Differential effects of antiretroviral treatment on immunity and gut microbiome composition in people living with HIV in rural versus urban Zimbabwe/Experiment 4
From BugSigDB
Reviewed Marked as Reviewed by Svetlana up on 2024-7-15
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
- Antiretroviral therapy (ART) experienced at baseline and after 24 weeks
- 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 on ART regimen and cotrimoxazole at both time points
- Group 0 sample size Number of subjects in the control (unexposed) group
- 42
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Use of antibiotics (apart from co-trimoxazole) within 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).
- centered log-ratio
- 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
- time, 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
Reviewed Marked as Reviewed by Svetlana up on 2024-7-15
Source: 4B
Description: Differential abundance of genera in ART experienced compared to HC using ANCOM-BC, significant differential log-fold changes between microbes were calculated relative to healthy controls using both time points.
Abundance in Group 1: increased abundance in Antiretroviral therapy (ART) experienced at baseline and after 24 weeks
| NCBI | Quality Control | Links |
|---|---|---|
| Megamonas | ||
| Lachnoclostridium | ||
| Bilophila |
Revision editor(s): Keamy
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-7-15
Source: 4B
Description: Differential abundance of genera in ART experienced compared to HC using ANCOM-BC, significant differential log-fold changes between microbes were calculated relative to healthy controls using both time points.
Abundance in Group 1: decreased abundance in Antiretroviral therapy (ART) experienced at baseline and after 24 weeks
| NCBI | Quality Control | Links |
|---|---|---|
| Blastocystis | ||
| Butyrivibrio | ||
| Turicibacter | ||
| clostridia UCG-014clostridia UCG-014 | ||
| Clostridium |
Revision editor(s): Keamy
