Compositional profile of mucosal bacteriome of smokers and smokeless tobacco users

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Reviewed Marked as Reviewed by Lwaldron on 2023-6-16
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Gopinath D, Wie CC, Banerjee M, Thangavelu L, Kumar R P, Nallaswamy D, Botelho MG, Johnson NW
Journal
Clinical oral investigations
Year
2022
Keywords:
Microbiome, Microbiota, Oral microbiome, Smokeless tobacco, Smoking, Tobacco
INTRODUCTION: Smoked, and especially smokeless, tobacco are major causes of oral cancer globally. Here, we examine the oral bacteriome of smokers and of smokeless tobacco users, in comparison to healthy controls, using 16S rRNA gene sequencing. METHODS: Oral swab samples were collected from smokers, smokeless tobacco users, and healthy controls (n = 44). Microbial DNA was extracted and the 16S rRNA gene profiled using the Illumina MiSeq platform. Sequencing reads were processed using DADA2, and taxonomical classification was performed using the phylogenetic placement method. Differentially abundant taxa were identified using DESeq2, while functional metagenomes based on KEGG orthology abundance were inferred using LIMMA. RESULTS: A significantly higher microbial diversity was observed in smokeless tobacco users and smokers relative to controls (P < 0.05). Compositional differences in microbial communities were observed in all comparisons with healthy controls (PERMANOVA P < 0.05) but not between smokers and smokeless tobacco users. Levels of Fusobacterium spp., Saccharibacterium spp., and members of Shuttleworthia were elevated in smokers when compared to controls (BH adj P < 0.01). In addition, the relative abundance of three bacterial taxa belonging to genera Fusobacterium spp., Catonella, and Fretibacterium spp. was significantly increased in smokeless tobacco users relative to controls (BH adj P < 0.01). Major functional pathways significantly increased in smokeless tobacco users relative to both controls, and smokers were similar and involved amino acid metabolism including glutamate and aspartate biosynthesis and degradation (log FC > 1.5; BH adj P < 0.01). CONCLUSIONS: A distinct taxonomic and functional profile of oral microbiome in smokers and smokeless tobacco users as compared to healthy controls implicates a significant role of microbes and their metabolites in diseases associated with tobacco use including oral cancer. CLINICAL RELEVANCE: Future efforts in preventive, diagnostic, curative, and prognostic strategies for diseases associated with tobacco use in smokers and smokeless tobacco users could incorporate the oral microbiome.

Experiment 1


Reviewed Marked as Reviewed by Lwaldron on 2023-6-16

Curated date: 2023/06/13

Curator: Atrayees

Revision editor(s): Atrayees, Lwaldron, Victoria

Subjects

Location of subjects
India
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
Chewing tobacco behavior Chewing tobacco behavior,chewing tobacco behavior
Group 0 name Corresponds to the control (unexposed) group for case-control studies
age-matched controls
Group 1 name Corresponds to the case (exposed) group for case-control studies
smokeless tobacco users
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Smokeless tobacco users with or without areca nut.
Group 0 sample size Number of subjects in the control (unexposed) group
13
Group 1 sample size Number of subjects in the case (exposed) group
14

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
V3-V4
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).
raw counts
Statistical test
DESeq2
Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
0.01
Matched on Factors on which subjects have been matched on in a case-control study
age, sex

Alpha Diversity

Pielou Quantifies how equal the community is numerically
increased
Shannon Estimator of species richness and species evenness: more weight on species richness
increased
Simpson Estimator of species richness and species evenness: more weight on species evenness
increased

Signature 1

Reviewed Marked as Reviewed by Lwaldron on 2023-6-16

Curated date: 2023/06/13

Curator: Atrayees

Revision editor(s): Atrayees, Lwaldron

Source: Figure 5

Description: Differentially abundant taxa identified in smokeless tobacco users and controls using DESeq2.

Abundance in Group 1: increased abundance in smokeless tobacco users

NCBI Quality ControlLinks
Catonella
Fretibacterium
Streptomyces plicatus

Revision editor(s): Atrayees, Lwaldron

Experiment 2


Reviewed Marked as Reviewed by Lwaldron on 2023-6-16

Curated date: 2023/06/13

Curator: Atrayees

Revision editor(s): Lwaldron, Atrayees, Victoria

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Smoking behavior smoking,Smoking behavior,smoking behavior
Group 1 name Corresponds to the case (exposed) group for case-control studies
Smokers who were using either bidis or cigarettes
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Smokers who were using either bidis (thin, hand-rolled cigarettes composed of tobacco wrapped in a “tendu” or “temburni” leaf) or cigarettes
Group 1 sample size Number of subjects in the case (exposed) group
17

Lab analysis

Statistical Analysis

Alpha Diversity

Pielou Quantifies how equal the community is numerically
increased
Shannon Estimator of species richness and species evenness: more weight on species richness
increased
Simpson Estimator of species richness and species evenness: more weight on species evenness
increased

Signature 1

Reviewed Marked as Reviewed by Lwaldron on 2023-6-16

Curated date: 2023/06/13

Curator: Atrayees

Revision editor(s): Atrayees, Lwaldron

Source: Figure 5

Description: Differentially abundant taxa identified in smokers and controls using DESeq2.

Abundance in Group 1: increased abundance in Smokers who were using either bidis or cigarettes

NCBI Quality ControlLinks
Fusobacterium
Shuttleworthella
unclassified Candidatus Saccharibacteria

Revision editor(s): Atrayees, Lwaldron

Experiment 3


Reviewed Marked as Reviewed by Lwaldron on 2023-6-16

Curated date: 2023/06/13

Curator: Atrayees

Revision editor(s): Lwaldron, Atrayees, Victoria

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Smokeless tobacco users
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
Smokers who were using either bidis or cigarettes
Group 0 sample size Number of subjects in the control (unexposed) group
14

Lab analysis

Statistical Analysis

Alpha Diversity

Pielou Quantifies how equal the community is numerically
increased
Shannon Estimator of species richness and species evenness: more weight on species richness
increased
Simpson Estimator of species richness and species evenness: more weight on species evenness
increased

Signature 1

Reviewed Marked as Reviewed by Lwaldron on 2023-6-16

Curated date: 2023/06/13

Curator: Atrayees

Revision editor(s): Atrayees

Source: Figure 5

Description: Differentially abundant taxa identified in smokeless tobacco users and smokers using DESeq2.

Abundance in Group 1: decreased abundance in Smokers

NCBI Quality ControlLinks
Fusobacterium
Campylobacter

Revision editor(s): Atrayees