Differential effects of antiretrovirals on microbial translocation and gut microbiota composition of HIV-infected patients/Experiment 1
Subjects
- Location of subjects
- Spain
- 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
- Alimentary part of gastrointestinal system GI tract,Alimentary system,Alimentary tract,Gastro-intestinal system,Gastroenterological system,Gastrointestinal (GI) tract,Gastrointestinal system,Gastrointestinal tract,Alimentary part of gastrointestinal system,alimentary part of gastrointestinal system
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- HIV infection [X]Human immunodeficiency virus disease,[X]Human immunodeficiency virus disease (disorder),[X]Unspecified human immunodeficiency virus [HIV] disease,[X]Unspecified human immunodeficiency virus [HIV] disease (disorder),HIV - Human immunodeficiency virus infection,HIV INFECT,HIV Infection,HIV infection,HIV Infections,HIV infectious disease,HTLV III INFECT,HTLV III Infections,HTLV III LAV INFECT,HTLV III LAV Infections,HTLV WIII INFECTIONS,HTLV WIII LAV INFECTIONS,HTLV-III Infection,HTLV-III Infections,HTLV-III-LAV Infection,HTLV-III-LAV Infections,HUMAN IMMUNO VIRUS DIS,human immunodeficiency virus,Human immunodeficiency virus [HIV] disease,HUMAN IMMUNOdeficiency VIRUS [HIV] INFECTION,Human immunodeficiency virus caused disease or disorder,Human immunodeficiency virus disease,Human immunodeficiency virus disease (disorder),Human immunodeficiency virus disease or disorder,Human immunodeficiency virus infection,Human immunodeficiency virus infection (disorder),Human immunodeficiency virus infection, NOS,Human immunodeficiency virus infectious disease,human immunodeficiency virus infectious disease,Infection, HIV,Infection, HTLV-III,Infection, HTLV-III-LAV,Infections, HIV,Infections, HTLV-III,Infections, HTLV-III-LAV,LYMPHOTROPIC VIRUS TYPE III INFECTIONS HUMAN T,T LYMPHOTROPIC VIRUS TYPE III INFECT HUMAN,T Lymphotropic Virus Type III Infections, Human,T-Lymphotropic Virus Type III Infections, Human,Unspecified human immunodeficiency virus [HIV] disease (disorder),hIV infection
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- non-infected volunteers
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- non-nucleoside reverse transcriptase inhibitors (NNRTIs)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Group 1, defined as NRTIs + non-nucleoside reverse transcriptase inhibitors (NNRTIs), consists of 22 HIV-infected patients who were on a combination of nucleoside reverse transcriptase inhibitors and non-nucleoside reverse transcriptase inhibitors as part of their antiretroviral therapy. This group was included to analyze the specific effects of this treatment regimen on microbial translocation and gut microbiota composition compared to other regimens.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 21
- Group 1 sample size Number of subjects in the case (exposed) group
- 22
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- The exclusion criteria for antibiotics in the study "Differential effects of antiretrovirals on microbial translocation and gut microbiota composition of HIV-infected patients" specified that patients treated with antibiotics within the last 3 months were excluded from participation. This was to ensure that any potential effects of antibiotics on gut microbiota composition and microbial translocation were not confounding factors in the study's findings.
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).
- raw counts
- Statistical test
- Chi-Square
- ANOVA
- Mann-Whitney (Wilcoxon)
- Pearson Correlation
- 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
- Matched on Factors on which subjects have been matched on in a case-control study
- age, Matched on: "gender" 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.gender, body mass index
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, Confounders controlled for: "gender" 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.gender, body mass index, 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: "other medications" 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.other medications, Confounders controlled for: "comorbid conditions" 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.comorbid conditions
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- decreased
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- decreased
- Richness Number of species
- decreased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- decreased
Signature 1
Source: Journal of the International AIDS Society
Description: The study investigates how different combinations of combined antiretroviral therapy (cART) impact bacterial translocation and gut microbiota in HIV-infected individuals. Conducted as a cross-sectional study with 45 HIV-infected patients, the research compares the effects of various cART regimens, including NRTIs combined with protease inhibitors, non-nucleoside reverse transcriptase inhibitors, and integrase strand transfer inhibitors. The findings reveal that the NRTIs + INSTIs regimen is associated with levels of systemic inflammation and microbial diversity similar to those of uninfected controls, while other regimens show varying impacts on gut microbiota composition. The study emphasizes the need for further longitudinal research to explore these relationships in depth.
Abundance in Group 1: increased abundance in non-nucleoside reverse transcriptase inhibitors (NNRTIs)
| NCBI | Quality Control | Links |
|---|---|---|
Revision editor(s): Joiejoie
Signature 2
Source: Journal of the International AIDS Society
Description: The study investigates how different combinations of combined antiretroviral therapy (cART) impact bacterial translocation and gut microbiota in HIV-infected individuals. Conducted as a cross-sectional study with 45 HIV-infected patients, the research compares the effects of various cART regimens, including NRTIs combined with protease inhibitors, non-nucleoside reverse transcriptase inhibitors, and integrase strand transfer inhibitors. The findings reveal that the NRTIs + INSTIs regimen is associated with levels of systemic inflammation and microbial diversity similar to those of uninfected controls, while other regimens show varying impacts on gut microbiota composition. The study emphasizes the need for further longitudinal research to explore these relationships in depth.
Abundance in Group 1: decreased abundance in non-nucleoside reverse transcriptase inhibitors (NNRTIs)
| NCBI | Quality Control | Links |
|---|---|---|
Revision editor(s): Joiejoie
Signature 3
Source: Journal of the International AIDS Society
Description: The study investigates how different combinations of combined antiretroviral therapy (cART) impact bacterial translocation and gut microbiota in HIV-infected individuals. Conducted as a cross-sectional study with 45 HIV-infected patients, the research compares the effects of various cART regimens, including NRTIs combined with protease inhibitors, non-nucleoside reverse transcriptase inhibitors, and integrase strand transfer inhibitors. The findings reveal that the NRTIs + INSTIs regimen is associated with levels of systemic inflammation and microbial diversity similar to those of uninfected controls, while other regimens show varying impacts on gut microbiota composition. The study emphasizes the need for further longitudinal research to explore these relationships in depth.
Abundance in Group 1: decreased abundance in non-nucleoside reverse transcriptase inhibitors (NNRTIs)
| NCBI | Quality Control | Links |
|---|---|---|
Revision editor(s): Joiejoie
