Alteration in Oral Microbiome Among Men Who Have Sex With Men With Acute and Chronic HIV Infection on Antiretroviral Therapy

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Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
Authors
Li S, Zhu J, Su B, Wei H, Chen F, Liu H, Wei J, Yang X, Zhang Q, Xia W, Wu H, He Q, Zhang T
Journal
Frontiers in cellular and infection microbiology
Year
2021
Keywords:
16S rRNA sequencing, antiretroviral therapy, human immunodeficiency virus, men who have sex with men, oral microbiome
Despite the antiretroviral therapy (ART), human immunodeficiency virus (HIV)-related oral disease remains a common problem for people living with HIV (PLWH). Evidence suggests that impairment of immune function in HIV infection might lead to the conversion of commensal bacteria to microorganisms with increased pathogenicity. However, limited information is available about alteration in oral microbiome in PLWH on ART. We performed a longitudinal comparative study on men who have sex with men (MSM) with acute HIV infection (n=15), MSM with chronic HIV infection (n=15), and HIV-uninfected MSM controls (n=15). Throat swabs were collected when these subjects were recruited (W0) and 12 weeks after ART treatment (W12) from the patients. Genomic DNAs were extracted and 16S rRNA gene sequencing was performed. Microbiome diversity was significantly decreased in patients with acute and chronic HIV infections compared with those in controls at the sampling time of W0 and the significant difference remained at W12. An increased abundance of unidentified Prevotellaceae was found in patients with acute and chronic HIV infections. Moreover, increased abundances of Prevotella in subjects with acute HIV infection and Streptococcus in subjects with chronic HIV infection were observed. In contrast, greater abundance in Lactobacillus, Rothia, Lautropia, and Bacteroides was found in controls. After effective ART, Bradyrhizobium was enriched in both acute and chronic HIV infections, whereas in controls, Lactobacillus, Rothia, Clostridia, Actinobacteria, and Ruminococcaceae were enriched. In addition, we found that lower CD4+ T-cell counts (<200 cells/mm3) were associated with lower relative abundances of Haemophilus, Actinomyces, unidentified Ruminococcaceae, and Rothia. This study has shown alteration in oral microbiome resulting from HIV infection and ART. The results obtained warrant further studies in a large number of subjects with different ethnics. It might contribute to improved oral health in HIV-infected individuals.

Experiment 1


Needs review

Curated date: 2024/04/29

Curator: Aleru Divine

Revision editor(s): Aleru Divine

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)
Participants who had used antibiotics within the previous 4 weeks were excluded

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).
relative abundances
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

Signature 1

Needs review

Curated date: 2024/04/30

Curator: Aleru Divine

Revision editor(s): Aleru Divine

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 ControlLinks
unclassified Prevotellaceae
Prevotella

Revision editor(s): Aleru Divine

Signature 2

Needs review

Curated date: 2024/04/30

Curator: Aleru Divine

Revision editor(s): Aleru Divine

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)

NCBI Quality ControlLinks
Leptotrichia
Lactobacillus
Rothia
Lautropia
Tannerella
unclassified Spirochaetaceae
unclassified Oscillospiraceae
Corynebacterium
Turicibacter
unclassified Lachnospiraceae
Roseburia
unclassified Eubacteriales
Romboutsia
Bacteroides
unclassified Leptotrichiaceae
Centipeda
Oscillibacter
Moraxella
Catonella

Revision editor(s): Aleru Divine

Experiment 2


Needs review

Curated date: 2024/04/30

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

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

Signature 1

Needs review

Curated date: 2024/04/30

Curator: Aleru Divine

Revision editor(s): Aleru Divine

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 ControlLinks
Streptococcus
unclassified Prevotellaceae

Revision editor(s): Aleru Divine

Signature 2

Needs review

Curated date: 2024/04/30

Curator: Aleru Divine

Revision editor(s): Aleru Divine

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)

NCBI Quality ControlLinks
Actinomyces
Lactobacillus
Rothia
Lautropia
Tannerella
unclassified Spirochaetaceae
unclassified Oscillospiraceae
Corynebacterium
Turicibacter
unclassified Lachnospiraceae
Roseburia
unclassified Eubacteriales
Romboutsia
Bacteroides
Centipeda
Oscillibacter
Moraxella
Stomatobaculum
Catonella
Oribacterium

Revision editor(s): Aleru Divine

Experiment 3


Needs review

Curated date: 2024/04/30

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

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

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

Signature 1

Needs review

Curated date: 2024/04/30

Curator: Aleru Divine

Revision editor(s): Aleru Divine

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 ControlLinks
Bradyrhizobium elkanii
Bradyrhizobium
Xanthobacteraceae
Hyphomicrobiales
Alphaproteobacteria
Haemophilus

