Intestinal microbiota, microbial translocation, and systemic inflammation in chronic HIV infection/Experiment 2
From BugSigDB
Reviewed Marked as Reviewed by Svetlana up on 2024-10-28
Subjects
- Location of subjects
- United States of America
- 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
- Response to antiviral drug Response to antiviral drug,response to antiviral drug
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- HIV-uninfected controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Chronic HIV-infected cases
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with HIV infection receiving suppressive ART and had an undetectable plasma HIV RNA levels
- Group 0 sample size Number of subjects in the control (unexposed) group
- 16
- Group 1 sample size Number of subjects in the case (exposed) group
- 21
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 4 weeks
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V5
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Roche454
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- Mann-Whitney (Wilcoxon)
- 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)?
- No
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Richness Number of species
- unchanged
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-10-28
Source: Figure 3C
Description: Differential abundance of microbiota between cases and controls using Mann-Whitney.
Abundance in Group 1: decreased abundance in Chronic HIV-infected cases
| NCBI | Quality Control | Links |
|---|---|---|
| Alistipes | ||
| Rikenellaceae |
Revision editor(s): KateRasheed
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-10-28
Source: Figure 3C
Description: Differential abundance of microbiota between cases and controls using Mann-Whitney.
Abundance in Group 1: increased abundance in Chronic HIV-infected cases
| NCBI | Quality Control | Links |
|---|---|---|
| Pseudomonadota | ||
| Gammaproteobacteria | ||
| Enterobacteriaceae | ||
| Erysipelotrichia | ||
| Erysipelotrichales | ||
| Enterobacterales | ||
| Erysipelotrichaceae | ||
| Barnesiella |
Revision editor(s): KateRasheed
