Alteration of salivary microbiome in periodontitis with or without type-2 diabetes mellitus and metformin treatment
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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.
Authors
Sun X, Li M, Xia L, Fang Z, Yu S, Gao J, Feng Q, Yang P
Journal
Scientific reports
Year
2020
We aimed to explore the effects of type-2 diabetes mellitus (T2DM) and hypoglycemic therapy on the salivary microbiome in periodontitis patients and identify the potential salivary micro-biomarker for the early warning of T2DM. Saliva samples were collected from healthy individuals (Health), periodontitis patients (P), T2DM patients, periodontitis patients with T2DM (DAP), and DAP patients treated with Metformin (Met). Samples were determined by16S rRNA gene sequencing. 29 phyla, 322 genera, and 333 species of salivary microbiome were annotated. Compared to the Health group, the P and DAP group showed a significantly higher diversity of saliva microbiota, while the T2DM and Met group had no significant difference in microbial abundance but showed a trend of increasing diversity. Other than well-known periodontitis-inducing pathogens, the proportion of Prevotella copri, Alloprevotella rava, and Ralstonia pickettii, etc. were also significantly increased in periodontitis patients with or without T2DM. After effective glycemic control, the abundance of Prevotella copri, Alloprevotella rava, Ralstonia pickettii, etc. decreased in periodontitis patients with companion T2DM. The accuracies of the classification models in differentiating Health-vs.-P, DAP-vs.-P, and T2DM-vs.-P were 100%, 96.3%, and 98.1%, respectively. Hypoglycemic therapy could reconstruct the saliva microbiota and hence improve the localized conditions of diabetes patients with periodontitis.
Experiment 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/06/22
Curated date: 2021/06/17
Curator: Madhubani Dey
Revision editor(s): Madhubani Dey, WikiWorks, Peace Sandy, Davvve
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
- Saliva Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva,saliva
- 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
- Healthy controls group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Individuals diagnosed with Periodontitis group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Individuals with Peridontitis; Periodontal disease was assessed by determining the PD, CAL, BI, GI, and PLI, which were then measured at six sites (i.e., mesiobuccal, buccal, distobuccal, distolingual, lingual, and mesiolingual) according to the Community Periodontal Index by an experienced dentist. Periodontitis patients had a PD of ≥ 5 mm and CAL of ≥ 3 mm.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 27
- Group 1 sample size Number of subjects in the case (exposed) group
- 31
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- patients treated with antibiotics within 3 months or those that received periodontal treatment within 6 months.
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V4
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/06/22
Source: Figure 3, text
Description: Increased abundance of bacterial species in individuals with Periodontitis as compared to healthy controls
Abundance in Group 1: increased abundance in Individuals diagnosed with Periodontitis group
| NCBI | Quality Control | Links |
|---|---|---|
| Porphyromonas endodontalis | ||
| Segatella copri | ||
| Treponema medium | ||
| Alloprevotella rava | ||
| unclassified Sutterella | ||
| Treponema amylovorum | ||
| Faecalibacterium prausnitzii |
Revision editor(s): Madhubani Dey, Claregrieve1
Experiment 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/06/22
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Individuals diagnosed with Periodontitis and Type 2 Diabetes Mellitus (DAP)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Individuals diagnosed with Periodontitis and Type 2 Diabetes Mellitus (DAP); Patients were classified into the DAP group when both periodontitis and T2DM were present.
- Group 1 sample size Number of subjects in the case (exposed) group
- 46
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- patients treated with antibiotics within 3 months or those that received periodontal treatment within 6 months
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- Not specified
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/06/22
Source: Supplementary Fig 3a
Description: Increased abundance of bacterial communities in individuals in DAP group compared to healthy controls
Abundance in Group 1: increased abundance in Individuals diagnosed with Periodontitis and Type 2 Diabetes Mellitus (DAP)
| NCBI | Quality Control | Links |
|---|---|---|
| Alloprevotella rava | ||
| Segatella copri | ||
| Ralstonia pickettii | ||
| Sutterella stercoricanis |
Revision editor(s): Madhubani Dey
Experiment 3
Reviewed Marked as Reviewed by Claregrieve1 on 2022/06/22
Curated date: 2021/06/17
Curator: Madhubani Dey
Revision editor(s): Madhubani Dey, WikiWorks, Peace Sandy
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 1 name Corresponds to the case (exposed) group for case-control studies
- Individuals diagnosed with Type 2 Diabetes Mellitus
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Individuals with Type 2 Diabetes; Type 2 Diabetes determined by a fasting blood sugar of > 7.0 mmol/L and an HbA1c concentration of > 7%, as stated by the American Diabetes Association in 201834
- Group 1 sample size Number of subjects in the case (exposed) group
- 9
- 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
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Experiment 4
Reviewed Marked as Reviewed by Claregrieve1 on 2022/06/22
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 1 name Corresponds to the case (exposed) group for case-control studies
- Individuals diagnosed with both Periodontitis and Type 2 Diabetes and treated with metformin (Met group)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with both Periodontitis and Type 2 Diabetes who received metformin for at least 6 months and achieved glycemic control (HbA1c < 6.5%, without any companion diseases), were classified into the Met group
- Group 1 sample size Number of subjects in the case (exposed) group
- 20
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- patients treated with antibiotics within 3 months or those that received periodontal treatment within 6 months
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- Not specified
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/06/22
Source: Supplementary Fig 3b
Description: Increased abundance of microbial communities in individuals in Met group compared to the controls
Abundance in Group 1: increased abundance in Individuals diagnosed with both Periodontitis and Type 2 Diabetes and treated with metformin (Met group)
Revision editor(s): Madhubani Dey, Claregrieve1
Experiment 5
Reviewed Marked as Reviewed by Claregrieve1 on 2022/06/22
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Individuals diagnosed with Periodontitis and Type 2 Diabetes Mellitus (DAP)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 46
Lab analysis
Statistical Analysis
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/06/22
Source: Figure 5c, 5d
Description: Decreased abundance of bacterial communities in Met group compared to DAP group
Abundance in Group 1: decreased abundance in Individuals diagnosed with both Periodontitis and Type 2 Diabetes and treated with metformin (Met group)
| NCBI | Quality Control | Links |
|---|---|---|
| Alloprevotella rava | ||
| Phyllobacterium myrsinacearum | ||
| Segatella copri | ||
| Ralstonia pickettii | ||
| Sutterella stercoricanis |
Revision editor(s): Madhubani Dey
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/06/22
Source: Figure 5c, 5d
Description: Increased abundance of bacterial communities in individuals of Met group compared to DAP group
Abundance in Group 1: increased abundance in Individuals diagnosed with both Periodontitis and Type 2 Diabetes and treated with metformin (Met group)
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotella jejuni | ||
| Streptobacillus moniliformis | ||
| Streptococcus mutans |
Revision editor(s): Madhubani Dey
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