Gut Microbiome Alterations Precede Cerebral Amyloidosis and Microglial Pathology in a Mouse Model of Alzheimer's Disease

Study information

EditHistoryDelete

Mark reviewed

Your review change was submittedAdd a new Experiment

• Quality control
  • Retracted paper
  • Contamination issues suspected
  • Batch effect issues suspected
  • Uncontrolled confounding suspected
  • Results are suspect (various reasons)
  • Apply tags

    Tags applied

Needs review

study design

time series / longitudinal observational
laboratory experiment

Citation

PMID PubMed identifier for scientific articles.

32596386

DOI Digital object identifier for electronic documents.

10.1155/2020/8456596

URI

Authors

Chen Y, Fang L, Chen S, Zhou H, Fan Y, Lin L, Li J, Xu J, Chen Y, Ma Y, Chen Y

Journal

BioMed research international

Year

2020

Emerging evidence suggests that the gut microbiome actively regulates cognitive functions and that gut microbiome imbalance is associated with Alzheimer's disease (AD), the most prevalent neurodegenerative disorder. However, the changes in gut microbiome composition in AD and their association with disease pathology, especially in the early stages, are unclear. Here, we compared the profiles of gut microbiota between APP/PS1 transgenic mice (an AD mouse model) and their wild-type littermates at different ages by amplicon-based sequencing of 16S ribosomal RNA genes. Microbiota composition started diverging between the APP/PS1 and wild-type mice at young ages (i.e., 1-3 months), before obvious amyloid deposition and plaque-localized microglial activation in the cerebral cortex in APP/PS1 mice. At later ages (i.e., 6 and 9 months), there were distinct changes in the abundance of inflammation-related bacterial taxa including Escherichia-Shigella, Desulfovibrio, Akkermansia, and Blautia in APP/PS1 mice. These findings suggest that gut microbiota alterations precede the development of key pathological features of AD, including amyloidosis and plaque-localized neuroinflammation. Thus, the investigation of gut microbiota might provide new avenues for developing diagnostic biomarkers and therapeutic targets for AD.

Experiment 1

EditHistoryDelete

Mark reviewed

Your review change was submittedDuplicate this ExperimentAdd a new Signature

Needs review

Curated date: 2024/09/19

Curator: AaishahM

Revision editor(s): AaishahM

Subjects

Location of subjects

China

Host species Species from which microbiome was sampled. Contact us to have more species added.

Mus musculus

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

Wild-type (WT)

Group 1 name Corresponds to the case (exposed) group for case-control studies

APP/PS1

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

Alzheimer's Disease (AD) mouse model 1-month-old

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

14

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

2.5

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

EditHistoryDelete

Mark reviewed

Your review change was submitted

Needs review

Curated date: 2024/10/06

Curator: AaishahM

Revision editor(s): AaishahM

Source: Table S2

Description: Significantly different taxa between WT and AD (APP/PS1) mice

Abundance in Group 1: increased abundance in APP/PS1

NCBI	Quality Control	Links
Enterobacteriaceae

Revision editor(s): AaishahM

Experiment 2

EditHistoryDelete

Mark reviewed

Your review change was submittedDuplicate this ExperimentAdd a new Signature

Needs review

Curated date: 2024/10/06

Curator: AaishahM

Revision editor(s): AaishahM

Differences from previous experiment shown

Subjects

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

Alzheimer's Disease (AD) mouse model 2-month-old

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

17

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

24

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

increased

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

unchanged

Richness Number of species

unchanged

Signature 1

EditHistoryDelete

Mark reviewed

Your review change was submitted

Needs review

Curated date: 2024/10/06

Curator: AaishahM

Revision editor(s): AaishahM

Source: Table S2

Description: Significantly different taxa between WT and AD (APP/PS1) mice

Abundance in Group 1: increased abundance in APP/PS1

NCBI	Quality Control	Links
Actinomycetota
Akkermansia
Allobaculum
Alloprevotella
Bifidobacterium
Erysipelotrichaceae
Prevotellaceae
Verrucomicrobiaceae
Verrucomicrobiota
Thomasclavelia

