Analysis of the effect of smoking on the buccal microbiome using next-generation sequencing technology

Study information

Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/8

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

31199220

DOI Digital object identifier for electronic documents.

10.1099/jmm.0.001003

URI

Authors

Karabudak S, Ari O, Durmaz B, Dal T, Basyigit T, Kalcioglu MT, Durmaz R

Journal

Journal of medical microbiology

Year

2019

Keywords:

buccal microbiome, metagenomic analysis, next-generation sequencing, smoking

PURPOSE: This study aimed to investigate the effect of smoking on the buccal microbiome and to analyse the descriptive ability of each of the seven hypervariable regions in their 16S rRNA genes. METHODOLOGY: Microbiome compositions of 40 buccal swab samples collected from smokers (n =20) and non-smokers (n =20) were determined using 16S rRNA sequencing. Seven different 16S rRNA hypervariable regions (V2, V3, V4, V6-7, V8 and V9) in each sample were amplified using the Ion Torrent 16S Metagenomics kit and were sequenced on the Ion S5 instrument. RESULTS: Seven hypervariable regions in the 16S rRNA gene were successfully sequenced for all samples tested. The data obtained with the V2 region was found to be informative but the consensus data generated according to a number of operational taxonomic unit reads gathered from all seven hypervariable regions gave the most accurate result. At the phylum level, no statistically significant difference was found between smokers and non-smokers whereas relative abundances of Veillonella atypica, Streptococcus australis, Prevotella melaninogenica, Prevotella salivae and Rothia mucilaginosa showed significant increases in the smoker group (P-adj=0.05). Alpha diversity results did not show a significant difference between the two groups; however, beta diversity analysis indicated that samples of smoker and non-smoker groups had a tendency to be clustered within themselves. CONCLUSION: The results of the current study indicate that smoking is a factor influencing buccal microbiome composition. In addition, sequencing of all seven hypervariable regions yielded more accurate results than those with any of the single variable regions.

Experiment 1

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Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/8

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Claregrieve1, WikiWorks

Subjects

Location of subjects: Turkey

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: Buccal mucosa Buccal mucosa,buccal mucosa

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

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

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

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Participants who smoke cigarettes that fulfilled the inclusion criteria for good health: no use of antibiotics in the past 3 months, no respiratory infections, no oral aphthous lesions on buccal mucosa, and absence of dental problems

Group 0 sample size Number of subjects in the control (unexposed) group: 20

Group 1 sample size Number of subjects in the case (exposed) group: 20

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: V2-V9

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Ion Torrent

Statistical Analysis

Statistical test: Mann-Whitney (Wilcoxon)

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

Richness Number of species: unchanged

Signature 1

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Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/8

Curated date: 2021/01/10

Curator: Victoria Goulbourne

Revision editor(s): WikiWorks

Source: Table 2

Description: Comparison of statistically significant differences between smoker and non-smoker groups at genus and species levels

Abundance in Group 1: increased abundance in smokers

NCBI	Quality Control	Links
Actinomyces
Veillonella
Streptococcus australis
Segatella salivae
Prevotella melaninogenica
Rothia mucilaginosa
Veillonella atypica

Revision editor(s): WikiWorks