Shifts in microbial diversity, composition, and functionality in the gut and genital microbiome during a natural SIV infection in vervet monkeys/Experiment 5
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
- Rectum Intestinum rectum,Rectal sac,Terminal portion of intestine,Terminal portion of large intestine,Rectum,rectum
- 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
- Free_State
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- KwaZulu-Natal
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- KwaZulu-Natal refers to vervet monkeys representing the Indian Ocean Coastal Belt (N = 33) and Savanna (N = 12) biomes from the KwaZulu-Natal Province (KZN)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 57
- Group 1 sample size Number of subjects in the case (exposed) group
- 45
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
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, sex, Confounders controlled for: "SIV infection status" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.SIV infection status
Signature 1
Needs review
Source: Supplementary Figure 5E
Description: Differentially abundant taxa between KZN and FS in rectal microbiome
Abundance in Group 1: increased abundance in KwaZulu-Natal
Revision editor(s): KateRasheed
Signature 2
Needs review
Source: Supplementary Figure 5E
Description: Differentially abundant taxa between KZN and FS in rectal microbiome
Abundance in Group 1: decreased abundance in KwaZulu-Natal
Revision editor(s): KateRasheed
