Molecular analysis of oral microflora in patients with primary Sjögren's syndrome by using high-throughput sequencing
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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
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
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
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
Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09
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
Revision editor(s): WikiWorks
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