Subgingival microbiota dysbiosis in systemic lupus erythematosus: association with periodontal status
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Corrêa JD, Calderaro DC, Ferreira GA, Mendonça SM, Fernandes GR, Xiao E, Teixeira AL, Leys EJ, Graves DT, Silva TA
Journal
Microbiome
Year
2017
Keywords:
Cytokine, Illumina sequencing, Lupus, Oral microbiota, Periodontitis, Subgingival dental plaque
BACKGROUND: Periodontitis results from the interaction between a subgingival biofilm and host immune response. Changes in biofilm composition are thought to disrupt homeostasis between the host and subgingival bacteria resulting in periodontal damage. Chronic systemic inflammatory disorders have been shown to affect the subgingival microbiota and clinical periodontal status. However, this relationship has not been examined in subjects with systemic lupus erythematosus (SLE). The objective of our study was to investigate the influence of SLE on the subgingival microbiota and its connection with periodontal disease and SLE activity. METHODS: We evaluated 52 patients with SLE compared to 52 subjects without SLE (control group). Subjects were classified as without periodontitis and with periodontitis. Oral microbiota composition was assessed by amplifying the V4 region of 16S rRNA gene from subgingival dental plaque DNA extracts. These amplicons were examined by Illumina MiSeq sequencing. RESULTS: SLE patients exhibited higher prevalence of periodontitis which occurred at a younger age compared to subjects of the control group. More severe forms of periodontitis were found in SLE subjects that had higher bacterial loads and decreased microbial diversity. Bacterial species frequently detected in periodontal disease were observed in higher proportions in SLE patients, even in periodontal healthy sites such as Fretibacterium, Prevotella nigrescens, and Selenomonas. Changes in the oral microbiota were linked to increased local inflammation, as demonstrated by higher concentrations of IL-6, IL-17, and IL-33 in SLE patients with periodontitis. CONCLUSIONS: SLE is associated with differences in the composition of the microbiota, independently of periodontal status.
Experiment 1
Subjects
- Location of subjects
- Brazil
- 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
- Systemic lupus erythematosus Disease, Libman-Sacks,disseminated lupus erythematosus,excess LMW-DNA,excess lymphocyte low molecular weight DNA,LIBMAN SACKS DIS,Libman Sacks Disease,Libman-Sacks Disease,lupus,Lupus Erythematosus Disseminatus,Lupus Erythematosus, Systemic,lupus erythematosus, systemic,SLE,SLE - lupus erythematosus, systemic,systemic lupus erythematosus,systemic lupus erythematosus (disease),Systemic lupus erythematosus
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Controls (C)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Systemic Lupus Erythematosus (SLE)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Systemic Lupus Erythematosus (SLE) patients with Non-periodontitis (NCP)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 24
- Group 1 sample size Number of subjects in the case (exposed) group
- 17
- 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
- V4
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Statistical test
- DESeq2
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- 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
- age, sex
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- increased
- Richness Number of species
- increased
Signature 1
Source: Figures 5a, 5b
Description: OTUs with different relative abundance in control subjects and SLE patients in non-periodontitis.
Abundance in Group 1: increased abundance in Systemic Lupus Erythematosus (SLE)
| NCBI | Quality Control | Links |
|---|---|---|
| unclassified Lachnospiraceae A IR009unclassified Lachnospiraceae A IR009 |
Experiment 2
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Systemic lupus erythematosus , PeriodontitisDisease, Libman-Sacks,disseminated lupus erythematosus,excess LMW-DNA,excess lymphocyte low molecular weight DNA,LIBMAN SACKS DIS,Libman Sacks Disease,Libman-Sacks Disease,lupus,Lupus Erythematosus Disseminatus,Lupus Erythematosus, Systemic,lupus erythematosus, systemic,SLE,SLE - lupus erythematosus, systemic,systemic lupus erythematosus,systemic lupus erythematosus (disease),Systemic lupus erythematosus,Periodontitis
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Systemic Lupus Erythematosus (SLE) patients with Chronic periodontitis (CP)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 28
- Group 1 sample size Number of subjects in the case (exposed) group
- 35
Lab analysis
Statistical Analysis
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Not specified
- Matched on Factors on which subjects have been matched on in a case-control study
- age, sex, health
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figures 5c, 5d
Description: OTUs with different relative abundance in control subjects and SLE samples in Chronic periodontitis.
