Alterations in Oral Microbiota in HIV Are Related to Decreased Pulmonary Function

From BugSigDB
Reviewed Marked as Reviewed by Claregrieve1 on 2022/06/30
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
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
Keywords:
HIV, lung function, microbiome, saliva, stool
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

Curated date: 2021/12/15

Curator: Joyessa

Revision editor(s): WikiWorks, LGeistlinger, Claregrieve1, Joyessa, Victoria

Subjects

Location of subjects
United States of America
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
Saliva Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva,saliva
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
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

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
relative abundances
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

Curated date: 2021/12/15

Curator: Joyessa

Revision editor(s): Joyessa, Claregrieve1

Source: Figure 1 D

Description: Differential abundance in saliva of HIV- individuals vs HIV+ individuals

Abundance in Group 1: decreased abundance in HIV+ individuals

NCBI Quality ControlLinks
Campylobacter
Capnocytophaga
Fusobacterium
Neisseria
Oribacterium
Prevotella
Tannerella
unclassified Candidatus Absconditabacteria
unclassified Neisseriaceae
Prevotella sp. 2-3
Butyrivibrio sp.

Revision editor(s): Joyessa, Claregrieve1

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 2022/06/30

Curated date: 2021/12/16

Curator: Joyessa

Revision editor(s): Joyessa, Claregrieve1

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 Quality ControlLinks
Bifidobacterium
Lactobacillus
Rothia
Streptococcus
Veillonella

Revision editor(s): Joyessa, Claregrieve1

Experiment 2


Reviewed Marked as Reviewed by Claregrieve1 on 2022/06/30

Curated date: 2021/12/15

Curator: Joyessa

Revision editor(s): WikiWorks, Claregrieve1, Joyessa, Victoria

Differences from previous experiment shown

Subjects

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,Nicotine dependence,Smoking behavior,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

Lab analysis

Statistical Analysis

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

Curated date: 2021/12/15

Curator: Joyessa

Revision editor(s): Joyessa, Claregrieve1

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 Quality ControlLinks
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

Curated date: 2021/12/16

Curator: Joyessa

Revision editor(s): Joyessa, Claregrieve1

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 Quality ControlLinks
Atopobium
Bifidobacterium
Lactobacillus
Streptococcus
Veillonella

Revision editor(s): Joyessa, Claregrieve1

Experiment 3


Reviewed Marked as Reviewed by Claregrieve1 on 2022/06/30

Curated date: 2021/12/16

Curator: Joyessa

Revision editor(s): WikiWorks, LGeistlinger, Claregrieve1, Joyessa, Victoria

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Abnormality on pulmonary function testing Abnormal pulmonary function test,Abnormal spirometry test,Abnormality on pulmonary function testing,abnormality on pulmonary function testing
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

Lab analysis

Statistical Analysis

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

Curated date: 2021/12/16

Curator: Joyessa

Revision editor(s): Joyessa, Claregrieve1

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 Quality ControlLinks
Lactobacillus
Streptococcus
Veillonella

Revision editor(s): Joyessa, Claregrieve1

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 2022/06/30

Curated date: 2021/12/16

Curator: Joyessa

Revision editor(s): Joyessa, Claregrieve1, Merit

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 Quality ControlLinks
Alloprevotella
Capnocytophaga
Fusobacterium
Lachnoanaerobaculum
Parvimonas
Prevotella
Stomatobaculum
unclassified Neisseriaceae
unclassified Prevotellaceae
Neisseria
Neisseria sp.
Neisseriaceae
Neisseriales
Parvimonas sp.
Fusobacteriaceae
Fusobacteriales

Revision editor(s): Joyessa, Claregrieve1, Merit