Investigation of the effect of type 2 diabetes mellitus on subgingival plaque microbiota by high-throughput 16S rDNA pyrosequencing/Experiment 1

From BugSigDB


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