Subgingival microbiome in smokers and non-smokers in Korean chronic periodontitis patients
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Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Experiment 1
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
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
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
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
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
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 |
Signature 6
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
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
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
Revision editor(s): Atrayees
Signature 9
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
Revision editor(s): Atrayees
Signature 10
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
Revision editor(s): Atrayees
