Stratification of the Gut Microbiota Composition Landscape across the Alzheimer's Disease Continuum in a Turkish Cohort/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Peace Sandy on 2024-2-13
Curated date: 2023/09/27
Curator: Janezhang
Revision editor(s): Janezhang, Chikamso, Joan Chuks, Peace Sandy
Subjects
- Location of subjects
- Turkey
- 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
- Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces
- 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
- Non-demented Controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Alzheimer's disease patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with Alzheimer's disease, mostly exhibiting mild to very mild dementia
- Group 0 sample size Number of subjects in the control (unexposed) group
- 51
- Group 1 sample size Number of subjects in the case (exposed) group
- 47
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 1 month
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
- Kruskall-Wallis
- 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
- Matched on Factors on which subjects have been matched on in a case-control study
- diet
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
Signature 1
Reviewed Marked as Reviewed by Peace Sandy on 2024-2-13
Source: Supplementary Table S2A and Supplementary Table S2CC
Description: Differentially Abundant Genus level Taxa Between Alzheimer's disease Patients and Non-demented control groups Detected by Limma-Voom Model (Age and Sex Adjusted)
Abundance in Group 1: increased abundance in Alzheimer's disease patients
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Collinsella | ||
| Escherichia/Shigella sp. | ||
| Odoribacter | ||
| Oscillospiraceae | ||
| Parabacteroides | ||
| Parabacteroides sp. | ||
| Paraprevotella | ||
| Prevotella | ||
| unclassified Erysipelotrichaceae |
Revision editor(s): Joan Chuks, Peace Sandy
Signature 2
Reviewed Marked as Reviewed by Peace Sandy on 2024-2-13
Curated date: 2023/10/24
Curator: Joan Chuks
Revision editor(s): Joan Chuks, Iram jamshed, Peace Sandy
Source: Supplementary Table S2A and Supplementary Table S2CC
Description: Differentially Abundant Genus level Taxa Between Alzheimer's disease Patients and Non-demented control groups Detected by Limma-Voom Model (Age and Sex Adjusted)
Abundance in Group 1: decreased abundance in Alzheimer's disease patients
| NCBI | Quality Control | Links |
|---|---|---|
| Butyricicoccus | ||
| Erysipelotrichaceae | ||
| Faecalibacterium | ||
| Lachnospiraceae | ||
| Parasutterella | ||
| Prevotella | ||
| Roseburia | ||
| unclassified Mollicutes |
Revision editor(s): Joan Chuks, Iram jamshed, Peace Sandy
