Subgingival microbiota dysbiosis in systemic lupus erythematosus: association with periodontal status

Study information

EditHistoryDelete

Flag for review

Your review change was submittedAdd a new Experiment

• Quality control
  • Retracted paper
  • Contamination issues suspected
  • Batch effect issues suspected
  • Uncontrolled confounding suspected
  • Results are suspect (various reasons)
  • Apply tags

    Tags applied

Reviewed Marked as Reviewed by Svetlana up on 2025-2-24

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

28320468

DOI Digital object identifier for electronic documents.

10.1186/s40168-017-0252-z

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

EditHistoryDelete

Flag for review

Your review change was submittedDuplicate this ExperimentAdd a new Signature

Reviewed Marked as Reviewed by Svetlana up on 2025-2-24

Curated date: 2025/02/14

Curator: Taofeecoh

Revision editor(s): Taofeecoh, WikiWorks

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

Control with Non-periodontitis (C-NCP)

Group 1 name Corresponds to the case (exposed) group for case-control studies

Systemic Lupus Erythematosus with Non-periodontitis (SLE-NCP)

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

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)

0.05

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

EditHistoryDelete

Flag for review

Your review change was submitted

Reviewed Marked as Reviewed by Svetlana up on 2025-2-24

Curated date: 2025/02/15

Curator: Taofeecoh

Revision editor(s): Taofeecoh, WikiWorks

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 with Non-periodontitis (SLE-NCP)

NCBI	Quality Control	Links
unclassified Lachnospiraceae A IR009unclassified Lachnospiraceae A IR009

Revision editor(s): Taofeecoh, WikiWorks

Signature 2

EditHistoryDelete

Flag for review

Your review change was submitted

Reviewed Marked as Reviewed by Svetlana up on 2025-2-24

Curated date: 2025/02/15

Curator: Taofeecoh

Revision editor(s): Taofeecoh, WikiWorks

Source: Figures 5a, 5b

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 with Non-periodontitis (SLE-NCP)

NCBI	Quality Control	Links
Mogibacterium
Sphingomonas

Revision editor(s): Taofeecoh, WikiWorks

Experiment 2

EditHistoryDelete

Flag for review

Your review change was submittedDuplicate this ExperimentAdd a new Signature

Reviewed Marked as Reviewed by Svetlana up on 2025-2-24

Curated date: 2025/02/15

Curator: Taofeecoh

Revision editor(s): Taofeecoh, WikiWorks

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies

Controls with Chronic periodontitis (C-CP)

Group 1 name Corresponds to the case (exposed) group for case-control studies

Systemic Lupus Erythematosus with Chronic periodontitis (SLE-CP)

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

EditHistoryDelete

Flag for review

Your review change was submitted

Reviewed Marked as Reviewed by Svetlana up on 2025-2-24

Curated date: 2025/02/15

Curator: Taofeecoh

Revision editor(s): Taofeecoh, WikiWorks

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 with Chronic periodontitis (SLE-CP)

NCBI	Quality Control	Links
Hoylesella pleuritidis
Pseudomonas
Segatella oulorum
Treponema maltophilum
Actinomyces IP073Actinomyces IP073
Bifidobacterium/ScardoviaBifidobacterium/Scardovia
Mogibacterium neglectum/vescumMogibacterium neglectum/vescum
Fretibacterium fastidiosum

Revision editor(s): Taofeecoh, WikiWorks

Signature 2

EditHistoryDelete

Flag for review

Your review change was submitted

Reviewed Marked as Reviewed by Svetlana up on 2025-2-24

Curated date: 2025/02/15

Curator: Taofeecoh

Revision editor(s): Taofeecoh, WikiWorks

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 with Chronic periodontitis (SLE-CP)

