Investigation of the effect of type 2 diabetes mellitus on subgingival plaque microbiota by high-throughput 16S rDNA pyrosequencing
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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 M, Rong R, Munro D, Zhu C, Gao X, Zhang Q, Dong Q
Journal
PloS one
Year
2013
Diabetes mellitus is a major risk factor for chronic periodontitis. We investigated the effects of type 2 diabetes on the subgingival plaque bacterial composition by applying culture-independent 16S rDNA sequencing to periodontal bacteria isolated from four groups of volunteers: non-diabetic subjects without periodontitis, non-diabetic subjects with periodontitis, type 2 diabetic patients without periodontitis, and type 2 diabetic patients with periodontitis. A total of 71,373 high-quality sequences were produced from the V1-V3 region of 16S rDNA genes by 454 pyrosequencing. Those 16S rDNA sequences were classified into 16 phyla, 27 classes, 48 orders, 85 families, 126 genera, and 1141 species-level OTUs. Comparing periodontally healthy samples with periodontitis samples identified 20 health-associated and 15 periodontitis-associated OTUs. In the subjects with healthy periodontium, the abundances of three genera (Prevotella, Pseudomonas, and Tannerella) and nine OTUs were significantly different between diabetic patients and their non-diabetic counterparts. In the subjects carrying periodontitis, the abundances of three phyla (Actinobacteria, Proteobacteria, and Bacteriodetes), two genera (Actinomyces and Aggregatibacter), and six OTUs were also significantly different between diabetics and non-diabetics. Our results show that type 2 diabetes mellitus could alter the bacterial composition in the subgingival plaque.
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 (if applicable)
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Subgingival dental plaque Subgingival plaque,Subgingival dental plaque
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- periodontitis chronic pericementitis,inflammation of periodontium,Pericementitides,Pericementitis,Periodontitides,periodontitis,Periodontitis (disorder),Periodontitis, NOS,periodontium inflammation,periodontosis
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- No Periodontitis within negative diabetic background only
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- periodontitis
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Periodontitis was defined by the following criteria: at least 30% of sites with probing depth and attachment loss, and more than four with probing depth >=4 mm and clinical attachment loss >=2 mm. Subjects with type 2 diabetes had been diagnosed for at least one year with HbA1c >= 6.5%, fasting plasma glucose test >=7.0 mmol/L, or OGTT 2 hour glucose test >=11.1 mmol/L
- Group 0 sample size Number of subjects in the control (unexposed) group
- 5
- Group 1 sample size Number of subjects in the case (exposed) group
- 6
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 3 months
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V1-V3
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Roche454
Statistical Analysis
- Statistical test
- Mann-Whitney (Wilcoxon)
- 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
Signature 1
Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09
Source: Table 1
Description: sognatures of Health-associated and periodontitis-associated OTUs
Abundance in Group 1: increased abundance in periodontitis
| NCBI | Quality Control | Links |
|---|---|---|
| Selenomonas sputigena | ||
| Prevotellaceae | ||
| Streptococcus gordonii |
Revision editor(s): WikiWorks
Signature 2
Reviewed Marked as Reviewed by Fatima on 2021/07/28
Source: Table 1
Description: sognatures of Health-associated and periodontitis-associated OTUs
Abundance in Group 1: decreased abundance in periodontitis
Experiment 2
Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- type II diabetes mellitus adult onset diabetes,Adult-Onset Diabetes,adult-onset diabetes,Adult-Onset Diabetes Mellitus,diabetes mellitis type 2,diabetes mellitis type II,DIABETES MELLITUS TYPE 02,diabetes mellitus type 2,Diabetes Mellitus, Adult Onset,Diabetes Mellitus, Adult-Onset,Diabetes Mellitus, Ketosis Resistant,Diabetes Mellitus, Ketosis-Resistant,Diabetes Mellitus, Maturity Onset,Diabetes Mellitus, Maturity-Onset,Diabetes Mellitus, Non Insulin Dependent,Diabetes Mellitus, Non-Insulin-Dependent,Diabetes Mellitus, Noninsulin Dependent,diabetes mellitus, noninsulin-dependent,Diabetes Mellitus, Slow Onset,Diabetes Mellitus, Slow-Onset,Diabetes Mellitus, Stable,Diabetes Mellitus, Type 2,diabetes mellitus, type 2,diabetes mellitus, type 2, protection against,Diabetes Mellitus, Type II,Diabetes, Type 2,diabetes, type 2,insulin resistance, susceptibility to,Ketosis-Resistant Diabetes Mellitus,Maturity Onset Diabetes Mellitus,maturity-onset diabetes,Maturity-Onset Diabetes Mellitus,MODY,NIDDM,Non-Insulin Dependent Diabetes,non-insulin dependent diabetes,Non-Insulin Dependent Diabetes Mellitus,non-insulin dependent diabetes mellitus,non-insulin-dependent diabetes mellitus,noninsulin dependent diabetes,noninsulin-dependent diabetes mellitus,Slow-Onset Diabetes Mellitus,Stable Diabetes Mellitus,T2DM - Type 2 Diabetes mellitus,T2DM - type 2 diabetes mellitus,Type 2 Diabetes,type 2 diabetes,Type 2 Diabetes Mellitus,type 2 diabetes mellitus,Type 2 Diabetes Mellitus Non-Insulin Dependent,type 2 diabetes mellitus non-insulin dependent,Type II Diabetes,type II diabetes,type II diabetes mellitus
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Non-diabetic within negative periodontitis
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Diabetic
- Group 1 sample size Number of subjects in the case (exposed) group
- 8
Lab analysis
Statistical Analysis
Signature 1
Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09
Source: Table 2
Description: Signature OTUs associated with diabetic and non-diabetic samples.
