Alterations in Oral Microbiota in HIV Are Related to Decreased Pulmonary Function
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI Uniform resource identifier for web resources.
Authors
Yang L, Dunlap DG, Qin S, Fitch A, Li K, Koch CD, Nouraie M, DeSensi R, Ho KS, Martinson JJ, Methé B, Morris A
Journal
American journal of respiratory and critical care medicine
Year
2020
Rationale: Mechanisms of HIV-associated chronic obstructive pulmonary disease (COPD) are poorly understood. The oral microbiome shapes the lung microbiome, and gut dysbiosis can affect lung diseases; however, relationships of the oral and gut microbiome to COPD in HIV have not been explored.Objectives: To examine alterations in the oral and gut microbiome associated with pulmonary disease in persons with HIV (PWH).Methods: Seventy-five PWH and 93 HIV-uninfected men from the MACS (Multicenter AIDS Cohort Study) performed pulmonary function testing. Sequencing of bacterial 16S ribosomal RNA in saliva and stool was performed. We used nonmetric multidimensional scaling, permutational multivariate ANOVA, and linear discriminant analysis to analyze communities by HIV and lung function.Measurements and Main Results: Oral microbiome composition differed by HIV and smoking status. Alterations of oral microbial communities were observed in PWH with abnormal lung function with increases in relative abundance of Veillonella, Streptococcus, and Lactobacillus. There were no significant associations between the oral microbiome and lung function in HIV-uninfected individuals. No associations with HIV status or lung function were seen with the gut microbiome.Conclusions: Alterations of oral microbiota in PWH were related to impaired pulmonary function and to systemic inflammation. These results suggest that the oral microbiome may serve as a biomarker of lung function in HIV and that its disruption may contribute to COPD pathogenesis.
Experiment 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/06/30
Subjects
- Location of subjects
- United States of America
- Host species Species from which microbiome was sampled (if applicable)
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Saliva Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Human immunodeficiency virus AIDS virus,HIV,Human immunodeficiency virus
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- HIV-uninfected individuals
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- HIV+ individuals
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- People with HIV
- Group 0 sample size Number of subjects in the control (unexposed) group
- 93
- Group 1 sample size Number of subjects in the case (exposed) group
- 75
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 5 days
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
- Statistical test
- LEfSe
- 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)?
- No
- 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
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/08/28
Source: Figure 1 D
Description: Differential abundance in saliva of HIV- individuals vs HIV+ individuals
Abundance in Group 1: decreased abundance in HIV+ individuals
Revision editor(s): Joyessa, Claregrieve1
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/06/30
Source: Figure 1 D
Description: Differential microbial abundance in saliva of HIV- individuals vs HIV+ individuals
Abundance in Group 1: increased abundance in HIV+ individuals
| NCBI | Links |
|---|---|
| Bifidobacterium | |
| Lactobacillus | |
| Rothia | |
| Streptococcus | |
| Veillonella |
Revision editor(s): Joyessa, Claregrieve1
Experiment 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/06/30
Subjects
- Location of subjects
- United States of America
- Host species Species from which microbiome was sampled (if applicable)
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Saliva Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- nicotine dependence , smoking behavior cigarette habituation, susceptibility to,Cigarette Smoking,Dependence, Nicotine,Dependence, Tobacco,Disorder, Nicotine Use,Disorder, Tobacco Use,Disorder, Tobacco-Use,Nicotine Addiction,nicotine addiction,nicotine addiction, susceptibility to,nicotine dependence,nicotine dependence, susceptibility to,NICOTINE USE DIS,Nicotine Use Disorder,Nicotine Use Disorders,smoking,smoking habit, susceptibility to,Smoking, Cigarette,Smoking, Tobacco,Smokings, Tobacco,susceptibility to tobacco addiction,tobacco addiction, susceptibility to,Tobacco Dependence,Tobacco Dependences,Tobacco Smoking,Tobacco Smokings,TOBACCO USE DIS,Tobacco Use Disorder,tobacco use disorder,Tobacco Use Disorders,Tobacco-Use Disorder,Use Disorder, Nicotine,smoking behavior
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- HIV+ non-smokers
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- HIV+ smokers
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- People with HIV who currently smoke cigarettes
- Group 0 sample size Number of subjects in the control (unexposed) group
- 26
- Group 1 sample size Number of subjects in the case (exposed) group
- 23
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 5 days
Lab analysis
- Sequencing type
- 16S
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Statistical test
- LEfSe
- 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)?
- No
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/06/30
Source: Figure 2E
Description: Differential bacterial abundance in oral samples from HIV+ individuals by smoking status
Abundance in Group 1: decreased abundance in HIV+ smokers
| NCBI | Links |
|---|---|
| Alloprevotella | |
| Bergeyella | |
| Campylobacter | |
| Fusobacterium | |
| Johnsonella | |
| Neisseria | |
| Prevotella | |
| unclassified Neisseriaceae | |
| unclassified Pasteurellaceae |
Revision editor(s): Joyessa, Claregrieve1
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/06/30
Source: Figure 2E
Description: Differential bacterial abundance in oral samples from HIV+ individuals by smoking status
Abundance in Group 1: increased abundance in HIV+ smokers
| NCBI | Links |
|---|---|
| Atopobium | |
| Bifidobacterium | |
| Lactobacillus | |
| Streptococcus | |
| Veillonella |
Revision editor(s): Joyessa, Claregrieve1
Experiment 3
Reviewed Marked as Reviewed by Claregrieve1 on 2022/06/30
Subjects
- Location of subjects
- United States of America
- Host species Species from which microbiome was sampled (if applicable)
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Saliva Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- lung functionlung function
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- HIV+ patients with normal DLCO
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- HIV+ patients with reduced DLCO
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- HIV+ patients with DLCO% predicted <80%
- Group 0 sample size Number of subjects in the control (unexposed) group
- 38
- Group 1 sample size Number of subjects in the case (exposed) group
- 37
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 5 days
Lab analysis
- Sequencing type
- 16S
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Statistical test
- LEfSe
- 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)?
- No
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/06/30
Source: Figure 3 I
Description: Differential microbial abundance between reduced DLCO HIV+ patients and normal DLCO HIV+ patients
Abundance in Group 1: increased abundance in HIV+ patients with reduced DLCO
| NCBI | Links |
|---|---|
| Lactobacillus | |
| Streptococcus | |
| Veillonella |
Revision editor(s): Joyessa, Claregrieve1
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/06/30
Source: Figure 3I
Description: Differential microbial abundance between reduced DLCO HIV+ patients and normal DLCO HIV+ patients
Abundance in Group 1: decreased abundance in HIV+ patients with reduced DLCO
| NCBI | Links |
|---|---|
| Alloprevotella | |
| Capnocytophaga | |
| Fusobacterium | |
| Lachnoanaerobaculum | |
| Parvimonas | |
| Prevotella | |
| Stomatobaculum | |
| Prevotella_2Prevotella_2 | |
| unclassified Prevotellaceae | |
| unclassified Neisseriaceae |
Revision editor(s): Joyessa, Claregrieve1
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