Revision editor(s): AaishahM

Experiment 3

EditHistoryDelete

Mark reviewed

Your review change was submittedDuplicate this ExperimentAdd a new Signature

Needs review

Curated date: 2024/10/07

Curator: AaishahM

Revision editor(s): AaishahM

Differences from previous experiment shown

Subjects

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

Alzheimer's Disease (AD) mouse model 3-month-old

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

Experiment 4

EditHistoryDelete

Mark reviewed

Your review change was submittedDuplicate this ExperimentAdd a new Signature

Needs review

Curated date: 2024/10/09

Curator: AaishahM

Revision editor(s): AaishahM

Differences from previous experiment shown

Subjects

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

Alzheimer's Disease (AD) mouse model 6-month-old

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

31

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

34

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

EditHistoryDelete

Mark reviewed

Your review change was submitted

Needs review

Curated date: 2024/10/09

Curator: AaishahM

Revision editor(s): AaishahM

Source: Table S2

Description: Significantly different taxa between WT and AD (APP/PS1) mice

Abundance in Group 1: increased abundance in APP/PS1

NCBI	Quality Control	Links
Verrucomicrobiota
Verrucomicrobiaceae
Akkermansia
Enterobacteriaceae
Blautia
Tyzzerella
Turicibacter
unclassified Enterobacteriaceae

Revision editor(s): AaishahM

Signature 2

EditHistoryDelete

Mark reviewed

Your review change was submitted

Needs review

Curated date: 2024/10/09

Curator: AaishahM

Revision editor(s): AaishahM

Source: Table S2

Description: Significantly different taxa between WT and AD (APP/PS1) mice

Abundance in Group 1: decreased abundance in APP/PS1

NCBI	Quality Control	Links
Bacteroidaceae
Rikenellaceae
Bacteroides
Escherichia/Shigella sp.

Revision editor(s): AaishahM

Experiment 5

EditHistoryDelete

Mark reviewed

Your review change was submittedDuplicate this ExperimentAdd a new Signature

Needs review

Curated date: 2024/10/09

Curator: AaishahM

Revision editor(s): AaishahM

Differences from previous experiment shown

Subjects

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

Alzheimer's Disease (AD) mouse model 9-month-old

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

18

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

18

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

increased

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

unchanged

Richness Number of species

increased

Signature 1

EditHistoryDelete

Mark reviewed

Your review change was submitted

Needs review

Curated date: 2024/10/09

Curator: AaishahM

Revision editor(s): AaishahM

Source: Table S2

Description: Significantly different taxa between WT and AD (APP/PS1) mice

Abundance in Group 1: increased abundance in APP/PS1

NCBI	Quality Control	Links
Verrucomicrobiota
Verrucomicrobiaceae
Akkermansia
Desulfovibrionaceae bacterium
Desulfovibrio
UnclassifiedUnclassified

Revision editor(s): AaishahM

Signature 2

EditHistoryDelete

Mark reviewed

Your review change was submitted

Needs review

Curated date: 2024/10/09

Curator: AaishahM

Revision editor(s): AaishahM

Source: Table S2

Description: Significantly different taxa between WT and AD(APP/PS1) mice

Abundance in Group 1: decreased abundance in APP/PS1

NCBI	Quality Control	Links
Carnobacteriaceae
Atopostipes
Alistipes

Revision editor(s): AaishahM

Experiment 6

EditHistoryDelete

Mark reviewed

Your review change was submittedDuplicate this ExperimentAdd a new Signature

Needs review

Curated date: 2024/10/24

Curator: AaishahM

Revision editor(s): AaishahM

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies

A combination of groups WT 2m, 3m, 6m, 9m

Group 1 name Corresponds to the case (exposed) group for case-control studies

WT 1m

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

Wild-type mouse 1-month-old

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

83

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

14

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

EditHistoryDelete

Mark reviewed

Your review change was submitted

Needs review

Curated date: 2024/10/24

Curator: AaishahM

Revision editor(s): AaishahM

Source: Figure S3 A

Description: Differentially represented bacterial taxa of WT

Abundance in Group 1: increased abundance in WT 1m

NCBI	Quality Control	Links
Bacteroidia
Bacteroidales
Candidatus Arthromitus
Clostridiaceae
Bacteroidota

