The semen microbiome and its relationship with local immunology and viral load in HIV infection/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Claregrieve1 on 2022/08/31
Curated date: 2022/01/11
Curator: Joyessa
Revision editor(s): WikiWorks, Claregrieve1, Joyessa, Victoria
Subjects
- Location of subjects
- Canada
- 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
- Semen Ejaculate,Sperm,Semen,semen
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- HIV-uninfected men
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- HIV-infected men
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- MSM with HIV infection
- Group 0 sample size Number of subjects in the control (unexposed) group
- 22
- Group 1 sample size Number of subjects in the case (exposed) group
- 27
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 6 months.
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V6
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Roche454
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- ANOVA
- 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
- Matched on Factors on which subjects have been matched on in a case-control study
- age
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Richness Number of species
- decreased
Signature 1
Needs review
Source: Table S2
Description: Differential microbial abundance between HIV- and HIV+ men
Abundance in Group 1: decreased abundance in HIV-infected men
Revision editor(s): Joyessa, Claregrieve1, WikiWorks
Signature 2
Needs review
Source: Table S2
Description: Differential microbial abundance between HIV- and HIV+ men
Abundance in Group 1: increased abundance in HIV-infected men
NCBI | Quality Control | Links |
---|---|---|
Veillonella | ||
Actinomycetospora |
Revision editor(s): Joyessa, Claregrieve1, WikiWorks