The penile microbiota of Black South African men: relationship with human papillomavirus and HIV infection/Experiment 2
From BugSigDB
Needs review
Subjects
- Location of subjects
- South Africa
- 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
- Skin of penis Penile skin,Penis skin,Penis zone of skin,Zone of skin of penis,Skin of penis,skin of penis
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Human papillomavirus Human Papilloma Virus,human papillomavirus HPV,Human papillomavirus,human papillomavirus
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- HR-HPV-uninfected in HIV-negative
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- HR-HPV-infected in HIV-negative
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- HR-HPV-infected in HIV-negative refers to the presence of High-Risk Human papillomavirus (HPV) in men that are not infected with HIV.
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)
- 0.2
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 3
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- unchanged
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
Signature 1
Needs review
Source: Additional file 5: Figure S3
Description: Significant differentially abundant taxa between HR-HPV-infected in HIV-negative and HR-HPV-uninfected in HIV-negative individuals.
Abundance in Group 1: decreased abundance in HR-HPV-infected in HIV-negative
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomycetales | ||
| Brevibacterium | ||
| Brachybacterium |
Revision editor(s): KateRasheed
