Differential effects of antiretrovirals on microbial translocation and gut microbiota composition of HIV-infected patients
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
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
- 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
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Non-infected volunteers (Control)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- HIV-positive (naive)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group includes untreated HIV-infected patients (HIV+(naive)) with an average viral load of 54,010 cop/mL (3,550–71,800 cop/mL))
- 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
- 5
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 3 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).
- relative abundances
- Statistical test
- Kruskall-Wallis
- 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, body mass index, sex
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- decreased
- Richness Number of species
- decreased
Signature 2
Source: Table 2
Description: The relative abundance of major phyla in the gut in HIV-positive (naive).
Abundance in Group 1: decreased abundance in HIV-positive (naive)
| NCBI | Quality Control | Links |
|---|---|---|
| Alphaproteobacteria |
Revision editor(s): Joiejoie, KateRasheed, WikiWorks
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- non-infected volunteers (Control)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- HIV-positive (cART)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group includes HIV-infected patients on cART (HIV+(cART)) for at least one year and with viral load of <20 cop/mL.
- Group 1 sample size Number of subjects in the case (exposed) group
- 45
Lab analysis
Statistical Analysis
Signature 1
Source: Table 2
Description: Relative abundance of major phyla present in the gut in HIV-positive (cART).
Abundance in Group 1: increased abundance in HIV-positive (cART)
| NCBI | Quality Control | Links |
|---|---|---|
| Deltaproteobacteria | ||
| Pseudomonadota | ||
| Lentisphaerota | ||
| Synergistota |
Revision editor(s): Joiejoie, KateRasheed, WikiWorks
Signature 2
Source: Table 2
Description: Relative abundance of major phyla present in the gut in HIV-positive (cART).
Abundance in Group 1: decreased abundance in HIV-positive (cART)
| NCBI | Quality Control | Links |
|---|---|---|
| Methanobacteriota |
Revision editor(s): Joiejoie, KateRasheed, WikiWorks
Experiment 3
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- NRTIs + PIs
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group includes patients on family treatment of nucleoside reverse transcriptase inhibitors (NRTIs) and protease inhibitors (PIs)
- Group 1 sample size Number of subjects in the case (exposed) group
- 15
Lab analysis
Statistical Analysis
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- decreased
- Richness Number of species
- decreased
Signature 2
Source: In-text result of "Gut microbiota diversity and composition"
Description: Relative abundance of major phyla present in the gut in NRTIs + PIs.
Abundance in Group 1: decreased abundance in NRTIs + PIs
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillota |
Revision editor(s): Joiejoie, KateRasheed, WikiWorks
Experiment 4
Curated date: 2025/01/08
Curator:
Revision editor(s):
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- NRTIs + PIs
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- NRTIs + NNRTIs
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group includes patients on family treatment of nucleoside reverse transcriptase inhibitors (NRTIs) and non-nucleoside reverse transcriptase inhibitors (NNRTIs)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 15
- Group 1 sample size Number of subjects in the case (exposed) group
- 22
Lab analysis
Statistical Analysis
- Matched on Factors on which subjects have been matched on in a case-control study
- Not specified
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- increased
- Richness Number of species
- increased
Signature 1
Source: Table 2
Description: Relative abundance of major phyla present in the gut in NRTIs + INSTIs.
Abundance in Group 1: increased abundance in
| NCBI | Quality Control | Links |
|---|---|---|
| Deltaproteobacteria |
Revision editor(s): Joiejoie, KateRasheed, WikiWorks
Experiment 5
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- NRTIs + NNRTIs
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- NRTIs + INSTIs
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group includes patients on family treatment of nucleoside reverse transcriptase inhibitors (NRTIs) with integrase strand transfer inhibitors (INSTIs)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 22
- Group 1 sample size Number of subjects in the case (exposed) group
- 8
Lab analysis
Statistical Analysis
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- increased
- Richness Number of species
- increased
Signature 1
Source: Table 2
Description: Relative abundance of major phyla present in the gut in NRTIs + INSTIs.
