Molecular analysis of oral microflora in patients with primary Sjögren's syndrome by using high-throughput sequencing

Study information

Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

30280027

DOI Digital object identifier for electronic documents.

10.7717/peerj.5649

URI

Authors

Zhou Z, Ling G, Ding N, Xun Z, Zhu C, Hua H, Chen X

Journal

PeerJ

Year

2018

Keywords:

Core microbiome, Dental caries, High-throughput sequencing, Oral microflora, Primary Sjögren’s syndrome

Background: The objective of this study was to characterize the oral microflora profile of primary Sjögren's syndrome (pSS) patients, thereby revealing the connection between oral bacterial composition and dental caries, and to identify the "core microbiome" in the oral cavities of pSS patients and systemic healthy individuals by using a high-throughput sequencing technique. Methods: Twenty-two pSS patients and 23 healthy controls were enrolled in this study. Their clinical data and oral rinse samples were collected. The V3-V4 hypervariable regions of the bacterial 16S rRNA gene of samples were amplified and analyzed by high-throughput sequencing on the Illumina Miseq PE300 platform. Results: Both two groups were age- and sex-matched. There were significantly higher decayed, missing and filled teeth (DMFT) and decayed, missing and filled surfaces (DMFS) in the pSS group than in the control group (p < 0.01). Alpha diversity was depleted in pSS patients, compared with healthy controls (p < 0.01), while beta diversity between the two groups was not significantly different. Seven discriminative genera (LDA > 4) were found between the two groups in LEfSe (LDA Effect Size) analysis. The relative abundance of Veillonella in pSS patients was fourfold higher, while Actinomyces, Haemophilus, Neisseria, Rothia, Porphyromonas and Peptostreptococcus were significantly lower in pSS patients than in healthy controls. However, the correlation between Veillonella and DMFT/DMFS was not significant (p > 0.05). In Venn diagram analysis, nine genera shared by all samples of two groups, which comprised 71.88% and 67.64% in pSS patients and controls, respectively. Discussion: These findings indicate a microbial dysbiosis in pSS patients; notably, Veillonella might be recognized as a biomarker in pSS patients. The core microbiome in pSS patients was similar to the systemic healthy population. These provide insight regarding advanced microbial prevention and treatment of severe dental caries in pSS patients. This study also provides basic data regarding microbiology in pSS.

Experiment 1

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Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Claregrieve1, WikiWorks, Victoria

Subjects

Location of subjects: China

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: Saliva

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Sjogren syndrome Mikulicz disease,primary Sjogren-Gougerot syndrome,primary Sjögren syndrome,primary Sjögren-Gougerot syndrome,Sicca (Sjogren's) syndrome,Sicca syndrome,sicca syndrome,Sicca syndrome (disorder),Sjgren's syndrome (disorder),Sjogren syndrome,Sjogren's disease,SJOGREN'S SYNDROME,Sjogren's syndrome,Sjogren's syndrome (disorder),Sjogrens Syndrome,Sjögren syndrome,Syndrome, Sicca,Syndrome, Sjogren's,syndrome, Sjogren's,xerodermosteosis,sjogren's syndrome,sjogren syndrome

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

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

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Patients with Sjogren syndrome

Group 0 sample size Number of subjects in the control (unexposed) group: 23

Group 1 sample size Number of subjects in the case (exposed) group: 22

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V3-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).: relative abundances

Statistical test: LEfSe

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)?: No

LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool: 4

Matched on Factors on which subjects have been matched on in a case-control study: age, sex

Alpha Diversity

Pielou Quantifies how equal the community is numerically: decreased

Shannon Estimator of species richness and species evenness: more weight on species richness: decreased

Chao1 Abundance-based estimator of species richness: unchanged

Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa: decreased

Signature 1

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Curated date: 2021/01/10

Curator: Rimsha Azhar

Revision editor(s): WikiWorks

Source: Figure 3

Description: Comparison of microbiota using LDA score by LEfSe analysis between primary sjogres patients(PSS) and healthy controls

Abundance in Group 1: increased abundance in PSS

NCBI	Quality Control	Links
Veillonella
Selenomonadales
Veillonellaceae
Gammaproteobacteria
Pseudomonadota

Revision editor(s): WikiWorks

Signature 2

Edit History Delete

Mark reviewed

Your review change was submitted

Needs review

Curated date: 2021/01/10

Curator: Rimsha Azhar

Revision editor(s): WikiWorks

Source: Figure 3

Description: Comparison of microbiota using LDA score by LEfSe analysis between primary sjogres patients(PSS) and healthy controls

Abundance in Group 1: decreased abundance in PSS

NCBI	Quality Control	Links
Actinomyces
Haemophilus
Neisseria
Rothia
Porphyromonas
Peptostreptococcus
Betaproteobacteria
Actinomycetaceae
Pasteurellaceae
Neisseriaceae
Neisseriales
Micrococcaceae
Porphyromonadaceae
Actinomycetales
Fusobacteriia
Fusobacteriota
Fusobacteriales
Clostridia
Eubacteriales
Pasteurellales
Actinomycetota

Revision editor(s): WikiWorks