Sustained gut dysbiosis and intestinal inflammation show correlation with weight gain in person with chronic HIV infection on antiretroviral therapy/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Folakunmi on 2024-11-1
Subjects
- Location of subjects
- Japan
- 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
- HIV-1 infection HIV-1 seropositive,Human Immunodeficiency Virus 1,Human Immunodeficiency Virus, Type 1,HIV-1 infection,hIV-1 infection
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Baseline
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Follow up
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Follow up refers to the study conducted four years after the initial gut microbiota analysis in 2018, where stool and blood samples were collected and analyzed for gut microbiota in 46 PWH(Person with human immunodeficiency virus type-1) receiving ART treatment. It is also referred to as second stool collection timepoint.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 46
- Group 1 sample size Number of subjects in the case (exposed) group
- 46
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-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
- MaAsLin2
- 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
- body mass index, age, sex, proton-pump inhibitor, Confounders controlled for: "antibiotic use" 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.antibiotic use, Confounders controlled for: "statins" 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.statins, alcohol drinking, smoking behavior
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-11-1
Source: Fig. 1B
Description: Significant abundance of gut microbiota in PWH ( patients with human immunodeficiency virus (HIV) type-1); from baseline to follow-up period.
Abundance in Group 1: increased abundance in Follow up
| NCBI | Quality Control | Links |
|---|---|---|
| Cutibacterium | ||
| Staphylococcus | ||
| unclassified Burkholderiaceae | ||
| unclassified Corynebacterium | ||
| unclassified Enterobacteriaceae | ||
| Esherichia/ShigellaEsherichia/Shigella |
Revision editor(s): KateRasheed
Signature 2
Reviewed Marked as Reviewed by Folakunmi on 2024-11-1
Source: Fig. 1B
Description: Significant abundance of gut microbiota in PWH ( patients with human immunodeficiency virus (HIV) type-1); from baseline to follow-up period.
Abundance in Group 1: decreased abundance in Follow up
| NCBI | Quality Control | Links |
|---|---|---|
| Blautia | ||
| Catenibacterium | ||
| Collinsella | ||
| Fusicatenibacter | ||
| Lysobacter | ||
| Ruminococcus gauvreauii |
Revision editor(s): KateRasheed