Revision editor(s): AaishahM

Experiment 7

EditHistoryDelete

Mark reviewed

Your review change was submittedDuplicate this ExperimentAdd a new Signature

Needs review

Curated date: 2024/10/24

Curator: AaishahM

Revision editor(s): AaishahM

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies

A combination of groups WT 1m, 3m, 6m, 9m

Group 1 name Corresponds to the case (exposed) group for case-control studies

WT 2m

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

Wild-type mouse 2-month-old

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

80

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

17

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

increased

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

unchanged

Richness Number of species

unchanged

Signature 1

EditHistoryDelete

Mark reviewed

Your review change was submitted

Needs review

Curated date: 2024/10/24

Curator: AaishahM

Revision editor(s): AaishahM

Source: Figure S3 A

Description: Differentially represented bacterial taxa of WT

Abundance in Group 1: increased abundance in WT 2m

NCBI	Quality Control	Links
Muribaculaceae
uncultured Muribaculaceae bacterium

Revision editor(s): AaishahM

Experiment 8

EditHistoryDelete

Mark reviewed

Your review change was submittedDuplicate this ExperimentAdd a new Signature

Needs review

Curated date: 2024/10/24

Curator: AaishahM

Revision editor(s): AaishahM

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies

A combination of groups WT 1m, 2m, 6m, 9m

Group 1 name Corresponds to the case (exposed) group for case-control studies

WT 3m

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

Wild-type mouse 3-month-old

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

EditHistoryDelete

Mark reviewed

Your review change was submitted

Needs review

Curated date: 2024/10/24

Curator: AaishahM

Revision editor(s): AaishahM

Source: Figure S3 A

Description: Differentially represented bacterial taxa of WT

Abundance in Group 1: increased abundance in WT 3m

NCBI	Quality Control	Links
Butyricicoccus
uncultured Oscillospiraceae bacterium
Peptococcus
Oscillibacter
Roseburia
Mucispirillum
Deferribacteres
Deferribacterales
Deferribacteraceae
Oscillospiraceae
uncultured Lachnospiraceae bacterium
Bacillota

Revision editor(s): AaishahM

Experiment 9

EditHistoryDelete

Mark reviewed

Your review change was submittedDuplicate this ExperimentAdd a new Signature

Needs review

Curated date: 2024/10/24

Curator: AaishahM

Revision editor(s): AaishahM

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies

A combination of groups WT 1m, 2m, 3m, 9m

Group 1 name Corresponds to the case (exposed) group for case-control studies

WT 6m

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

Wild-type mouse 6-month-old

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

66

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

31

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

EditHistoryDelete

Mark reviewed

Your review change was submitted

Needs review

Curated date: 2024/10/24

Curator: AaishahM

Revision editor(s): AaishahM

Source: Figure S3 A

Description: Differentially represented bacterial taxa of WT

Abundance in Group 1: increased abundance in WT 6m

NCBI	Quality Control	Links
Alloprevotella
Allobaculum
uncultured Peptococcaceae bacterium
Peptococcaceae

Revision editor(s): AaishahM

Experiment 10

EditHistoryDelete

Mark reviewed

Your review change was submittedDuplicate this ExperimentAdd a new Signature

Needs review

Curated date: 2024/10/24

Curator: AaishahM

Revision editor(s): AaishahM

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies

A combination of groups WT 1m, 2m, 3m, 6m

Group 1 name Corresponds to the case (exposed) group for case-control studies

WT 9m

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

Wild-type mouse 9-month-old

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

79

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

18

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

increased

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

unchanged

Richness Number of species

increased

Signature 1

EditHistoryDelete

Mark reviewed

Your review change was submitted

Needs review

Curated date: 2024/10/25

Curator: AaishahM

Revision editor(s): AaishahM

Source: Figure S3 A

Description: Differentially represented bacterial taxa of WT

Abundance in Group 1: increased abundance in WT 9m

NCBI	Quality Control	Links
Lachnoclostridium
Rhodospirillales
Rhodospirillaceae
Verrucomicrobiaceae
Verrucomicrobiia
Erysipelotrichaceae
Erysipelotrichia
Erysipelotrichales
uncultured Gastranaerophilales bacterium
Verrucomicrobiales
Verrucomicrobiota
Cyanobacteriota
Akkermansia
Candidatus Gastranaerophilales
Candidatus Melainabacteria

Revision editor(s): AaishahM

Experiment 11

EditHistoryDelete

Mark reviewed

Your review change was submittedDuplicate this ExperimentAdd a new Signature

Needs review

Curated date: 2024/10/25

Curator: AaishahM

Revision editor(s): AaishahM

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies

A combination of groups APP/PS1 2m, 3m, 6m, 9m

Group 1 name Corresponds to the case (exposed) group for case-control studies

APP/PS1 1m

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

Alzheimer's Disease (AD) mouse model 1-month-old

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

100

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

21

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

EditHistoryDelete

Mark reviewed

Your review change was submitted

Needs review

Curated date: 2024/10/25

Curator: AaishahM

Revision editor(s): AaishahM

Source: Figure S3 B

Description: Differentially represented bacterial taxa of APP/PS1 1m

Abundance in Group 1: increased abundance in APP/PS1 1m

NCBI	Quality Control	Links
Clostridiaceae
Candidatus Arthromitus
Alistipes
Bacteroidaceae
Bacteroides
Gammaproteobacteria
Enterobacteriaceae
Escherichia/Shigella sp.
Enterobacterales
Rikenellaceae
Lactobacillales
Lactobacillus
Lactobacillaceae

