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

From BugSigDB
Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
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


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 Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva,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

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

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 ControlLinks
Veillonella
Selenomonadales
Veillonellaceae
Gammaproteobacteria
Pseudomonadota

Revision editor(s): WikiWorks

Signature 2

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

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 ControlLinks
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