Alteration in Oral Microbiome Among Men Who Have Sex With Men With Acute and Chronic HIV Infection on Antiretroviral Therapy
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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
- China
- 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
- Throat Gula,Throat,throat
- 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
- HIV-uninfected MSM - controls (D)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Acute HIV-infected participants at baseline (A0)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Men who have sex with men (MSM) with acute HIV infection at baseline (A0).
- 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
- 15
- 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
- V4-V5
- 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
- T-Test
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
Alpha Diversity
- 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
- Richness Number of species
- decreased
Signature 1
Source: Figure 2a
Description: Differences in the composition of oral microbiome between controls and people living with HIV (PLWH).
Abundance in Group 1: increased abundance in Acute HIV-infected participants at baseline (A0)
| NCBI | Quality Control | Links |
|---|---|---|
| unclassified Prevotellaceae | ||
| Prevotella |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 2a
Description: Differences in the composition of oral microbiome between controls and people living with HIV (PLWH).
Abundance in Group 1: decreased abundance in Acute HIV-infected participants at baseline (A0)
Revision editor(s): Aleru Divine
Experiment 2
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Chronic HIV-infected participants at baseline (B0)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Men who have sex with men (MSM) with Chronic HIV infection at baseline (B0).
Lab analysis
Statistical Analysis
Alpha Diversity
- 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
- Richness Number of species
- decreased
Signature 1
Source: Figure 2b
Description: Differences in the composition of oral microbiome between controls and people living with HIV (PLWH).
Abundance in Group 1: increased abundance in Chronic HIV-infected participants at baseline (B0)
| NCBI | Quality Control | Links |
|---|---|---|
| Streptococcus | ||
| unclassified Prevotellaceae |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 2b
Description: Differences in the composition of oral microbiome between controls and people living with HIV (PLWH).
Abundance in Group 1: decreased abundance in Chronic HIV-infected participants at baseline (B0)
Revision editor(s): Aleru Divine
Experiment 3
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Acute HIV-infected participants (A12)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Men who have sex with men (MSM) with Acute HIV infection after 12 weeks of Antiretroviral Therapy (ART).
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- LEfSe
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2.0
Alpha Diversity
- 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
- Richness Number of species
- decreased
Signature 1
Source: Figure 3a
Description: Linear discriminative analysis (LDA) effect size (LefSe) at the genus level shown between Acute HIV-infected participants (A12) and control (D) groups.
Abundance in Group 1: increased abundance in Acute HIV-infected participants (A12)
| NCBI | Quality Control | Links |
|---|---|---|
| Bradyrhizobium elkanii | ||
| Bradyrhizobium | ||
| Xanthobacteraceae | ||
| Hyphomicrobiales | ||
| Alphaproteobacteria | ||
| Haemophilus |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 3a
Description: Linear discriminative analysis (LDA) effect size (LefSe) at the genus level shown between Acute HIV-infected participants (A12) and control (D) groups.
Abundance in Group 1: decreased abundance in Acute HIV-infected participants (A12)
Revision editor(s): Aleru Divine
Experiment 4
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Chronic HIV-infected participants (B12)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Men who have sex with men (MSM) with Chronic HIV infection after 12 weeks of Antiretroviral Therapy (ART).
Lab analysis
Statistical Analysis
Alpha Diversity
- 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
- Richness Number of species
- decreased
Signature 1
Source: Figure 3c
Description: Linear discriminative analysis (LDA) effect size (LefSe) at the genus level shown between Chronic HIV-infected participants (B12) and control (D) groups.
Abundance in Group 1: increased abundance in Chronic HIV-infected participants (B12)
| NCBI | Quality Control | Links |
|---|---|---|
| Ihuprevotella massiliensis | ||
| Bradyrhizobium elkanii | ||
| Bradyrhizobium | ||
| Xanthobacteraceae | ||
| Hyphomicrobiales | ||
| Alphaproteobacteria |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 3c
Description: Linear discriminative analysis (LDA) effect size (LefSe) at the genus level shown between Chronic HIV-infected participants (B12) and control (D) groups.
Abundance in Group 1: decreased abundance in Chronic HIV-infected participants (B12)
Revision editor(s): Aleru Divine
Experiment 5
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Acute HIV-infected participants at baseline (A0)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Acute HIV-infected participants on Antiretroviral Therapy (A12)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Men who have sex with men (MSM) with Acute HIV infection after 12 weeks of Antiretroviral Therapy (ART).
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure 4a
Description: Linear discriminative analysis (LDA) effect size (LefSe) at the genus level shown between Acute HIV-infected participants on Antiretroviral Therapy(A12) and Acute HIV-infected participants (A0).
Abundance in Group 1: increased abundance in Acute HIV-infected participants on Antiretroviral Therapy (A12)
| NCBI | Quality Control | Links |
|---|---|---|
| Alphaproteobacteria | ||
| Bradyrhizobium | ||
| Bradyrhizobium elkanii | ||
| Hyphomicrobiales | ||
| Xanthobacteraceae |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 4a
Description: Linear discriminative analysis (LDA) effect size (LefSe) at the genus level shown between Acute HIV-infected participants on Antiretroviral Therapy(A12) and Acute HIV-infected participants (A0).
