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

From BugSigDB
Reviewed Marked as Reviewed by Claregrieve1 on 8 July 2022
study design
Karabudak S, Ari O, Durmaz B, Dal T, Basyigit T, Kalcioglu MT, Durmaz R
Journal of medical microbiology
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

Reviewed Marked as Reviewed by Claregrieve1 on 8 July 2022

Curated date: 2021/01/10

Curator: WikiWorks743

Revision editor(s): WikiWorks753, WikiWorks743, Claregrieve1


Location of subjects Country from which study subjects were recruited
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
Buccal mucosa Buccal mucosa
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
Group 1 name Corresponds to the case (exposed) group for case-control studies
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
Group 1 sample size Number of subjects in the case (exposed) group
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 Experimental technique used for quantifying microbial abundance
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Ion Torrent

Statistical Analysis

Statistical test Statistical test or computational tool used for differential abundance testing
Mann-Whitney (Wilcoxon)
Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
Chao1 Abundance-based estimator of species richness
Richness Number of species

Signature 1

Reviewed Marked as Reviewed by Claregrieve1 on 8 July 2022

Curated date: 2020-07-16

Curator: Victoria Goulbourne

Revision editor(s): WikiWorks743

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 Links
Streptococcus australis
Prevotella salivae
Prevotella melaninogenica
Rothia mucilaginosa
Veillonella atypica

Revision editor(s): WikiWorks743