Oral microbiome in HIV-associated periodontitis

Study information

Reviewed Marked as Reviewed by Claregrieve1 on 2022/08/31

study design

cross-sectional observational, not case-control

Citation

PMID PubMed identifier for scientific articles.

28328799

DOI Digital object identifier for electronic documents.

10.1097/MD.0000000000005821

URI

https://pubmed.ncbi.nlm.nih.gov/28328799/

Authors

Noguera-Julian M, Guillén Y, Peterson J, Reznik D, Harris EV, Joseph SJ, Rivera J, Kannanganat S, Amara R, Nguyen ML, Mutembo S, Paredes R, Read TD, Marconi VC

Journal

Medicine

Year

2017

HIV-associated periodontal diseases (PD) could serve as a source of chronic inflammation. Here, we sought to characterize the oral microbial signatures of HIV+ and HIV- individuals at different levels of PD severity.This cross-sectional study included both HIV+ and HIV- patients with varying degrees of PD. Two tooth, 2 cheek, and 1 saliva samples were obtained for microbiome analysis. Mothur/SILVADB were used to classify sequences. R/Bioconductor (Vegan, PhyloSeq, and DESeq2) was employed to assess overall microbiome structure differences and differential abundance of bacterial genera between groups. Polychromatic flow cytometry was used to assess immune activation in CD4 and CD8 cell populations.Around 250 cheek, tooth, and saliva samples from 50 participants (40 HIV+ and 10 HIV-) were included. Severity of PD was classified clinically as None/Mild (N), Moderate (M), and Severe (S) with 18 (36%), 16 (32%), and 16 (32%) participants in each category, respectively. Globally, ordination analysis demonstrated clustering by anatomic site (R2 = 0.25, P < 0.001). HIV status and PD severity showed a statistically significant impact on microbiome composition but only accounted for a combined 2% of variation. HIV+ samples were enriched in genera Abiotrophia, Neisseria, Kingella, and unclassified Neisseriaceae and depleted in Leptotrichia and Selenomonas. The Neisseria genus was consistently enriched in HIV+ participants regardless of sampling site and PD level. Immune markers were altered in HIV+ participants but did not show association with the oral microbiome.HIV-associated changes in oral microbiome result in subtle microbial signatures along different stages of PD that are common in independent oral anatomic sites.

Experiment 1

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Reviewed Marked as Reviewed by Claregrieve1 on 2022/08/31

Curated date: 2022/01/10

Curator: Joyessa

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

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: Dental plaque , Internal cheek pouch , Saliva Bacterial plaque,Plaque,Dental plaque,dental plaque,Internal buccal pouch,Internal cheek pouch,internal cheek pouch,Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva,saliva

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Periodontitis chronic pericementitis,inflammation of periodontium,Pericementitides,Pericementitis,Periodontitides,periodontitis,Periodontitis (disorder),Periodontitis, NOS,periodontium inflammation,periodontosis,Periodontitis

Group 0 name Corresponds to the control (unexposed) group for case-control studies: HIV–

Group 1 name Corresponds to the case (exposed) group for case-control studies: HIV+

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Participants who were positive for HIV-1 infection, as verified by ELISA and confirmed by Western blot.

Group 0 sample size Number of subjects in the control (unexposed) group: 10

Group 1 sample size Number of subjects in the case (exposed) group: 40

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: Wald Test

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

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

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Reviewed Marked as Reviewed by Claregrieve1 on 2022/08/31

Curated date: 2022/01/10

Curator: Joyessa

Revision editor(s): Joyessa, Claregrieve1

Source: Table 1, Figure 3

Description: Differential microbial abundance between HIV+ and HIV- participants

Abundance in Group 1: increased abundance in HIV+

NCBI	Quality Control	Links
Aggregatibacter
Kingella
Neisseria
Rothia
unclassified Neisseriaceae
unclassified Pasteurellaceae
Abiotrophia

Revision editor(s): Joyessa, Claregrieve1

Signature 2

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Reviewed Marked as Reviewed by Claregrieve1 on 2022/08/31

Curated date: 2022/01/10

Curator: Joyessa

Revision editor(s): Joyessa, Claregrieve1

Source: Table 1, Figure 3

Description: Differential microbial abundance between HIV+ and HIV- participants

Abundance in Group 1: decreased abundance in HIV+

NCBI	Quality Control	Links
Centipeda
Tannerella
Leptotrichia
Selenomonas
Treponema
unclassified Veillonellaceae
Prevotella

Revision editor(s): Joyessa, Claregrieve1