Associations between the gut microbiome, inflammation and cardiovascular profiles in people with HIV/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Svetlana up on 2025-4-11
Subjects
- Location of subjects
- Ireland
- 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
- Human immunodeficiency virus AIDS virus,HIV,Human immunodeficiency virus,human immunodeficiency virus
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- People Without HIV
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- People With HIV
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Individuals who have been diagnosed with HIV (Human Immunodeficiency Virus)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 37
- Group 1 sample size Number of subjects in the case (exposed) group
- 44
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).
- centered log-ratio
- Statistical test
- ANCOM-BC
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.1
- 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, antiretroviral therapy, Confounders controlled for: "comorbidities" 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.comorbidities, 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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2025-4-11
Source: Fig 2 And Fig-S2
Description: Differential abundance (DA) analysis of species and genus in people with human immunodeficiency virus (HIV) compared to those without HIV.
Abundance in Group 1: increased abundance in People With HIV
Revision editor(s): Aiyshaaaa
Signature 3
Reviewed Marked as Reviewed by Svetlana up on 2025-4-11
Source: Fig 2 And S2
Description: Differential abundance (DA) analysis of species in people with human immunodeficiency virus (HIV) compared to those without HIV.
Abundance in Group 1: decreased abundance in People With HIV
Revision editor(s): Aiyshaaaa
