Alterations in the oral microbiome in HIV-infected participants after antiretroviral therapy administration are influenced by immune status
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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
Presti RM, Handley SA, Droit L, Ghannoum M, Jacobson M, Shiboski CH, Webster-Cyriaque J, Brown T, Yin MT, Overton ET
Journal
AIDS (London, England)
Year
2018
OBJECTIVE: To characterize the oral bacterial microbiome in HIV-infected participants at baseline and after 24 weeks of EFV/FTC/TDF. DESIGN: Thirty-five participants co-enrolled in two AIDS Clinical Trials Group (ACTG) studies, A5272 and A5280, with paired saliva samples and complete data sets were assessed. METHODS: Paired saliva samples were evaluated for bacterial microbiome using 16S rDNA PCR followed by Illumina sequencing. Diversity and differential abundance was compared between groups. A random forest classification scheme was used to determine the contribution of parameters in classifying participants' CD4+ T-cell count. RESULTS: Bacterial communities demonstrated considerable variability both within participants and between timepoints, although they became more similar after 24 weeks of ART. At baseline, both the number of taxa detected and the average alpha diversity were variable between participants, but did not differ significantly based on CD4+ cell count, viral load or other factors. After 24 weeks of ART samples obtained from participants with persistently low CD4+ T-cell counts had significantly higher bacterial richness and diversity. Several differentially abundant taxa, including Porphyromonas species associated with periodontal disease, were identified, which discriminated between baseline and posttreatment samples. Analysis demonstrated that although inflammatory markers are important in untreated disease, the salivary microbiome may play an important role in CD4+ T-cell count recovery after ART. CONCLUSION: Shifts in the oral microbiome after ART initiation are complex, and may play an important role in immune function and inflammatory disease.
Experiment 1
Subjects
- Location of subjects
- United States of America
- 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
- Saliva Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- response to antiviral drug response to antiviral drug
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Baseline low CD4 samples
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Week 24 low CD4 samples
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Samples collected following 24 weeks of administering Anti Retroviral Therapy, showing low CD4 count
- Group 0 sample size Number of subjects in the control (unexposed) group
- 35
- Group 1 sample size Number of subjects in the case (exposed) group
- 35
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- N/A
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V4-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).
- relative abundances
- Statistical test
- 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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Richness Number of species
- increased
Experiment 2
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Baseline samples
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Week 24 samples
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Analyzing the changes in bacterial taxa abundance in saliva samples after 24 weeks of antiretroviral therapy
Lab analysis
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V4
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure 2 :Table S1
Description: Bacterial taxa differentially abundant in saliva prior to and following 24 weeks of antiretroviral therapy
Abundance in Group 1: increased abundance in Week 24 samples
| NCBI | Quality Control | Links |
|---|---|---|
| Treponema lecithinolyticum |
Revision editor(s): MyleeeA
Signature 2
Source: Figure 2 :Table S1
Description: Bacterial taxa differentially abundant in saliva prior to and following 24 weeks of antiretroviral therapy
Abundance in Group 1: decreased abundance in Week 24 samples
| NCBI | Quality Control | Links |
|---|---|---|
| Muribaculum intestinale |
Revision editor(s): MyleeeA
Experiment 3
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- CD4-positive T-lymphocyte count CD4-positive T-lymphocyte count
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Baseline CD4+ low samples
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Baseline CD4+ high samples
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Baseline CD4+ high samples before administering Anti Retroviral Therapy
Lab analysis
Statistical Analysis
- Statistical test
- DESeq2
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure 3 :Table S2
Description: The effect of CD4+ T-cell counts on the salivary bacterial microbiome: Differential abundance of bacterial taxa in CD4+ low vs. CD4+ high patient saliva.
Abundance in Group 1: increased abundance in Baseline CD4+ high samples
| NCBI | Quality Control | Links |
|---|---|---|
| Haemophilus parainfluenzae |
Revision editor(s): MyleeeA
Experiment 4
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- week 24 CD4+ low samples
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- week 24 CD4+ high samples
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Week 24 CD4+ high samples following Anti Retroviral Therapy
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure 3 :Table S2
Description: The effect of CD4+ T-cell counts on the salivary bacterial microbiome: Differential abundance of bacterial taxa in CD4+ low vs. CD4+ high patient saliva.
Abundance in Group 1: decreased abundance in week 24 CD4+ high samples
| NCBI | Quality Control | Links |
|---|---|---|
| Haemophilus parainfluenzae |
Revision editor(s): MyleeeA
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