTB and negative sputum samples. 2(B) Bar plots display differentially abundant bacterial taxa across various taxonomic ranks. 4(B) Bar plots display differentially abundant fungal taxa across various taxonomic ranks.
Abundance in Group 1: increased abundance in Mycobacterium tuberculosis-positive
| NCBI | Quality Control | Links |
|---|---|---|
| Stenotrophomonas maltophilia | ||
| Mycobacterium tuberculosis | ||
| Candida orthopsilosis |
Revision editor(s): Nuerteye
Signature 2
Source: Figure 2B; 4B; S2
Description: Differential abundance analysis was performed using Linear Discriminant Analysis Effect Size (LEfSe) on MTB and negative sputum samples. 2(B) Bar plots display differentially abundant bacterial taxa across various taxonomic ranks. 4(B) Bar plots display differentially abundant fungal taxa across various taxonomic ranks.
Abundance in Group 1: decreased abundance in Mycobacterium tuberculosis-positive
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotella melaninogenica | ||
| Veillonella parvula | ||
| Corynebacterium striatum | ||
| Pseudomonas aeruginosa | ||
| Aureobasidium leucospermiAureobasidium leucospermi | ||
| Wallemia muriaeWallemia muriae |
Revision editor(s): Nuerteye
