Shifts in microbial diversity, composition, and functionality in the gut and genital microbiome during a natural SIV infection in vervet monkeys/Experiment 4
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.
- Chlorocebus pygerythrus
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Vagina Vagina,vagina,Distal oviductal region,Distal portion of oviduct,Vaginae
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Simian immunodeficiency virus infection Simian immunodeficiency virus caused disease or disorder,Simian immunodeficiency virus disease or disorder,simian immunodeficiency virus infection,Simian immunodeficiency virus infectious disease,SIV,Simian immunodeficiency virus infection
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Alkaline
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Acidic
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Acidic refers to the vaginal-PH below 7. It is found in vagitype A of vervets monkeys.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 21
- Group 1 sample size Number of subjects in the case (exposed) group
- 16
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).
- raw counts
- Statistical test
- DESeq2
- 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
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Needs review
Source: Supplementary Figure 4D
Description: Differentially abundant microbial genera in acidic vaginal samples vs. alkaline vaginal samples.
Abundance in Group 1: increased abundance in Acidic
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces | ||
| Bacteroides | ||
| Blautia | ||
| Sarcina | ||
| Ureaplasma | ||
| Streptococcus | ||
| Aerococcus | ||
| Trichococcus | ||
| Carnobacteriaceae | ||
| family XIfamily XI |
Revision editor(s): KateRasheed
Signature 2
Needs review
Source: Supplementary Figure 4D
Description: Differentially abundant microbial genera in acidic vaginal samples vs. alkaline vaginal samples.
Abundance in Group 1: decreased abundance in Acidic
Revision editor(s): KateRasheed
