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

From BugSigDB
Reviewed Marked as Reviewed by Lwaldron on 2023-4-4
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
Authors
Moon JH, Lee JH, Lee JY
Journal
Molecular oral microbiology
Year
2015
Keywords:
Korean, periodontitis, pyrosequencing, smoking, subgingival microflora
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


Reviewed Marked as Reviewed by Lwaldron on 2023-4-4

Curated date: 2023/03/13

Curator: Atrayees

Revision editor(s): Atrayees, Lwaldron

Subjects

Location of subjects
Republic of Korea
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
Subgingival dental plaque Subgingival plaque,Subgingival dental plaque,subgingival dental plaque
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
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
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Roche454

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
relative abundances
Matched on Factors on which subjects have been matched on in a case-control study
age, sex

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

Signature 1

Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-4

Curated date: 2023/03/13

Curator: Atrayees

Revision editor(s): Atrayees, Lwaldron, Claregrieve1

Source: text, Figure 1, Figure 2, Figure 3

Description: Genera, phylum and species showing differences in relative abundance.

Abundance in Group 1: increased abundance in Smokers

NCBI Quality ControlLinks
Bacteroides
Campylobacter concisus
Campylobacter showae
Corynebacterium
Corynebacterium matruchotii
Desulfobulbus
Eubacterium
Filifactor
Filifactor alocis
Fretibacterium
Fusobacteriia
Fusobacterium
Fusobacterium nucleatum
Gemella
Granulicatella
Hoylesella oralis
Lachnoanaerobaculum orale
Lachnoanaerobaculum saburreum
Lautropia
Leptotrichiaceae
Mogibacterium
Neisseria oralis
Neisseria sicca
Parvimonas
Segatella baroniae
Segatella buccae
Segatella maculosa
Segatella salivae
Rothia
Spirochaetia
Streptococcus
Synergistota
Tannerella
Veillonella
Veillonella dispar
unclassified Catonella
unclassified Leptotrichia
unclassified Porphyromonadaceae
unclassified Treponema
unclassified Veillonellaceae

Revision editor(s): Atrayees, Lwaldron, Claregrieve1

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-4

Curated date: 2023/03/13

Curator: Atrayees

Revision editor(s): Atrayees, Aiyshaaaa, Claregrieve1

Source: text, Figure 1, Figure 2, Figure 3

Description: Genera, phylum and species showing differences in relative abundance

Abundance in Group 1: decreased abundance in Smokers

NCBI Quality ControlLinks
Actinomyces johnsonii
Actinomyces viscosus
Aggregatibacter
Aggregatibacter segnis
Bacteroidia
Campylobacter
Capnocytophaga ochracea
Capnocytophaga sputigena
Cardiobacterium
Fusobacterium canifelinum
Granulicatella adiacens
Haemophilus
Hallella seregens
Lautropia mirabilis
Leptotrichia buccalis
Leptotrichia trevisanii
Megasphaera micronuciformis
Mogibacterium timidum
Neisseria bacilliformis
Neisseria elongata
Neisseria flavescens
Neisseria mucosa
Neisseria perflava
Porphyromonadaceae
Prevotella
Prevotella denticola
Prevotella intermedia
Prevotella melaninogenica
Prevotella nigrescens
Segatella oulorum
Prevotella pallens
Prevotellaceae
Pseudomonadota
Rothia aeria
Rothia dentocariosa
Schaalia odontolytica
Selenomonas noxia
Streptococcus cristatus
Streptococcus oralis
Streptococcus pseudopneumoniae
Streptococcus sanguinis
Treponema amylovorum
Treponema lecithinolyticum
Veillonella parvula
Veillonella rodentium
[Eubacterium] brachy
[Eubacterium] nodatum
[Eubacterium] saphenum
[Eubacterium] yurii
unclassified Aggregatibacter
unclassified Fretibacterium
unclassified Neisseria
unclassified Porphyromonas
unclassified Prevotella
unclassified Selenomonas
unclassified Treponema

Revision editor(s): Atrayees, Aiyshaaaa, Claregrieve1