Differential effects of antiretroviral treatment on immunity and gut microbiome composition in people living with HIV in rural versus urban Zimbabwe/Experiment 1
From BugSigDB
Needs review
Subjects
- Location of subjects
- Zimbabwe
- 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
- Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Clinical treatment Clinical treatment,clinical treatment
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy controls (HC).
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- ART Naïve
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- PLWH(People living with HIV) who were not on ART at the first timepoint but who subsequently commenced first-line ART with efavirenz/lamivudine/tenofovir disoproxil fumarate (EFV/3TC/TDF) and the prophylactic antibiotic cotrimoxazole (ART Naïve) - Baseline
- Group 0 sample size Number of subjects in the control (unexposed) group
- 42
- Group 1 sample size Number of subjects in the case (exposed) group
- 67
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Subjects were excluded from all cohorts if they had used antibiotics (apart from co-trimoxazole) within the prior 2 months.
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).
- relative abundances
- Statistical test
- ANCOM
- 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
- Confounders controlled for: "location" 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.location, Confounders controlled for: "viral load" 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.viral load
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Needs review
Source: Figure 4A
Description: Differential abundance of genera in ART-naïve compared to HC using ANCOM-BC, significant differential log-fold changes between microbes were calculated relative to healthy controls using only baseline values.
Abundance in Group 1: decreased abundance in ART Naïve
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridium |
Revision editor(s): Nwajei Edgar, Ayibatari, Keamy
