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
- Saliva Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva,saliva
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Alzheimer's disease [X]Dementia in Alzheimer's disease,[X]Dementia in Alzheimer's disease (disorder),AD,AD - Alzheimer's disease,Alzheimer Dementia,Alzheimer dementia,Alzheimer Dementia, Presenile,ALZHEIMER DIS,Alzheimer Disease,Alzheimer disease,Alzheimer disease, familial,Alzheimer Type Dementia,Alzheimer's,Alzheimer's Dementia,Alzheimer's dementia,Alzheimer's disease,Alzheimer's disease (disorder),Alzheimer's disease, NOS,Alzheimers,Alzheimers Dementia,Alzheimers dementia,ALZHEIMERS DIS,Alzheimers disease,DAT - Dementia Alzheimer's type,Dementia in Alzheimer's disease,Dementia in Alzheimer's disease (disorder),Dementia in Alzheimer's disease, unspecified (disorder),Dementia of the Alzheimer's type,Dementia, Alzheimer Type,Dementia, Presenile,Dementia, Presenile Alzheimer,Disease, Alzheimer,Disease, Alzheimer's,Presenile Alzheimer Dementia,sporadic Alzheimer's disease,alzheimer'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 |
Revision editor(s): AaishahM
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 |
Revision editor(s): AaishahM
