Alteration in Oral Microbiome Among Men Who Have Sex With Men With Acute and Chronic HIV Infection on Antiretroviral Therapy/Experiment 4
From BugSigDB
Reviewed Marked as Reviewed by Svetlana up on 2024-10-9
Subjects
- Location of subjects
- China
- 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
- Throat Gula,Throat,throat
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Human immunodeficiency virus AIDS virus,HIV,Human immunodeficiency virus,human immunodeficiency virus
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- HIV-uninfected MSM - controls (D)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Chronic HIV-infected participants (B12)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Men who have sex with men (MSM) with Chronic HIV infection after 12 weeks of Antiretroviral Therapy (ART).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 15
- Group 1 sample size Number of subjects in the case (exposed) group
- 15
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 4 weeks
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V4-V5
- 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
- LEfSe
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2.0
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Richness Number of species
- decreased
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-10-9
Source: Figure 3c
Description: Linear discriminative analysis (LDA) effect size (LefSe) at the genus level shown between Chronic HIV-infected participants (B12) and control (D) groups.
Abundance in Group 1: increased abundance in Chronic HIV-infected participants (B12)
| NCBI | Quality Control | Links |
|---|---|---|
| Ihuprevotella massiliensis | ||
| Bradyrhizobium elkanii | ||
| Bradyrhizobium | ||
| Xanthobacteraceae | ||
| Hyphomicrobiales | ||
| Alphaproteobacteria |
Revision editor(s): Aleru Divine
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-10-9
Source: Figure 3c
Description: Linear discriminative analysis (LDA) effect size (LefSe) at the genus level shown between Chronic HIV-infected participants (B12) and control (D) groups.
Abundance in Group 1: decreased abundance in Chronic HIV-infected participants (B12)
Revision editor(s): Aleru Divine
