Tongue microbiome of smokeless tobacco users

Study information

Reviewed Marked as Reviewed by Atrayees on 2023-7-12

study design

cross-sectional observational, not case-control

Citation

PMID PubMed identifier for scientific articles.

32640977

DOI Digital object identifier for electronic documents.

10.1186/s12866-020-01883-8

URI

Authors

Halboub E, Al-Ak'hali MS, Alamir AH, Homeida HE, Baraniya D, Chen T, Al-Hebshi NN

Journal

BMC microbiology

Year

2020

Keywords:

Microbiota, Mouth neoplasms, Rothia mucilaginosa, high-throughput nucleotide sequencing, Tobacco, Tongue

BACKGROUND: The possibility that smokeless tobacco may contribute to oral carcinogenesis by influencing the oral microbiome has not been explored. This preliminary cross-sectional study sought to assess the effect of using shammah, a form of smokeless tobacco prevalent in Arabia, on the tongue microbiome. Tongue scarping samples were obtained from 29 shammah users (SU; 27.34 ± 6.9 years) and 23 shammah non-users (SNU; 27.7 ± 7.19 years) and analyzed with 16S rRNA gene sequencing (V1-V3). Species-level taxonomy assignment of the high-quality, merged reads was obtained using a previously described BLASTn-based algorithm. Downstream analyses were performed with QIIME, LEfSe, and R. RESULTS: A total of 178 species, belonging to 62 genera and 8 phyla were identified. Genera Streptococcus, Leptotrichia, Actinomyces, Veillonella, Haemophilus, Prevotella and Neisseria accounted for more than 60% of the average microbiome. There were no differences between the two groups in species richness and alpha-diversity, but PCoA showed significant separation (P = 0.015, ANOSIM). LEfSe analysis identified 22 species to be differentially abundant between the SU and SNU. However, only 7 species maintained a false discovery rate of ≤0.2 and could cluster the two groups separately: Rothia mucilaginosa, Streptococcus sp. oral taxon 66, Actinomyces meyeri, Streptococcus vestibularis Streptococcus sanguinis and a potentially novel Veillonella species in association with SU, and Oribacterium asaccharolyticum with SNU. CONCLUSION: These preliminary results indicate that shammah use induces tongue microbiome changes including enrichment of several species with high acetaldehyde production potential, which warrants further investigation.

Experiment 1

Edit History Delete

Flag for review

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Atrayees on 2023-7-12

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Atrayees

Subjects

Location of subjects: Saudi Arabia

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: Tongue Glossus,Tongue,tongue

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-shammah users

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

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: participants who used shammah daily for at least one year without a period of cessation and those who had no history of shammah use

Group 0 sample size Number of subjects in the control (unexposed) group: 23

Group 1 sample size Number of subjects in the case (exposed) group: 29

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-V3

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: LEfSe

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): 0.015

MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?: Yes

Matched on Factors on which subjects have been matched on in a case-control study: sex

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

Edit History Delete

Flag for review

Your review change was submitted

Reviewed Marked as Reviewed by Atrayees on 2023-7-12

Curated date: 2021/01/10

Curator: Victoria Goulbourne

Revision editor(s): WikiWorks

Source: Figure 3 a & b

Description: Differentially abundant taxa

Abundance in Group 1: increased abundance in shammah users

NCBI	Quality Control	Links
Streptococcus
Rothia
Lactobacillus
Alloscardovia
Rothia mucilaginosa
Streptococcus sp.
Schaalia meyeri
Alloscardovia omnicolens
Limosilactobacillus gastricus
Streptococcus mitis
Streptococcus vestibularis
Haemophilus pittmaniae
Neisseria flavescens
Veillonella parvula
Neisseria flava
Leptotrichia hongkongensis
Actinomyces sp.
Streptococcus sanguinis
Neisseria elongata