The lung microbiome in HIV-positive patients with active pulmonary tuberculosis
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Ueckermann V, Lebre P, Geldenhuys J, Hoosien E, Cowan D, van Rensburg LJ, Ehlers M
Journal
Scientific reports
Year
2022
Tuberculosis poses one of the greatest infectious disease threats of our time, especially when associated with human immunodeficiency virus (HIV) infection. Very little data is available on the lung microbiome in pulmonary tuberculosis (PTB) in HIV-positive patients. Three patient cohorts were studied: (i) HIV-positive with no respiratory disease (control cohort), (ii) HIV-positive with pneumonia and (iii) HIV-positive with PTB. Sputum specimens were collected in all patients and where possible a paired BALF was collected. DNA extraction was performed using the QIAamp DNA mini kit (QIAGEN, Germany) and extracted DNA specimens were sent to Inqaba Biotechnical Industries (Pty) Ltd for 16S rRNA gene sequence analysis using the Illumina platform (Illumina Inc, USA). Data analysis was performed using QIMME II and R Studio version 3.6.2 (2020). The lung microbiomes of patients with PTB, in the context of HIV co-infection, were dominated by Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes. Loss of biodiversity and dysbiosis was found in these patients when compared to the HIV-positive control cohort. Microbial community structure was also distinct from the control cohort, with the dominance of genera such as Achromobacter, Mycobacterium, Acinetobacter, Stenotrophomonas and Pseudomonas in those patients with PTB. This is the first study to describe the lung microbiome in patients with HIV and PTB co-infection and to compare findings with an HIV-positive control cohort. The lung microbiomes of patients with HIV and PTB were distinct from the HIV-positive control cohort without PTB, with an associated loss of microbial diversity.
Experiment 1
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
Experiment 2
Needs review
Differences from previous experiment shown
Subjects
- 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 with Pneumonia
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients who were HIV-positive with pneumonia but TB cultures negative (“Pneumonia” cohort)
- Group 1 sample size Number of subjects in the case (exposed) group
- 31
Lab analysis
Statistical Analysis
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 (Pneumonia cohort) and HIV-positive control cohort (sputum (SPU).
Abundance in Group 1: increased abundance in HIV positive with Pneumonia
| NCBI | Quality Control | Links |
|---|---|---|
| Achromobacter | ||
| Acinetobacter | ||
| Corynebacterium | ||
| Mycobacterium | ||
| Pseudomonas | ||
| Stenotrophomonas |
Revision editor(s): AishatBolarinwa, MyleeeA
Experiment 3
Needs review
Differences from previous experiment shown
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Bronchoalveolar duct junction , Sputum Bronchoalveolar duct junction,bronchoalveolar duct junction,Expectoration,Sputum,sputum
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- HIV positive with Pneumonia
- 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
- Patients who were HIV-positive with pneumonia and Tuberculosis (TB) cultures positive. Sputum and Broncho-alveolar lavage fluid (BALF) were gotten.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 31
- 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
Statistical Analysis
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 2
Description: Differential abundance analysis of the genera in HIV positive (Pneumonia cohort) and HIV-positive TB cohort (sputum (SPU) and BALF).
Abundance in Group 1: increased abundance in HIV positive (Tuberculosis cohort)
| NCBI | Quality Control | Links |
|---|---|---|
| Stenotrophomonas |
Revision editor(s): AishatBolarinwa, MyleeeA
Signature 2
Source: Supplementary File 4
Description: Differential abundance analysis of the genera in HIV positive (Pneumonia cohort) and HIV-positive TB cohort (sputum (SPU) and BALF).
Abundance in Group 1: decreased abundance in HIV positive (Tuberculosis cohort)
| NCBI | Quality Control | Links |
|---|---|---|
| Neisseria | ||
| Corynebacterium | ||
| Dialister | ||
| Prevotella |
Revision editor(s): MyleeeA
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