Altered microbiomes distinguish Alzheimer's disease from amnestic mild cognitive impairment and health in a Chinese cohort
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Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Experiment 1
Subjects
- Location of subjects
- China
- Host species Species from which microbiome was sampled (if applicable)
- 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
- 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
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- healthy controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Alzheimer’s disease
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with dementia stage of alzheimer's disease.
- 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
- 33
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Two months
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
- 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
- Matched on Factors on which subjects have been matched on in a case-control study
- age, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Richness Number of species
- unchanged
Signature 1
Source: Figure 2
Description: Differential microbial abundance between Alzheimers patients and healthy controls
Abundance in Group 1: decreased abundance in Alzheimer’s disease
Revision editor(s): Sophy, Aiyshaaaa, Claregrieve1
Signature 2
Source: Figure 2
Description: Differential microbial abundance between Alzheimers patients and healthy controls
Abundance in Group 1: increased abundance in Alzheimer’s disease
NCBI | Quality Control | Links |
---|---|---|
Gammaproteobacteria | ||
Pseudomonadota | ||
Enterobacterales | ||
Enterobacteriaceae |
Revision editor(s): Sophy, Aiyshaaaa, Claregrieve1
Experiment 2
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- aMCI patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with amnestic mild cognitive impairment of alzheimer's disease.
- Group 1 sample size Number of subjects in the case (exposed) group
- 32
Lab analysis
Statistical Analysis
Alpha Diversity
- 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
- Richness Number of species
- unchanged
Signature 1
Source: Figure 2
Description: Differential microbial abundance between aMCI patients and healthy controls
Abundance in Group 1: decreased abundance in aMCI patients
NCBI | Quality Control | Links |
---|---|---|
Clostridiaceae | ||
Lachnospiraceae | ||
Blautia |
Revision editor(s): Sophy, Claregrieve1
Signature 2
Source: Figure 2
Description: Differential microbial abundance between aMCI patients and healthy controls
Abundance in Group 1: increased abundance in aMCI patients
NCBI | Quality Control | Links |
---|---|---|
Veillonellaceae | ||
Bacteroidia | ||
Bacteroidales | ||
Bacteroidaceae | ||
Bacteroides |
Revision editor(s): Sophy, Claregrieve1
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Alzheimers patients in dementia stage
- Group 0 sample size Number of subjects in the control (unexposed) group
- 33
Lab analysis
Statistical Analysis
Alpha Diversity
- 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
- Richness Number of species
- unchanged
Signature 1
Source: Figure 2
Description: Differential microbial abundance between Alzheimers patients with dementia and aMCI patients
Abundance in Group 1: decreased abundance in aMCI patients
NCBI | Quality Control | Links |
---|---|---|
Enterobacterales | ||
Enterobacteriaceae | ||
Gammaproteobacteria | ||
Pseudomonadota |
Revision editor(s): Sophy, Aiyshaaaa, Claregrieve1
Signature 2
Source: Figure 2
Description: Differential microbial abundance between Alzheimers patients with dementia and aMCI patients
Abundance in Group 1: increased abundance in aMCI patients
NCBI | Quality Control | Links |
---|---|---|
Clostridiaceae | ||
Ruminococcus | ||
Clostridia | ||
Bacteroidia | ||
Clostridiales bacterium | ||
Bacteroidales | ||
Oscillospiraceae | ||
Bacteroidaceae | ||
Bacteroides |
Revision editor(s): Sophy, Claregrieve1