Abundance in Group 1: increased abundance in NRTIs + INSTIs
| NCBI | Quality Control | Links |
|---|---|---|
| Alphaproteobacteria |
Revision editor(s): Joiejoie, KateRasheed, WikiWorks
Experiment 6
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- non-infected volunteers (Control)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- NRTIs+PIs
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group includes patients on family treatment of nucleoside reverse transcriptase inhibitors (NRTIs) and protease inhibitors (PIs)
- 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
- 15
Lab analysis
Statistical Analysis
- Statistical test
- Mann-Whitney (Wilcoxon)
- Matched on Factors on which subjects have been matched on in a case-control study
- age, body mass index, sex
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- decreased
- Richness Number of species
- decreased
Signature 2
Source: Table 3
Description: Relative abundance of taxonomical groups (order, family, genus, species) in NRTIs+PIs
Abundance in Group 1: decreased abundance in NRTIs+PIs
Revision editor(s): Joiejoie, KateRasheed, WikiWorks
Signature 3
Source: Table 3
Description: Relative abundance of taxonomical groups (order, family, genus, species) in NRTIs+PIs
Abundance in Group 1: increased abundance in NRTIs+PIs
| NCBI | Quality Control | Links |
|---|---|---|
| Eggerthella | ||
| Clostridiales bacterium | ||
| Lachnospiraceae | ||
| Blautia sp. 3Blautia sp. 3 | ||
| Flavonifractor plautii |
Revision editor(s): KateRasheed, WikiWorks
Experiment 7
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- NRTIs + NNRTIs
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group includes patients on family treatment of nucleoside reverse transcriptase inhibitors (NRTIs) and non-nucleoside reverse transcriptase inhibitors (NNRTIs)
- Group 1 sample size Number of subjects in the case (exposed) group
- 22
Lab analysis
Statistical Analysis
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- decreased
- Richness Number of species
- decreased
Signature 1
Source: Table 3
Description: Combined antiretroviral therapy modified the relative abundance of taxonomical groups (order, family, genus, species) in NRTIs+NNRTIs
Abundance in Group 1: increased abundance in NRTIs + NNRTIs
| NCBI | Quality Control | Links |
|---|---|---|
| Coriobacteriaceae | ||
| Coriobacteriales | ||
| Lachnospiraceae | ||
| Pseudomonas |
Revision editor(s): Joiejoie, KateRasheed, WikiWorks
Signature 2
Source: Table 3
Description: Combined antiretroviral therapy modified the relative abundance of taxonomical groups (order, family, genus, species) in NRTIs+NNRTIs
Abundance in Group 1: decreased abundance in NRTIs + NNRTIs
Revision editor(s): Joiejoie, KateRasheed, WikiWorks
Experiment 8
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- NRTIs + INSTIs
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group includes patients on family treatment of nucleoside reverse transcriptase inhibitors (NRTIs) with integrase strand transfer inhibitors (INSTIs)
- Group 1 sample size Number of subjects in the case (exposed) group
- 8
Lab analysis
Statistical Analysis
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- decreased
- Richness Number of species
- decreased
Signature 1
Source: Table 3
Description: Combined antiretroviral therapy modified the relative abundance of taxonomical groups (order, family, genus, species) in NRTIs+INSTIs
Abundance in Group 1: increased abundance in NRTIs + INSTIs
| NCBI | Quality Control | Links |
|---|---|---|
| Desulfovibrionales | ||
| Selenomonadales | ||
| Lachnospiraceae | ||
| Desulfovibrionaceae | ||
| Desulfovibrio | ||
| Blautia sp. 3Blautia sp. 3 | ||
| Parabacteroides merdae |
Signature 2
Source: Table 3
Description: Combined antiretroviral therapy modified the relative abundance of taxonomical groups (order, family, genus, species) in NRTIs+INSTIs
Abundance in Group 1: decreased abundance in NRTIs + INSTIs
Revision editor(s): Joiejoie, KateRasheed, WikiWorks
Experiment 9
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Control
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- HIV non coinfected patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group includes HIV-infected patients who are not coinfected with other infections such as hepatitis B virus (HBV) or hepatitis C virus (HCV).
- Group 1 sample size Number of subjects in the case (exposed) group
- 25
Lab analysis
Statistical Analysis
Signature 2
Source: Supplementary Table 1
Description: Relative abundance of major phyla present in the gut in non-coinfected HIV patients
Abundance in Group 1: decreased abundance in HIV non coinfected patients
| NCBI | Quality Control | Links |
|---|---|---|
| Gammaproteobacteria |
Revision editor(s): Joiejoie, KateRasheed, WikiWorks
Experiment 10
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- HIV coinfected patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group includes HIV-infected patients who are also coinfected with either hepatitis B virus (HBV) or hepatitis C virus (HCV).
Lab analysis
Statistical Analysis
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- decreased
- Richness Number of species
- decreased
Signature 1
Source: Supplementary Table 1
Description: Relative abundance of major phyla present in the gut in coinfected patients.
Abundance in Group 1: increased abundance in HIV coinfected patients
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomycetota | ||
| Deltaproteobacteria | ||
| Pseudomonadota |
Revision editor(s): Joiejoie, KateRasheed, WikiWorks
Experiment 11
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Non-coinfected
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- coinfected patients
- Group 0 sample size Number of subjects in the control (unexposed) group
- 25
Lab analysis
Statistical Analysis
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Supplementary Table 2, Supplementary Table 1
Description: Abundance of lower taxonomic levels (genus and species) which were significantly increased in feces from coinfected patients
Abundance in Group 1: increased abundance in coinfected patients
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Parabacteroides | ||
| Parabacteroides merdae | ||
| Gammaproteobacteria | ||
| Actinomycetota |
Revision editor(s): Joiejoie, KateRasheed, WikiWorks
Signature 2
Source: Supplementary Table 2
Description: Abundance of lower taxonomic levels (genus and species) which were significantly decreased in feces from coinfected patients
Abundance in Group 1: decreased abundance in coinfected patients
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridium | ||
| Coriobacterium | ||
| Pseudomonas | ||
| Roseburia | ||
| Roseburia inulinivorans | ||
| Ruminococcus | ||
| Sinorhizobium sp. |
Revision editor(s): Joiejoie, KateRasheed, WikiWorks
