The lung microbiome in HIV-positive patients with active pulmonary tuberculosis/Experiment 1
From BugSigDB
Needs review
Subjects
- Location of subjects
- South Africa
- 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
- HIV-positive control cohort
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- HIV positive (Tuberculosis cohort)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- HIV-positive with pneumonia and Tuberculosis (TB) cultures positive.
- 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
- 20
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 6 Weeks
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).
- raw counts
- Statistical test
- DESeq2
- 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)?
- No
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- decreased
- Richness Number of species
- decreased
Signature 1
Needs review
Source: Supplementary File 3
Description: Differential abundance analysis of the genera in HIV positive (Tuberculosis cohort) and HIV-positive control cohort (sputum (SPU).
Abundance in Group 1: increased abundance in HIV positive (Tuberculosis cohort)
| NCBI | Quality Control | Links |
|---|---|---|
| Achromobacter | ||
| Acinetobacter | ||
| Mycobacterium | ||
| Pseudomonas | ||
| Stenotrophomonas |
Revision editor(s): AishatBolarinwa, MyleeeA
Signature 2
Needs review
Source: Supplementary File 3
Description: Differential abundance analysis of the genera in HIV positive (Tuberculosis cohort) and HIV-positive control cohort (sputum (SPU).
Abundance in Group 1: decreased abundance in HIV positive (Tuberculosis cohort)
| NCBI | Quality Control | Links |
|---|---|---|
| Filifactor | ||
| Haemophilus | ||
| Lautropia | ||
| Neisseria |
Revision editor(s): AishatBolarinwa, MyleeeA