Abundance in Group 1: increased abundance in Diabetic
| NCBI | Quality Control | Links |
|---|---|---|
| Neisseriales | ||
| Actinomycetales | ||
| Tannerella forsythia | ||
| Burkholderiales |
Revision editor(s): WikiWorks
Signature 2
Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09
Source: Table 2
Description: Signature OTUs associated with diabetic and non-diabetic samples.
Abundance in Group 1: decreased abundance in Diabetic
| NCBI | Quality Control | Links |
|---|---|---|
| Corynebacterium matruchotii | ||
| Hoylesella loescheii | ||
| Cardiobacterium valvarum | ||
| Neisseria flavescens | ||
| Capnocytophaga ochracea |
Revision editor(s): WikiWorks
Experiment 3
Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Non-diabetic within positive periodontitis
- Group 0 sample size Number of subjects in the control (unexposed) group
- 6
- Group 1 sample size Number of subjects in the case (exposed) group
- 12
Lab analysis
Statistical Analysis
Signature 1
Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09
Source: Table 2
Description: Signature OTUs associated with diabetic and non-diabetic samples.
Abundance in Group 1: increased abundance in Diabetic
| NCBI | Quality Control | Links |
|---|---|---|
| Propionibacteriaceae | ||
| Capnocytophaga sputigena |
Revision editor(s): WikiWorks
Experiment 4
Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- periodontitis chronic pericementitis,inflammation of periodontium,Pericementitides,Pericementitis,Periodontitides,periodontitis,Periodontitis (disorder),Periodontitis, NOS,periodontium inflammation,periodontosis
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- No Periodontitis within positive diabetic background only
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- periodontitis
- Group 0 sample size Number of subjects in the control (unexposed) group
- 8
Lab analysis
Statistical Analysis
Signature 1
Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09
Source: Table 1
Description: sognatures of Health-associated and periodontitis-associated OTUs
Abundance in Group 1: increased abundance in periodontitis
| NCBI | Quality Control | Links |
|---|---|---|
| Porphyromonas gingivalis | ||
| Leptotrichia | ||
| Treponema medium | ||
| Bacteroidales | ||
| Tannerella forsythia | ||
| Synergistaceae | ||
| Porphyromonas endodontalis | ||
| Filifactor alocis |
Revision editor(s): WikiWorks
Signature 2
Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09
Source: Table 1
Description: sognatures of Health-associated and periodontitis-associated OTUs
Abundance in Group 1: decreased abundance in periodontitis
| NCBI | Quality Control | Links |
|---|---|---|
| Neisseria elongata | ||
| Rothia dentocariosa | ||
| Veillonella | ||
| Haemophilus parainfluenzae | ||
| Neisseria |
Revision editor(s): WikiWorks
Experiment 5
Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- No Periodontitis within both positive and negative diabetic background
- Group 0 sample size Number of subjects in the control (unexposed) group
- 13
- Group 1 sample size Number of subjects in the case (exposed) group
- 18
Lab analysis
Statistical Analysis
Signature 1
Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09
Source: Table 1
Description: sognatures of Health-associated and periodontitis-associated OTUs
Abundance in Group 1: increased abundance in periodontitis
| NCBI | Quality Control | Links |
|---|---|---|
| Treponema denticola | ||
| Prevotella intermedia | ||
| Prevotellaceae |
Revision editor(s): WikiWorks
Signature 2
Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09
Source: Table 1
Description: sognatures of Health-associated and periodontitis-associated OTUs
Abundance in Group 1: decreased abundance in periodontitis
| NCBI | Quality Control | Links |
|---|---|---|
| Streptococcus infantis | ||
| Streptococcus gordonii | ||
| Actinomyces naeslundii |
Revision editor(s): WikiWorks
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