Subgingival microbiome in smokers and non-smokers in Korean chronic periodontitis patients

From BugSigDB
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study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI Uniform resource identifier for web resources.
Authors
Moon JH, Lee JH, Lee JY
Journal
Molecular oral microbiology
Year
2015
Smoking is a major environmental factor associated with periodontal diseases. However, we still have a very limited understanding of the relationship between smoking and subgingival microflora in the global population. Here, we investigated the composition of subgingival bacterial communities from the pooled plaque samples of smokers and non-smokers, 134 samples in each group, in Korean patients with moderate chronic periodontitis using 16S rRNA gene-based pyrosequencing. A total of 17,927 reads were analyzed and classified into 12 phyla, 126 genera, and 394 species. Differences in bacterial communities between smokers and non-smokers were examined at all phylogenetic levels. The genera Fusobacterium, Fretibacterium, Streptococcus, Veillonella, Corynebacterium, TM7, and Filifactor were abundant in smokers. On the other hand, Prevotella, Campylobacter, Aggregatibacter, Veillonellaceae GQ422718, Haemophilus, and Prevotellaceae were less abundant in smokers. Among species-level taxa occupying > 1% of whole subgingival microbiome of smokers, higher abundance (≥ 2.0-fold compared to non-smokers) of seven species or operational taxonomic units (OTUs) was found: Fusobacterium nucleatum, Neisseria sicca, Neisseria oralis, Corynebacterium matruchotii, Veillonella dispar, Filifactor alocis, and Fretibacterium AY349371. On the other hand, lower abundance of 11 species or OTUs was found in smokers: Neisseria elongata, six Prevotella species or OTUs, Fusobacterium canifelinum, Aggregatibacter AM420165, Selenomonas OTU, and Veillonellaceae GU470897. Species richness and evenness were similar between the groups whereas diversity was greater in smokers than non-smokers. Collectively, the results of the present study indicate that differences exist in the subgingival bacterial community between smoker and non-smoker patients with chronic moderate periodontitis in Korea, suggesting that cigarette smoking considerably affects subgingival bacterial ecology.

Experiment 1


Needs review

Curated date: 2023/03/13

Curator: Atrayees

Revision editor(s): Atrayees

Subjects

Location of subjects
Republic of Korea
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
chronic periodontitis chronic pericementitis,Chronic pericementitis (disorder),Chronic periodontitis,chronic periodontitis,chronic periodontitis (disorder),Chronic periodontitis NOS,chronic periodontitis NOS (disorder),periodontitis, chronic
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
A patient was defined as a smoker if he was currently smoking and had been smoking five or more cigarettes a day for at least 10 years.
Group 0 sample size Number of subjects in the control (unexposed) group
36
Group 1 sample size Number of subjects in the case (exposed) group
57
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
Patients were excluded if they had received antibiotic therapy within the past 3 months.

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
V1-V3

Statistical Analysis

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, Matched on: "gender" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.gender, Matched on: "tobacco exposure" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.tobacco exposure, Matched on: "full mouth periodontal profile" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.full mouth periodontal profile, Matched on: "profile of sample sites" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.profile of sample sites

Alpha Diversity

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
unchanged
Richness Number of species
unchanged
Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
increased

Signature 1

Needs review

Curated date: 2023/03/13

Curator: Atrayees

Revision editor(s): Atrayees

Source: text, Figure 2

Description: Genera showing differences in relative abundance greater than 1.5-fold (These genera occupied > 1% of the subgingival microflora).

Abundance in Group 1: increased abundance in Smokers

NCBI Links
Corynebacterium
Filifactor
Fretibacterium
Fusobacterium
Streptococcus
Veillonella
TM7TM7

Revision editor(s): Atrayees

Signature 2

Needs review

Curated date: 2023/03/13

Curator: Atrayees

Revision editor(s): Atrayees

Source: text, Figure 2A

Description: Genera showing differences in relative abundance greater than 1.5-fold (These genera occupied > 1% of the subgingival microflora).

Abundance in Group 1: decreased abundance in Smokers

NCBI Links
Haemophilus
Prevotellaceae
Prevotella
Aggregatibacter
Campylobacter
veillonellaceae GQ422718veillonellaceae GQ422718

Revision editor(s): Atrayees

Signature 3

Needs review

Curated date: 2023/03/24

Curator: Atrayees

Revision editor(s): Atrayees

Source: text, Figure 2

Description: Genera showing differences in relative abundance greater than 1.5-fold (These genera occupied < 1% of the subgingival microflora).

Abundance in Group 1: increased abundance in Smokers

NCBI Links
Bacteroides
Desulfobulbus
Eubacterium
Gemella
Granulicatella
Lautropia
Leptotrichiaceae
Mogibacterium
Parvimonas
Rothia
Tannerella

Revision editor(s): Atrayees

Signature 4

Needs review

Curated date: 2023/03/24

Curator: Atrayees

Revision editor(s): Atrayees

Source: text, Figure 2B

Description: Genera showing differences in relative abundance greater than 1.5-fold (These genera occupied < 1% of the subgingival microflora).

