Classifying dementia progression using microbial profiling of saliva/Experiment 9
From BugSigDB
Subjects
- Location of subjects
- Switzerland
- 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
- SalivaSaliva
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Alzheimer's diseaseAlzheimer's disease
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Cognitively Normal Healthy (CNh)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Alzheimer's Disease (AD) patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with Alzheimer's Disease
- 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
- 17
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
- LEfSe
- 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
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2.0
Signature 1
Source: Figure S2E + Figure S2F
Description: Significantly different bacterial taxa in AD patients and CNh
Abundance in Group 1: increased abundance in Alzheimer's Disease (AD) patients
| NCBI | Quality Control | Links |
|---|---|---|
| Aminiphilus | ||
| Calothrix | ||
| Kocuria | ||
| Cyanophyceae | ||
| Aminiphilus circumscriptus | ||
| Kocuria rosea | ||
| Streptococcus sobrinus |
Signature 2
Source: Figure S2E + Figure S2F
Description: Significantly different bacterial taxa in AD patients and CNh
Abundance in Group 1: decreased abundance in Alzheimer's Disease (AD) patients
| NCBI | Quality Control | Links |
|---|---|---|
| Spirochaetaceae | ||
| Treponema | ||
| Peptoniphilus methioninivorax | ||
| Spirochaetia | ||
| Spirochaetales | ||
| Alloprevotella tannerae | ||
| Filifactor villosus |