Abundance in Group 1: decreased abundance in Acute HIV-infected participants on Antiretroviral Therapy (A12)
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotella histicola | ||
| Prevotella melaninogenica | ||
| Bacteroidia | ||
| Bacteroidota | ||
| Prevotellaceae | ||
| Bacteroidales | ||
| unclassified Prevotellaceae |
Revision editor(s): Aleru Divine
Experiment 6
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Chronic HIV-infected participants at baseline (B0)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Chronic HIV-infected participants on Antiretroviral Therapy(B12)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Men who have sex with men (MSM) with Chronic HIV infection after 12 weeks of Antiretroviral Therapy (ART).
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- increased
Signature 1
Source: Figure 4c
Description: Linear discriminative analysis (LDA) effect size (LefSe) at the genus level shown between Chronic HIV-infected participants on Antiretroviral Therapy(B12) and Chronic HIV-infected participants (B0).
Abundance in Group 1: increased abundance in Chronic HIV-infected participants on Antiretroviral Therapy(B12)
| NCBI | Quality Control | Links |
|---|---|---|
| Alphaproteobacteria | ||
| Hyphomicrobiales | ||
| Xanthobacteraceae | ||
| Bradyrhizobium | ||
| Bradyrhizobium elkanii |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 4c
Description: Linear discriminative analysis (LDA) effect size (LefSe) at the genus level shown between Chronic HIV-infected participants on Antiretroviral Therapy(B12) and Chronic HIV-infected participants (B0).
Abundance in Group 1: decreased abundance in Chronic HIV-infected participants on Antiretroviral Therapy(B12)
| NCBI | Quality Control | Links |
|---|---|---|
| Negativicutes | ||
| Prevotella histicola | ||
| Selenomonadales | ||
| Veillonellaceae | ||
| unclassified Prevotellaceae | ||
| Veillonella |
Revision editor(s): Aleru Divine
Experiment 7
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Acute HIV-infected participants at baseline (A0)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Chronic HIV-infected participants at baseline (B0)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Men who have sex with men (MSM) with Chronic HIV infection.
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- raw counts
- Statistical test
- T-Test
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- Not specified
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- decreased
Signature 1
Source: Figure 4e
Description: Comparisons of the relative abundance in oral microbiota at the genus level between people living with acute HIV infection at baseline (A0) and people living with chronic HIV infection at baseline (B0).
Abundance in Group 1: decreased abundance in Chronic HIV-infected participants at baseline (B0)
| NCBI | Quality Control | Links |
|---|---|---|
| Oribacterium |
Revision editor(s): Aleru Divine
Experiment 8
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Acute HIV-infected participants on Antiretroviral Therapy(A12)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Chronic HIV-infected participants on Antiretroviral Therapy(B12)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Men who have sex with men (MSM) with Chronic HIV infection after 12 weeks of Antiretroviral Therapy (ART).
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure 4f
Description: Comparisons of the relative abundance in oral microbiota at the genus level between people living with acute HIV infection after 12 weeks of ART (A12) and people living with chronic HIV infection after 12 weeks of ART (B12).
Abundance in Group 1: increased abundance in Chronic HIV-infected participants on Antiretroviral Therapy(B12)
| NCBI | Quality Control | Links |
|---|---|---|
| Campylobacter |
Revision editor(s): Aleru Divine
Experiment 9
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Uninfected Controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- CD4+ T cells < 200 cells/mm3
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Subjects whose CD4+ T cells were defined as < 200 cells/mm3.
- Group 1 sample size Number of subjects in the case (exposed) group
- Not specified
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 5
Description: The relationship between the alteration observed in the oral microbiome and the CD4+ T-cell count of patients.
Abundance in Group 1: decreased abundance in CD4+ T cells < 200 cells/mm3
| NCBI | Quality Control | Links |
|---|---|---|
| Haemophilus | ||
| Actinomyces | ||
| Rothia | ||
| unclassified Oscillospiraceae |
Revision editor(s): Aleru Divine
Experiment 10
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- CD4+ T cells > 200 cells/mm3
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Subjects whose CD4+ T cells were defined as > 200 cells/mm3.
Lab analysis
Statistical Analysis
Signature 2
Source: Figure 5
Description: The relationship between the alteration observed in the oral microbiome and the CD4+ T-cell count of patients.
Abundance in Group 1: decreased abundance in CD4+ T cells > 200 cells/mm3
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces | ||
| unclassified Oscillospiraceae | ||
| Rothia |
Revision editor(s): Aleru Divine
Experiment 11
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- CD4+ T cells < 200 cells/mm3
- Group 0 sample size Number of subjects in the control (unexposed) group
- Not specified
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 5
Description: The relationship between the alteration observed in the oral microbiome and the CD4+ T-cell count of patients.
Abundance in Group 1: increased abundance in CD4+ T cells > 200 cells/mm3
| NCBI | Quality Control | Links |
|---|---|---|
| Haemophilus | ||
| Actinomyces | ||
| unclassified Oscillospiraceae | ||
| Rothia |
Revision editor(s): Aleru Divine
