Investigation of the effect of type 2 diabetes mellitus on subgingival plaque microbiota by high-throughput 16S rDNA pyrosequencing
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Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Experiment 1
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
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
Source: Table 1
Description: sognatures of Health-associated and periodontitis-associated OTUs
Abundance in Group 1: decreased abundance in periodontitis
Experiment 2
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
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 |
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Neisseriales | ||
Actinomycetales | ||
Tannerella forsythia | ||
Burkholderiales |
Revision editor(s): WikiWorks
Signature 2
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
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
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
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
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
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
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
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
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