NCBI	Quality Control	Links
Capnocytophaga gingivalis
Comamonadaceae
Eubacteriales
Granulicatella adiacens
Haemophilus parainfluenzae
Prevotella fusca
Roseateles puraquae
Sphingomonas
Streptococcus sanguinis
Ralstonia oral taxon 027Ralstonia oral taxon 027
Leptotrichia oral taxon A71Leptotrichia oral taxon A71
Rothia aeria

Revision editor(s): Taofeecoh, WikiWorks

Experiment 3

EditHistoryDelete

Flag for review

Your review change was submittedDuplicate this ExperimentAdd a new Signature

Reviewed Marked as Reviewed by Svetlana up on 2025-2-24

Curated date: 2025/02/20

Curator: Taofeecoh

Revision editor(s): Taofeecoh

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies

Control with Non-periodontitis (C-NCP)

Group 1 name Corresponds to the case (exposed) group for case-control studies

Systemic Lupus Erythematosus with Non-periodontitis (SLE-NCP)

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

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).

relative abundances

Statistical test

LEfSe

MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?

No

LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool

2

Alpha Diversity

Chao1 Abundance-based estimator of species richness

increased

Richness Number of species

increased

Signature 1

EditHistoryDelete

Flag for review

Your review change was submitted

Reviewed Marked as Reviewed by Svetlana up on 2025-2-24

Curated date: 2025/02/20

Curator: Taofeecoh

Revision editor(s): Taofeecoh

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 with Non-periodontitis (SLE-NCP)

NCBI	Quality Control	Links
Aggregatibacter
Cryptobacterium curtum
Hallella multisaccharivorax
Leptotrichia
Oribacterium sinus
Prevotella nigrescens
Segatella oris
Segatella oulorum
Selenomonas noxia
Treponema amylovorum
Streptococcus intermedius/constellatusStreptococcus intermedius/constellatus
Capnocytophaga leadbetteri

Revision editor(s): Taofeecoh

Signature 2

EditHistoryDelete

Flag for review

Your review change was submitted

Reviewed Marked as Reviewed by Svetlana up on 2025-2-24

Curated date: 2025/02/20

Curator: Taofeecoh

Revision editor(s): Taofeecoh

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 with Non-periodontitis (SLE-NCP)

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

EditHistoryDelete

Flag for review

Your review change was submittedDuplicate this ExperimentAdd a new Signature

Reviewed Marked as Reviewed by Svetlana up on 2025-2-24

Curated date: 2025/02/20

Curator: Taofeecoh

Revision editor(s): Taofeecoh

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies

Control with Chronic periodontitis (C-CP)

Group 1 name Corresponds to the case (exposed) group for case-control studies

Systemic Lupus Erythematosus Chronic periodontitis (SLE-CP)

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

EditHistoryDelete

Flag for review

Your review change was submitted

Reviewed Marked as Reviewed by Svetlana up on 2025-2-24

Curated date: 2025/02/20

Curator: Taofeecoh

Revision editor(s): Taofeecoh

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 Chronic periodontitis (SLE-CP)

NCBI	Quality Control	Links
Segatella oulorum
Fretibacterium oral taxon 360 453Fretibacterium oral taxon 360 453
TM7 oral taxon 437TM7 oral taxon 437
Hallella multisaccharivorax
Fretibacterium fastidiosum
Sphingomonas
Anaeroglobus geminatus

Revision editor(s): Taofeecoh

Signature 2

EditHistoryDelete

Flag for review

Your review change was submitted

Reviewed Marked as Reviewed by Svetlana up on 2025-2-24

Curated date: 2025/02/20

Curator: Taofeecoh

Revision editor(s): Taofeecoh

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 Chronic periodontitis (SLE-CP)

NCBI	Quality Control	Links
Prevotella intermedia
Rothia aeria
Bergeyella 602D02Bergeyella 602D02
Brevundimonas nbw914f05c1Brevundimonas nbw914f05c1
Peptococcus BU014Peptococcus BU014

Revision editor(s): Taofeecoh