The blood pressure lowering effect of beetroot juice is impaired in periodontitis and recovered after periodontal treatment
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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
- Mexico
- 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
- PeriodontitisPeriodontitis
- 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
- Periodontitis Baseline (BL)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Periodontitis before any periodontal treatment
- 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
- 13
- 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
- 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).
- log transformation
- Statistical test
- ANCOM-BC
- 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)?
- Yes
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- increased
- Richness Number of species
- increased
Signature 1
Source: Supplementary Figure 2A and Figure 6A
Description: Bar graphs show comparisons between healthy individuals (H) and periodontitis patients at baseline (BL) in subgingival plaque
Abundance in Group 1: decreased abundance in Periodontitis Baseline (BL)
Signature 2
Source: Supplementary Figure 2A and Figure 6A
Description: Bar graphs show comparisons between healthy individuals (H) and periodontitis patients at baseline (BL) in subgingival plaque
Abundance in Group 1: increased abundance in Periodontitis Baseline (BL)
Experiment 2
Curated date: 2025/01/29
Curator:
Revision editor(s):
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Periodontitis BL
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Periodontitis D70
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Periodontitis after 70 days of periodontal treatment
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Richness Number of species
- decreased
Signature 1
Source: Supplementary Figure 2B and Figure 6B
Description: Bar graphs show comparisons between D70 and BL in subgingival plaque.
Abundance in Group 1: increased abundance in
Signature 2
Source: Supplementary Figure 2B and Figure 6B
Description: Bar graphs show comparisons between D70 and BL in subgingival plaque
Abundance in Group 1: decreased abundance in
NCBI | Quality Control | Links |
---|---|---|
Filifactor | ||
Fretibacterium | ||
Peptostreptococcus | ||
Porphyromonas | ||
Tannerella forsythia | ||
unclassified Fretibacterium | ||
Rickenellaceae RC9Rickenellaceae RC9 |
Experiment 3
Curated date: 2025/01/31
Curator:
Revision editor(s):
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Tongue Glossus,Tongue,tongue
- 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
- Periodontitis Baseline (BL)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Periodontitis before any periodontal treatment
- Group 1 sample size Number of subjects in the case (exposed) group
- 14
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- increased
- Richness Number of species
- increased
Signature 1
Source: Supplementary Figure 2C and Figure 6C
Description: Bar graphs show comparisons between H and BL in tongue coating.
Abundance in Group 1: decreased abundance in
NCBI | Quality Control | Links |
---|---|---|
Actinobacillus | ||
Cardiobacterium | ||
Gemella | ||
Gemella sanguinis | ||
Haemophilus | ||
Rothia dentocariosa | ||
Veillonella rogosae | ||
unclassified Veillonella |
Experiment 4
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Periodontitis Baseline (D70)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Periodontitis after 70 days of periodontal treatment
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- increased
- Richness Number of species
- increased
Experiment 5
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Periodontitis BL
- Group 0 sample size Number of subjects in the control (unexposed) group
- 14
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Richness Number of species
- unchanged