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

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

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 ControlLinks
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 ControlLinks
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


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 ControlLinks
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 ControlLinks
Capnocytophaga ochracea
Cardiobacterium valvarum
Corynebacterium matruchotii
Hoylesella loescheii
Neisseria flavescens

Revision editor(s): WikiWorks, ChiomaBlessing

Experiment 3


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 ControlLinks
Capnocytophaga sputigena
Propionibacteriaceae

Revision editor(s): WikiWorks, ChiomaBlessing

Experiment 4


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
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 ControlLinks
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 ControlLinks
Haemophilus parainfluenzae
Neisseria
Neisseria elongata
Rothia dentocariosa
Veillonella

Revision editor(s): WikiWorks, ChiomaBlessing

Experiment 5


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 ControlLinks
Prevotella intermedia
Prevotellaceae
Treponema denticola

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 both the diabetes-positive and diabetes-negative background

Abundance in Group 1: decreased abundance in periodontitis

NCBI Quality ControlLinks
Actinomyces naeslundii
Streptococcus gordonii
Streptococcus infantis

Revision editor(s): WikiWorks, ChiomaBlessing