Profiles of subgingival microbiomes and gingival crevicular metabolic signatures in patients with amnestic mild cognitive impairment and Alzheimer's disease/Experiment 1

Needs review

Curated date: 2024/03/23

Curator: Aananditaa

Revision editor(s): Aananditaa

Subjects

Location of subjects: China

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: Lower first secondary molar tooth , Upper first secondary molar tooth , Lower first secondary premolar tooth , Upper first secondary premolar tooth , Central incisor tooth Lower first permanent molar tooth,Mandibular first secondary molar tooth,Lower first secondary molar tooth,lower first secondary molar tooth,Maxillary first secondary molar tooth,Upper first permanent molar tooth,Upper first secondary molar tooth,upper first secondary molar tooth,Lower first permanent premolar tooth,Mandibular first secondary premolar tooth,Permanent first lower premolar tooth,Secondary first lower premolar tooth,Lower first secondary premolar tooth,lower first secondary premolar tooth,Maxillary first secondary premolar tooth,Permanent first upper premolar tooth,Secondary first upper premolar tooth,Upper first permanent premolar tooth,Upper first secondary premolar tooth,upper first secondary premolar tooth,Central incisor,Central incisor tooth,central incisor tooth

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 people

Group 1 name Corresponds to the case (exposed) group for case-control studies: Patients with AD dementia

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Patients with AD dementia who were diagnosed following the National Institute on Aging and Alzheimer’s Association guidelines

Group 0 sample size Number of subjects in the control (unexposed) group: 32

Group 1 sample size Number of subjects in the case (exposed) group: 32

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: Not specified

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Non-quantitative PCR, PacBio RS

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)?: Yes

LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool: 2

Alpha Diversity

Pielou Quantifies how equal the community is numerically: unchanged

Shannon Estimator of species richness and species evenness: more weight on species richness: unchanged

Chao1 Abundance-based estimator of species richness: unchanged

Simpson Estimator of species richness and species evenness: more weight on species evenness: unchanged

Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample: unchanged

Signature 1

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Curated date: 2024/03/23

Curator: Aananditaa

Revision editor(s): Aananditaa

Source: Figure 3

Description: Relative abundances of candidate microbial biomarkers. Taxon abundances at the species level were statistically compared in group 0 and group 1

Abundance in Group 1: increased abundance in Patients with AD dementia