Revision editor(s): Aleru Divine

Signature 2

Needs review

Curated date: 2024/04/30

Curator: Aleru Divine

Revision editor(s): Aleru Divine

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)

NCBI Quality ControlLinks
Clostridia
Eubacteriales
Actinomycetota
unclassified Actinomycetota
Lactobacillus
Lactobacillaceae
Oscillospiraceae
Actinomycetaceae
Actinomycetales
Actinomyces
Lautropia
Burkholderiaceae
Rothia
Micrococcaceae

Revision editor(s): Aleru Divine

Experiment 4


Needs review

Curated date: 2024/04/30

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

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

Signature 1

Needs review

Curated date: 2024/04/30

Curator: Aleru Divine

Revision editor(s): Aleru Divine

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 ControlLinks
Ihuprevotella massiliensis
Bradyrhizobium elkanii
Bradyrhizobium
Xanthobacteraceae
Hyphomicrobiales
Alphaproteobacteria

Revision editor(s): Aleru Divine

Signature 2

Needs review

Curated date: 2024/04/30

Curator: Aleru Divine

Revision editor(s): Aleru Divine

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)

NCBI Quality ControlLinks
Clostridia
Eubacteriales
Lactobacillus
Lactobacillaceae
Actinomycetota
unclassified Actinomycetota
Oscillospiraceae
Actinomycetaceae
Actinomycetales
Actinomyces
Haemophilus parahaemolyticus
Actinobacillus

Revision editor(s): Aleru Divine

Experiment 5


Needs review

Curated date: 2024/04/30

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

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

Signature 1

Needs review

Curated date: 2024/04/30

Curator: Aleru Divine

Revision editor(s): Aleru Divine

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 ControlLinks
Alphaproteobacteria
Bradyrhizobium
Bradyrhizobium elkanii
Hyphomicrobiales
Xanthobacteraceae

Revision editor(s): Aleru Divine

Signature 2

Needs review

Curated date: 2024/04/30

Curator: Aleru Divine

Revision editor(s): Aleru Divine

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 ControlLinks
Prevotella histicola
Prevotella melaninogenica
Bacteroidia
Bacteroidota
Prevotellaceae
Bacteroidales
unclassified Prevotellaceae

Revision editor(s): Aleru Divine

Experiment 6


Needs review

Curated date: 2024/04/30

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

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

Signature 1

Needs review

Curated date: 2024/04/30

Curator: Aleru Divine

Revision editor(s): Aleru Divine

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 ControlLinks
Alphaproteobacteria
Hyphomicrobiales
Xanthobacteraceae
Bradyrhizobium
Bradyrhizobium elkanii

Revision editor(s): Aleru Divine

Signature 2

Needs review

Curated date: 2024/04/30

Curator: Aleru Divine

Revision editor(s): Aleru Divine

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 ControlLinks
Negativicutes
Prevotella histicola
Selenomonadales
Veillonellaceae
unclassified Prevotellaceae
Veillonella

Revision editor(s): Aleru Divine

Experiment 7


Needs review

Curated date: 2024/04/30

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

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

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

Signature 1

Needs review

Curated date: 2024/04/30

Curator: Aleru Divine

Revision editor(s): Aleru Divine

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 ControlLinks
Oribacterium

Revision editor(s): Aleru Divine

Experiment 8


Needs review

Curated date: 2024/04/30

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

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

Signature 1

Needs review

Curated date: 2024/04/30

Curator: Aleru Divine

Revision editor(s): Aleru Divine

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 ControlLinks
Campylobacter

Revision editor(s): Aleru Divine

Experiment 9


Needs review

Curated date: 2024/05/01

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

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

Needs review

Curated date: 2024/05/01

Curator: Aleru Divine

Revision editor(s): Aleru Divine

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 ControlLinks
Haemophilus
Actinomyces
Rothia
unclassified Oscillospiraceae

Revision editor(s): Aleru Divine

Experiment 10


Needs review

Curated date: 2024/05/01

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

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

Needs review

Curated date: 2024/05/01

Curator: Aleru Divine

Revision editor(s): Aleru Divine

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 ControlLinks
Actinomyces
unclassified Oscillospiraceae
Rothia

Revision editor(s): Aleru Divine

Experiment 11


Needs review

Curated date: 2024/05/01

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Differences from previous experiment shown

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

Needs review

Curated date: 2024/05/01

Curator: Aleru Divine

Revision editor(s): Aleru Divine

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 ControlLinks
Haemophilus
Actinomyces
unclassified Oscillospiraceae
Rothia

Revision editor(s): Aleru Divine