Abundance in Group 1: increased abundance in Systemic Lupus Erythematosus (SLE)
Signature 2
Source: Figures 5c, 5d
Description: OTUs with different relative abundance in control subjects and SLE samples in Chronic periodontitis.
Abundance in Group 1: decreased abundance in Systemic Lupus Erythematosus (SLE)
Experiment 3
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Systemic lupus erythematosus Disease, Libman-Sacks,disseminated lupus erythematosus,excess LMW-DNA,excess lymphocyte low molecular weight DNA,LIBMAN SACKS DIS,Libman Sacks Disease,Libman-Sacks Disease,lupus,Lupus Erythematosus Disseminatus,Lupus Erythematosus, Systemic,lupus erythematosus, systemic,SLE,SLE - lupus erythematosus, systemic,systemic lupus erythematosus,systemic lupus erythematosus (disease),Systemic lupus erythematosus
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Systemic Lupus Erythematosus (SLE) patients with Non-periodontitis (NCP)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 24
- Group 1 sample size Number of subjects in the case (exposed) group
- 17
Lab analysis
Statistical Analysis
- Statistical test
- LEfSe
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- Not specified
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
- Matched on Factors on which subjects have been matched on in a case-control study
- age, sex
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- increased
- Richness Number of species
- increased
Signature 1
Source: Figure 6a
Description: OTUs with different relative abundance in control subjects and SLE patients in non-periodontitis.
Abundance in Group 1: increased abundance in Systemic Lupus Erythematosus (SLE)
Revision editor(s): Taofeecoh
Signature 2
Source: Figure 6a
Description: OTUs with different relative abundance in control subjects and SLE samples in non-periodontitis.
Abundance in Group 1: decreased abundance in Systemic Lupus Erythematosus (SLE)
| NCBI | Quality Control | Links |
|---|---|---|
| Aggregatibacter aphrophilus | ||
| Comamonadaceae | ||
| Streptococcus anginosus | ||
| Treponema E D 05 72Treponema E D 05 72 | ||
| unclassified Burkholderiales | ||
| Sphingomonas |
Revision editor(s): Taofeecoh
Experiment 4
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Systemic lupus erythematosus , PeriodontitisDisease, Libman-Sacks,disseminated lupus erythematosus,excess LMW-DNA,excess lymphocyte low molecular weight DNA,LIBMAN SACKS DIS,Libman Sacks Disease,Libman-Sacks Disease,lupus,Lupus Erythematosus Disseminatus,Lupus Erythematosus, Systemic,lupus erythematosus, systemic,SLE,SLE - lupus erythematosus, systemic,systemic lupus erythematosus,systemic lupus erythematosus (disease),Systemic lupus erythematosus,Periodontitis
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Systemic Lupus Erythematosus (SLE) patients with Chronic periodontitis (CP)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 28
- Group 1 sample size Number of subjects in the case (exposed) group
- 35
Lab analysis
Statistical Analysis
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure 6b
Description: OTUs with different relative abundance in control subjects and SLE samples in Chronic periodontitis.
Abundance in Group 1: increased abundance in Systemic Lupus Erythematosus (SLE)
Revision editor(s): Taofeecoh
Signature 2
Source: Figure 6b
Description: OTUs with different relative abundance in control subjects and SLE samples in Chronic periodontitis.
Abundance in Group 1: decreased abundance in Systemic Lupus Erythematosus (SLE)
| NCBI | Quality Control | Links |
|---|---|---|
| Rothia aeria | ||
| Preptococcus BU014Preptococcus BU014 | ||
| Bergeyella 602D02Bergeyella 602D02 | ||
| Prevotella intermedia | ||
| Brevundimonas nbw914f05c1Brevundimonas nbw914f05c1 |
Revision editor(s): Taofeecoh
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