The subgingival microbiome of clinically healthy current and never smokers

Study information

Reviewed Marked as Reviewed by Claregrieve1 on 2023-3-28

study design

cross-sectional observational, not case-control

Citation

PMID PubMed identifier for scientific articles.

25012901

DOI Digital object identifier for electronic documents.

https://doi.org/10.1038/ismej.2014.114

URI

https://pubmed.ncbi.nlm.nih.gov/25012901/

Authors

Mason MR, Preshaw PM, Nagaraja HN, Dabdoub SM, Rahman A, Kumar PS

Journal

The ISME journal

Year

2015

Dysbiotic oral bacterial communities have a critical role in the etiology and progression of periodontal diseases. The goal of this study was to investigate the extent to which smoking increases risk for disease by influencing the composition of the subgingival microbiome in states of clinical health. Subgingival plaque samples were collected from 200 systemically and periodontally healthy smokers and nonsmokers. 16S pyrotag sequencing was preformed generating 1,623,713 classifiable sequences, which were compared with a curated version of the Greengenes database using the quantitative insights into microbial ecology pipeline. The subgingival microbial profiles of smokers and never-smokers were different at all taxonomic levels, and principal coordinate analysis revealed distinct clustering of the microbial communities based on smoking status. Smokers demonstrated a highly diverse, pathogen-rich, commensal-poor, anaerobic microbiome that is more closely aligned with a disease-associated community in clinically healthy individuals, suggesting that it creates an at-risk-for-harm environment that is primed for a future ecological catastrophe.

Experiment 1

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Reviewed Marked as Reviewed by Claregrieve1 on 2023-3-28

Curated date: 2023/03/13

Curator: Kelvin Joseph

Revision editor(s): Kelvin Joseph, Claregrieve1

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: Subgingival dental plaque Subgingival plaque,Subgingival dental plaque

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: smoking behavior smoking,smoking behavior

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Never smokers
Group 1 name Corresponds to the case (exposed) group for case-control studies: Healthy Current Smokers
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: people who are current smokers
Group 0 sample size Number of subjects in the control (unexposed) group: 100
Group 1 sample size Number of subjects in the case (exposed) group: 100
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): 3 months

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V1-V9

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Roche454

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
MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?: No
Matched on Factors on which subjects have been matched on in a case-control study: age, education level, race, sex, socioeconomic status

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: increased

Signature 1

Subject page title:	The subgingival microbiome of clinically healthy current and never smokers/Experiment 1/Signature 1
Reviewer:	Claregrieve1
Review date:	2023-3-28
Review state:	Reviewed
Quality control tags:

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Curated date: 2023/03/14

Curator: Kelvin Joseph

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Source: Text

Description: The relative abundance of selected species in current smokers and nonsmokers.

Abundance in Group 1: increased abundance in Healthy Current Smokers

NCBI	Quality Control	Links
Acinetobacter baumannii
Acinetobacter guillouiae
Acinetobacter haemolyticus
Acinetobacter johnsonii
Acinetobacter schindleri
Anaeroglobus geminatus
Desulfobulbus sp.
Dialister micraerophilus
Filifactor alocis
Fusobacterium naviforme
Fusobacterium nucleatum
Megasphaera elsdenii
Megasphaera micronuciformis
Megasphaera sueciensis
Pseudomonas oleovorans
Pseudoramibacter alactolyticus

Revision editor(s): Kelvin Joseph, Claregrieve1

Signature 2

Subject page title:	The subgingival microbiome of clinically healthy current and never smokers/Experiment 1/Signature 2
Reviewer:	Claregrieve1
Review date:	2023-3-28
Review state:	Reviewed
Quality control tags:

Edit History Delete

Mark reviewed

Your review change was submitted

Needs review

Curated date: 2023/03/14

Curator: Kelvin Joseph

Revision editor(s): Kelvin Joseph, Claregrieve1

Source: Text

Description: The relative abundance of selected species in current smokers and nonsmokers.

Abundance in Group 1: decreased abundance in Healthy Current Smokers

NCBI	Quality Control	Links
Actinomyces israelii
Actinomyces viscosus
Granulicatella adiacens
Granulicatella elegans
Haemophilus parainfluenzae
Neisseria subflava
Streptococcus oralis
Streptococcus parasanguinis
Streptococcus sanguinis
Actinomyces dentalis

Revision editor(s): Kelvin Joseph, Claregrieve1