Classifying dementia progression using microbial profiling of saliva/Experiment 8

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Needs review

Curated date: 2024/12/16

Curator:

Revision editor(s):

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
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

Needs review

Curated date: 2024/12/16

Curator: AaishahM

Revision editor(s): AaishahM, WikiWorks

Source: Figure S2C + Figure S2D

Description: Significantly different bacterial taxa in MCI and CNh

Abundance in Group 1: increased abundance in

NCBI Quality ControlLinks
Leptotrichia
Leptotrichiaceae
Fusobacteriales
Streptococcus mutans
Streptococcus troglodytae
Leptotrichia wadei
Fusobacteriia

Revision editor(s): AaishahM, WikiWorks

Signature 2

Needs review

Curated date: 2024/12/16

Curator: AaishahM

Revision editor(s): AaishahM, WikiWorks

Source: Figure S2C + Figure S2D

Description: Significantly different bacterial taxa in MCI and CNh

Abundance in Group 1: decreased abundance in

NCBI Quality ControlLinks
Synergistales
Synergistaceae
Spirochaetaceae
Treponema
Treponema lecithinolyticum
Dialister
Erysipelothrix
Filifactor
Spirochaetia
Spirochaetales
Alloprevotella tannerae
Prevotella intermedia
Dialister invisus
Prevotella nigrescens
Synergistia
Synergistota
Synechococcales
Bacteroides xylanisolvens
Streptococcus intermedius
Filifactor villosus
Limosilactobacillus fermentum

Revision editor(s): AaishahM, WikiWorks