Carious status and supragingival plaque microbiota in hemodialysis patients

From BugSigDB
Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/15
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

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): 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
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

Curated date: 2021/01/10

Curator: Fatima Zohra

Revision editor(s): Claregrieve1, WikiWorks

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 ControlLinks
Actinomyces
Bergeyella
Corynebacterium
Rothia
Streptococcus
Lactobacillus

Revision editor(s): Claregrieve1, WikiWorks

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/22

Curated date: 2021/01/10

Curator: Fatima Zohra

Revision editor(s): Claregrieve1, WikiWorks

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 ControlLinks
Fusobacterium
Porphyromonas

Revision editor(s): Claregrieve1, WikiWorks

Experiment 2


Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/22

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Victoria

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

NCBI Quality ControlLinks
Actinomyces naeslundii
Campylobacter curvus
Capnocytophaga sp.
Ligilactobacillus salivarius
Limosilactobacillus fermentum
Streptococcus mitis
Streptococcus mutans
Streptococcus sobrinus
[Eubacterium] infirmum

Revision editor(s): Claregrieve1, Atrayees, WikiWorks

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/22

Curated date: 2022/07/15

Curator: Claregrieve1

Revision editor(s): Claregrieve1

Source: Figure 4

Description: Differential microbial abundance between CKD patients and healthy controls

Abundance in Group 1: decreased abundance in Chronic kidney disease

NCBI Quality ControlLinks
Acholeplasmatales bacterium canine oral taxon 172
Capnocytophaga haemolytica
Haemophilus haemolyticus
Johnsonella ignava
Neisseria sp. GHG17
Oribacterium sp. CM12
Prevotella genomosp. P6
Prevotella intermedia 17
Prevotella melaninogenica
Hoylesella nanceiensis
Prevotella sp. oral clone GU027
Pseudoleptotrichia goodfellowii

Revision editor(s): Claregrieve1

Experiment 4


Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/22

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Victoria

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

Curated date: 2021/01/10

Curator: Fatima Zohra

Revision editor(s): Claregrieve1, WikiWorks

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 ControlLinks
Streptococcus mutans

Revision editor(s): Claregrieve1, WikiWorks