Classifying dementia progression using microbial profiling of saliva
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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.
URI
Authors
Bathini P, Foucras S, Dupanloup I, Imeri H, Perna A, Berruex JL, Doucey MA, Annoni JM, Auber Alberi L
Journal
Alzheimer's & dementia (Amsterdam, Netherlands)
Year
2020
Keywords:
Alzheimer's disease, cytokines, olfaction, oral microbiome
INTRODUCTION: There is increasing evidence linking periodontal infections to Alzheimer's disease (AD). Saliva sampling can reveal information about the host and pathogen interactions that can inform about physiological and pathological brain states. METHODS: A cross-sectional cohort of age-matched participants (78) was segmented according to their chemosensory (University of Pennsylvania Smell Identification Test; UPSIT) and cognitive scores (Mini-Mental State Exam; MMSE and clinical dementia rating; CDR). Mid-morning saliva was sampled from each participant and processed for microbiome composition and cytokine analysis. Linear discriminant analysis (LDA) was used to unravel specific changes in microbial and immunological signatures and logistic regression analysis (LRA) was employed to identify taxa that varied in abundance among patient groups. RESULTS: Using olfaction we distinguish in the cognitively normal population a segment with high chemosensory scores (CNh, 27) and another segment with chemosensory scores (CNr, 16) as low as mild cognitive impairment (MCI, 21) but higher than the AD group (17). We could identify stage-specific microbial signatures changes but no clearly distinct cytokine profiles. Periodontal pathogen species as Filifactor villosus decline with the increasing severity of AD, whereas opportunistic oral bacteria such as Leptotrichia wadei show a significant enrichment in MCI. CONCLUSIONS: The salivary microbiome indicates stage-dependent changes in oral bacteria favoring opportunistic species at the expense of periodontal bacteria, whereas the inflammatory profiles remain mainly unchanged in the sampled population.
Experiment 2
Differences from previous experiment shown
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
- Mild Cognitive Impairment (MCI)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with Mild Cognitive Impairment (MCI)
- 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
- 21
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
- ANOVA
- 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
Experiment 3
Differences from previous experiment shown
Subjects
- 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 1 sample size Number of subjects in the case (exposed) group
- 17
Lab analysis
Statistical Analysis
Experiment 4
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Cognitively Normal at risk (CNr)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Cognitively normal people with hyposmia
- Group 1 sample size Number of subjects in the case (exposed) group
- 15
Signature 1
Source: Figure 1D + Figure 1E
Description: Significantly different bacterial taxa in CNr and CNh
Abundance in Group 1: decreased abundance in Cognitively Normal at risk (CNr)
| NCBI | Quality Control | Links |
|---|---|---|
| Alloprevotella tannerae | ||
| Porphyromonas gingivalis | ||
| Filifactor alocis | ||
| Cardiobacterium valvarum |
Experiment 5
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Mild Cognitive Impairment (MCI)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with Mild Cognitive Impairment (MCI)
- Group 1 sample size Number of subjects in the case (exposed) group
- 21
Lab analysis
Statistical Analysis
Experiment 7
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Cognitively Normal at risk (CNr)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Cognitively normal people with hyposmia
- Group 1 sample size Number of subjects in the case (exposed) group
- 15
Lab analysis
Statistical Analysis
- Statistical test
- LEfSe
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2.0
Experiment 9
Differences from previous experiment shown
Subjects
- 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 1 sample size Number of subjects in the case (exposed) group
- 17
Lab analysis
Statistical Analysis
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 |
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