Oral and gut microbial profiling in periodontitis and Parkinson's disease/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Svetlana up on 2024-11-20
Subjects
- Location of subjects
- Turkey
- 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 (HC)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Periodontitis group (P)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants in this group were diagnosed with Stage III, Grade B periodontitis.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 17
- Group 1 sample size Number of subjects in the case (exposed) group
- 18
- 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
- Illumina
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- centered log-ratio
- Statistical test
- ANCOM
- 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
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-11-20
Source: Figure 4 and Figure 6
Description: Differential abundance in the oral microbiome profiles of the healthy control, Parkinson’s and non-Parkinson’s groups.
Abundance in Group 1: increased abundance in Periodontitis group (P)
Revision editor(s): Aleru Divine
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-11-20
Source: Figure 4 and Figure 6
Description: Differential abundance in the oral microbiome profiles of the healthy control, Parkinson’s and non-Parkinson’s groups.
Abundance in Group 1: decreased abundance in Periodontitis group (P)
| NCBI | Quality Control | Links |
|---|---|---|
| Gemella sanguinis | ||
| Prevotella melaninogenica | ||
| Prevotella pallens | ||
| Prevotellaceae bacterium | ||
| Rothia dentocariosa | ||
| Neisseria sp. |
Revision editor(s): Aleru Divine