Abundance in Group 1: decreased abundance in Smokers

NCBI Links
Porphyromonadaceae
Cardiobacterium
Neisseriaceae FJ976399Neisseriaceae FJ976399

Revision editor(s): Atrayees

Signature 5

Needs review

Curated date: 2023/03/24

Curator: Atrayees

Revision editor(s): Atrayees, Aiyshaaaa

Source: text, Figure 1

Description: Phylum showing differences in relative abundance. (Note: The 'Synergistota' phylum as mentioned below is a homotypic synonym of the 'Synergistetes' phylum)

Abundance in Group 1: increased abundance in Smokers

NCBI Links
Fusobacteriia
Synergistota
TM7TM7
SR1SR1
Spirochaetia

Revision editor(s): Atrayees, Aiyshaaaa

Signature 6

Needs review

Curated date: 2023/03/24

Curator: Atrayees

Revision editor(s): Atrayees

Source: text, Figure 1

Description: Phylum showing differences in relative abundance. (Note: The phylum 'Pseudomonadota' as mentioned below is equivalent to 'Proteobacteria')

Abundance in Group 1: decreased abundance in Smokers

NCBI Links
bacteroidetesbacteroidetes
Pseudomonadota

Revision editor(s): Atrayees

Signature 7

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Curated date: 2023/03/24

Curator: Atrayees

Revision editor(s): Atrayees

Source: text, Figure 3A

Description: species-level taxa (that occupied > 1% of the subgingival microflora of smokers or non-smokers) showing differences in relative abundance greater than 2.0-fold between smokers and non-smokers as compared with each other

Abundance in Group 1: increased abundance in Smokers

NCBI Links
Fusobacterium nucleatum
Neisseria sicca
Neisseria oralis
Corynebacterium matruchotii
Veillonella dispar
Filifactor alocis
Fretibacterium AY349371Fretibacterium AY349371

Revision editor(s): Atrayees

Signature 8

Needs review

Curated date: 2023/03/24

Curator: Atrayees

Revision editor(s): Atrayees

Source: text, Figure 1

Description: species-level taxa (that occupied > 1% of the subgingival microflora of smokers or non-smokers) showing differences in relative abundance greater than 2.0-fold between smokers and non-smokers as compared with each other

Abundance in Group 1: decreased abundance in Smokers

NCBI Links
Prevotella denticola
Prevotella oulorum
Prevotella nigrescens
Prevotella intermedia
Prevotella AM419982Prevotella AM419982
Neisseria elongata
Fusobacterium canifelinum
Aggregatibacter AM420165Aggregatibacter AM420165
Veillonellaceae GU470897Veillonellaceae GU470897
unclassified Selenomonas
unclassified Prevotella

Revision editor(s): Atrayees

Signature 9

Needs review

Curated date: 2023/03/24

Curator: Atrayees

Revision editor(s): Atrayees

Source: Figure 3C

Description: species-level taxa (that occupied < 1% of the subgingival microflora of smokers or non-smokers) showing differences in relative abundance greater than 2.0-fold between smokers and non-smokers as compared with each other

Abundance in Group 1: decreased abundance in Smokers

NCBI Links
unclassified Treponema
unclassified Catonella
unclassified Porphyromonadaceae
Lachnoanaerobaculum saburreum
Lachnoanaerobaculum orale
unclassified Leptotrichia
Hoylesella oralis
unclassified Bacteroidales
Selenomonas dianae
Prevotella dentalis
unclassified Veillonellaceae
Prevotella salivae
Prevotella maculosa
Prevotella buccae
Prevotella baroniae
Campylobacter concisus
Campylobacter showae

Revision editor(s): Atrayees

Signature 10

Needs review

Curated date: 2023/03/24

Curator: Atrayees

Revision editor(s): Atrayees

Source: Figure 3B

Description: species-level taxa (that occupied < 1% of the subgingival microflora of smokers or non-smokers) showing differences in relative abundance greater than 2.0-fold between smokers and non-smokers as compared with each other

Abundance in Group 1: increased abundance in Smokers

NCBI Links
Veillonella parvula
Lautropia mirabilis
Streptococcus sanguinis
Streptococcus cristatus
Capnocytophaga ochracea
Prevotella melaninogenica
Neisseria bacilliformis
Leptotrichia buccalis
Streptococcus pseudopneumoniae
Capnocytophaga sputigena
Neisseria perflava
Selenomonas noxia
Aggregatibacter segnis
Rothia aeria
Treponema lecithinolyticum
unclassified Treponema
unclassified Fretibacterium
Actinomyces viscosus
unclassified Neisseria
Rothia dentocariosa
Streptococcus oralis
Granulicatella adiacens
unclassified Porphyromonas
Prevotella pallens
Veillonella rodentium
[Eubacterium] nodatum
Actinomyces johnsonii
Schaalia odontolytica
Neisseria mucosa
Treponema amylovorum
Hallella seregens
Megasphaera micronuciformis
Neisseria flavescens
unclassified Aggregatibacter
[Eubacterium] yurii
[Eubacterium] brachy
[Eubacterium] saphenum
Mogibacterium timidum
Leptotrichia trevisanii

Revision editor(s): Atrayees