Alterations in the oral microbiome in HIV-infected participants after antiretroviral therapy administration are influenced by immune status/Experiment 2
From BugSigDB
Reviewed Marked as Reviewed by Folakunmi on 2024-1-8
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,saliva
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Response to antiviral drug Response to antiviral drug,response to antiviral drug
- 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
- Saliva samples after 24 weeks of antiretroviral therapy
- 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
- 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
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-1-8
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
Reviewed Marked as Reviewed by Folakunmi on 2024-1-8
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 |
