Investigation of the effect of type 2 diabetes mellitus on subgingival plaque microbiota by high-throughput 16S rDNA pyrosequencing

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Claregrieve1, WikiWorks, Peace Sandy

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: Subgingival dental plaque Subgingival plaque,Subgingival dental 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,Periodontitis

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

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).: relative abundances

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

Curated date: 2021/01/10

Curator: Yaseen Javaid

Revision editor(s): WikiWorks, ChiomaBlessing

Source: Table 1

Description: Significant differential abundant bacteria in periodontitis group VS healthy group within the diabetes-negative group

Abundance in Group 1: increased abundance in periodontitis

NCBI	Quality Control	Links
Prevotellaceae
Selenomonas sputigena
Streptococcus gordonii

Revision editor(s): WikiWorks, ChiomaBlessing

Signature 2

Reviewed Marked as Reviewed by Fatima on 2021/07/28

Curated date: 2021/01/10

Curator: Yaseen Javaid

Revision editor(s): Fatima, WikiWorks, ChiomaBlessing

Source: Table 1

Description: Significant differential abundant bacteria in periodontitis group VS healthy group within the diabetes-negative group

Abundance in Group 1: decreased abundance in periodontitis

NCBI	Quality Control	Links
Aggregatibacter
Capnocytophaga sputigena
Cardiobacterium hominis
Cardiobacterium valvarum
Corynebacterium matruchotii
Hoylesella loescheii
Leptotrichia
Leptotrichiaceae
Neisseria flavescens
Porphyromonas sp.
Propionibacteriaceae
Selenomonas noxia

Revision editor(s): Fatima, WikiWorks, ChiomaBlessing

Experiment 2

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Claregrieve1, WikiWorks, ChiomaBlessing

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,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

Curated date: 2021/01/10

Curator: Yaseen Javaid

Revision editor(s): WikiWorks, ChiomaBlessing

Source: Table 2

Description: Significant differential abundant bacteria in diabetic VS non-diabetic group within periodontitis-negative samples

Abundance in Group 1: increased abundance in Diabetic

NCBI	Quality Control	Links
Actinomycetales
Burkholderiales
Neisseriales
Tannerella forsythia

Revision editor(s): WikiWorks, ChiomaBlessing

Signature 2

Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09

Curated date: 2021/01/10

Curator: Yaseen Javaid

Revision editor(s): WikiWorks, ChiomaBlessing

Source: Table 2

Description: Significant differential abundant bacteria in diabetic VS non-diabetic group within periodontitis-negative samples

Abundance in Group 1: decreased abundance in Diabetic

NCBI	Quality Control	Links
Capnocytophaga ochracea
Cardiobacterium valvarum
Corynebacterium matruchotii
Hoylesella loescheii
Neisseria flavescens

Revision editor(s): WikiWorks, ChiomaBlessing

Experiment 3

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Claregrieve1, WikiWorks, ChiomaBlessing

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

Curated date: 2021/01/10

Curator: Shaimaa Elsafoury

Revision editor(s): WikiWorks, ChiomaBlessing

Source: Table 2

Description: Significant differential abundant bacteria in diabetic VS non-diabetic group within periodontitis-positive samples

Abundance in Group 1: increased abundance in Diabetic

NCBI	Quality Control	Links
Capnocytophaga sputigena
Propionibacteriaceae

Revision editor(s): WikiWorks, ChiomaBlessing

Experiment 4

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, ChiomaBlessing, Claregrieve1

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,Periodontitis

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

Curated date: 2021/01/10

Curator: Shaimaa Elsafoury

Revision editor(s): WikiWorks, ChiomaBlessing

Source: Table 1

Description: Significant differential abundant bacteria in periodontitis group VS healthy group within the diabetes-positive background

Abundance in Group 1: increased abundance in periodontitis

NCBI	Quality Control	Links
Bacteroidales
Filifactor alocis
Leptotrichia
Porphyromonas endodontalis
Porphyromonas gingivalis
Synergistaceae
Tannerella forsythia
Treponema medium

Revision editor(s): WikiWorks, ChiomaBlessing

Signature 2

Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09

Curated date: 2021/01/10

Curator: Shaimaa Elsafoury

Revision editor(s): WikiWorks, ChiomaBlessing

Source: Table 1

Description: Significant differential abundant bacteria in periodontitis group VS healthy group within the diabetes-positive background

Abundance in Group 1: decreased abundance in periodontitis

NCBI	Quality Control	Links
Haemophilus parainfluenzae
Neisseria
Neisseria elongata
Rothia dentocariosa
Veillonella

Revision editor(s): WikiWorks, ChiomaBlessing

Experiment 5

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Claregrieve1, WikiWorks, ChiomaBlessing

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

Curated date: 2021/01/10

Curator: Shaimaa Elsafoury

Revision editor(s): WikiWorks, ChiomaBlessing

Source: Table 1

Description: Significant differential abundant bacteria in periodontitis group VS healthy group within both the diabetes-positive and diabetes-negative background

Abundance in Group 1: increased abundance in periodontitis

NCBI	Quality Control	Links
Prevotella intermedia
Prevotellaceae
Treponema denticola

Revision editor(s): WikiWorks, ChiomaBlessing

Signature 2