Carious status and supragingival plaque microbiota in hemodialysis patients
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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
Yue Q, Yin FT, Zhang Q, Yuan C, Ye MY, Wang XL, Li JJ, Gan YH
Journal
PloS one
Year
2018
OBJECTIVE: The aim of this study was to evaluate the carious status and the microbial profiles of supragingival plaque in patients with chronic kidney disease undergoing hemodialysis. METHODS: This study included 30 patients with chronic kidney disease undergoing hemodialysis as well as 30 control subjects. Dental examination was performed and the decayed-missing-filled-teeth was recorded. Supragingival plaque was taken and analyzed using 16S rRNA gene amplicon by Illumina MiSeq sequencing to detect microbial composition and community diversity and structure. RESULTS: The level of decayed-missing-filled-teeth was higher in the hemodialysis group than that in the control group. Microbial analysis showed a decrease in α diversity and a increase in relative abundance and prevalence of many acidogenic and aciduric caries related species in the supragingival plaque samples of the hemodialysis patients, including Streptococcus mutans, Lactobacillus salivarius, Lactobacillus fermentum, Lactobacillus vaginalis, Scardovia wiggsiae F0424, and Actinomyces naeslundii. CONCLUSION: Our results suggested that the hemodialysis patients were more susceptible to caries. More attentions for caries prevention and treatment should be paid to improve their life quality, and even to reduce their cardiovascular events and survival.
Experiment 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/15
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
- Gingiva Gingival mucosa,Gum,Gum tissue,Gums,Gingiva,gingiva
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Chronic kidney disease chronic kidney disease,chronic kidney failure,Chronic Kidney Insufficiencies,Chronic Kidney Insufficiency,chronic renal disease,Chronic Renal Failure,chronic renal failure syndrome,Chronic Renal Insufficiencies,chronic renal insufficiency,CKD,CKD - chronic kidney disease,Disease, End-Stage Kidney,Disease, End-Stage Renal,END STAGE KIDNEY DIS,End Stage Kidney Disease,END STAGE RENAL DIS,End Stage Renal Disease,End-Stage Kidney Disease,End-Stage Renal Disease,End-Stage Renal Failure,ESRD,kidney disease, chronic,Kidney Disease, End-Stage,Kidney Failure, Chronic,Kidney Insufficiencies, Chronic,Kidney Insufficiency, Chronic,RENAL DIS END STAGE,Renal Disease, End Stage,Renal Disease, End-Stage,renal failure - chronic,Renal Failure, Chronic,Renal Failure, End Stage,Renal Failure, End-Stage,Renal Insufficiencies, Chronic,Renal Insufficiency, Chronic,Chronic kidney disease
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- healthy controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Chronic kidney disease
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- chronic kidney disease patients undergoing hemodialysis
- Group 0 sample size Number of subjects in the control (unexposed) group
- 30
- Group 1 sample size Number of subjects in the case (exposed) group
- 30
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 30 days
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
- Metastats
- 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
- Matched on Factors on which subjects have been matched on in a case-control study
- age, smoking behavior, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Richness Number of species
- decreased
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/22
Source: Figure 3
Description: Differential microbial abundance between CKD patients and healthy controls
Abundance in Group 1: increased abundance in Chronic kidney disease
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces | ||
| Bergeyella | ||
| Corynebacterium | ||
| Rothia | ||
| Streptococcus | ||
| Lactobacillus |
Revision editor(s): Claregrieve1, WikiWorks
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/22
Source: Figure 3
Description: Differential microbial abundance between CKD patients and healthy controls
Abundance in Group 1: decreased abundance in Chronic kidney disease
| NCBI | Quality Control | Links |
|---|---|---|
| Fusobacterium | ||
| Porphyromonas |
Revision editor(s): Claregrieve1, WikiWorks
Experiment 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/22
Differences from previous experiment shown
Subjects
Lab analysis
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V5
Statistical Analysis
- Statistical test
- LEfSe
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Richness Number of species
- decreased
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/22
Curated date: 2021/01/10
Curator: Fatima Zohra
Revision editor(s): Claregrieve1, Atrayees, WikiWorks
Source: Figure 4
Description: Differential microbial abundance between CKD patients and healthy controls
Abundance in Group 1: increased abundance in Chronic kidney disease
Revision editor(s): Claregrieve1, Atrayees, WikiWorks
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/22
Source: Figure 4
Description: Differential microbial abundance between CKD patients and healthy controls
Abundance in Group 1: decreased abundance in Chronic kidney disease
Revision editor(s): Claregrieve1
Experiment 4
Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/22
Differences from previous experiment shown
Subjects
Lab analysis
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V6
Statistical Analysis
- Statistical test
- Mann-Whitney (Wilcoxon)
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- Not specified
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Richness Number of species
- decreased
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/22
Source: Figure 5
Description: Differential abundance of Streptococcus mutans in supragingival plaque measured by quantitative real-time PCR between kidney disease patients and healthy controls
Abundance in Group 1: increased abundance in Chronic kidney disease
| NCBI | Quality Control | Links |
|---|---|---|
| Streptococcus mutans |
Revision editor(s): Claregrieve1, WikiWorks
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