Alterations in the oral microbiome in HIV-infected participants after antiretroviral therapy administration are influenced by immune status

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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


Needs review

Curated date: 2023/10/10

Curator: MyleeeA

Revision editor(s): MyleeeA

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


Needs review

Curated date: 2023/10/13

Curator: MyleeeA

Revision editor(s): MyleeeA

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

Needs review

Curated date: 2023/10/16

Curator: MyleeeA

Revision editor(s): MyleeeA

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 ControlLinks
Treponema lecithinolyticum

Revision editor(s): MyleeeA

Signature 2

Needs review

Curated date: 2023/10/16

Curator: MyleeeA

Revision editor(s): MyleeeA

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 ControlLinks
Muribaculum intestinale

Revision editor(s): MyleeeA

Experiment 3


Needs review

Curated date: 2023/10/16

Curator: MyleeeA

Revision editor(s): MyleeeA

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

Needs review

Curated date: 2023/10/16

Curator: MyleeeA

Revision editor(s): MyleeeA

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 ControlLinks
Haemophilus parainfluenzae

Revision editor(s): MyleeeA

Experiment 4


Needs review

Curated date: 2023/10/16

Curator: MyleeeA

Revision editor(s): MyleeeA

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

Needs review

Curated date: 2023/10/16

Curator: MyleeeA

Revision editor(s): MyleeeA

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 ControlLinks
Haemophilus parainfluenzae

Revision editor(s): MyleeeA