Oral Microbiome in HIV-Infected Women: Shifts in the Abundance of Pathogenic and Beneficial Bacteria Are Associated with Aging, HIV Load, CD4 Count, and Antiretroviral Therapy/Experiment 4
From BugSigDB
Reviewed Marked as Reviewed by Folakunmi on 2024-2-25
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
- Coinfection , Age Coinfection,coinfection,Age,age
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- young HIV-infected group without coinfection
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- aging HIV-infected women with coinfections
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- aging HIV-infected women with coinfections; Hairy leukoplakia, oral candida, kaposi's sarcoma, HPV
- Group 0 sample size Number of subjects in the control (unexposed) group
- 4
- Group 1 sample size Number of subjects in the case (exposed) group
- 4
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).
- relative abundances
- Statistical test
- LEfSe
- 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
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-2-24
Source: Figure 5
Description: LEfSe was performed to identify statistically different bacterial taxa in their relative abundance between young adult HIV-infected women versus aging HIV-infected women with coinfection.
Abundance in Group 1: increased abundance in aging HIV-infected women with coinfections
Signature 2
Reviewed Marked as Reviewed by Folakunmi on 2024-2-24
Source: Figure 5
Description: LEfSe was performed to identify statistically different bacterial taxa in their relative abundance between young adult HIV-infected women versus aging HIV-infected women with coinfection.
Abundance in Group 1: decreased abundance in aging HIV-infected women with coinfections
| NCBI | Quality Control | Links |
|---|---|---|
| Solobacterium moorei | ||
| Bulleidia sp. | ||
| Veillonella parvula | ||
| unclassified Mycoplasmatota |
Revision editor(s): Atrayees