Revision editor(s): AaishahM

Experiment 12

EditHistoryDelete

Mark reviewed

Your review change was submittedDuplicate this ExperimentAdd a new Signature

Needs review

Curated date: 2024/10/25

Curator: AaishahM

Revision editor(s): AaishahM

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies

A combination of groups APP/PS1 1m, 3m, 6m, 9m

Group 1 name Corresponds to the case (exposed) group for case-control studies

APP/PS1 2m

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

Alzheimer's Disease (AD) mouse model 2-month-old

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

97

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

24

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

increased

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

unchanged

Richness Number of species

unchanged

Signature 1

EditHistoryDelete

Mark reviewed

Your review change was submitted

Needs review

Curated date: 2024/10/25

Curator: AaishahM

Revision editor(s): AaishahM

Source: Figure S3 B

Description: Differentially represented bacterial taxa of APP/PS1 2m

Abundance in Group 1: increased abundance in APP/PS1 2m

NCBI	Quality Control	Links
Staphylococcus
Staphylococcaceae
Bacillales
Muribaculaceae
uncultured Muribaculaceae bacterium

Revision editor(s): AaishahM

Experiment 13

EditHistoryDelete

Mark reviewed

Your review change was submittedDuplicate this ExperimentAdd a new Signature

Needs review

Curated date: 2024/10/25

Curator: AaishahM

Revision editor(s): AaishahM

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies

A combination of groups APP/PS1 1m, 2m, 6m, 9m

Group 1 name Corresponds to the case (exposed) group for case-control studies

APP/PS1 3m

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

Alzheimer's Disease (AD) mouse model 3-month-old

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

EditHistoryDelete

Mark reviewed

Your review change was submitted

Needs review

Curated date: 2024/10/25

Curator: AaishahM

Revision editor(s): AaishahM

Source: Figure S3 B

Description: Differentially represented bacterial taxa of APP/PS1 3m

Abundance in Group 1: increased abundance in APP/PS1 3m

NCBI	Quality Control	Links
uncultured Oscillospiraceae bacterium
Blautia
Anaerotruncus
Peptococcus
Oscillibacter
Roseburia
Ruminiclostridium
Oscillospiraceae
Mucispirillum
Deferribacteres
Deferribacterales
Deferribacteraceae
uncultured Lachnospiraceae bacterium

Revision editor(s): AaishahM

Experiment 14

EditHistoryDelete

Mark reviewed

Your review change was submittedDuplicate this ExperimentAdd a new Signature

Needs review

Curated date: 2024/10/25

Curator: AaishahM

Revision editor(s): AaishahM

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies

A combination of groups APP/PS1 1m, 2m, 3m, 9m

Group 1 name Corresponds to the case (exposed) group for case-control studies

APP/PS1 6m

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

Alzheimer's Disease (AD) mouse model 6-month-old

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

87

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

34

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

EditHistoryDelete

Mark reviewed

Your review change was submitted

Needs review

Curated date: 2024/10/25

Curator: AaishahM

Revision editor(s): AaishahM

Source: Figure S3 B

Description: Differentially represented bacterial taxa of APP/PS1 6m

Abundance in Group 1: increased abundance in APP/PS1 6m

NCBI	Quality Control	Links
Allobaculum

Revision editor(s): AaishahM

Experiment 15

EditHistoryDelete

Mark reviewed

Your review change was submittedDuplicate this ExperimentAdd a new Signature

Needs review

Curated date: 2024/10/25

Curator: AaishahM

Revision editor(s): AaishahM

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies

A combination of groups APP/PS1 1m, 2m, 3m, 6m

Group 1 name Corresponds to the case (exposed) group for case-control studies

APP/PS1 9m

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

Alzheimer's Disease (AD) mouse model 9-month-old

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

103

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

18

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

increased

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

unchanged

Richness Number of species

increased

Signature 1

EditHistoryDelete

Mark reviewed

Your review change was submitted

Needs review

Curated date: 2024/10/25

Curator: AaishahM

Revision editor(s): AaishahM

Source: Figure S3 B

Description: Differentially represented bacterial taxa of APP/PS1 9m

Abundance in Group 1: increased abundance in APP/PS1 9m

NCBI	Quality Control	Links
uncultured Peptococcaceae bacterium
Lachnoclostridium
Rhodospirillaceae
Peptococcaceae
Rhodospirillales
Turicibacter
Desulfovibrio
Desulfovibrionales
Desulfovibrionaceae
Deltaproteobacteria
uncultured Gastranaerophilales bacterium
Candidatus Gastranaerophilales
Cyanobacteriota
Pseudomonadota
Actinomycetota
Bifidobacterium
Bifidobacteriaceae
Bifidobacteriales

Revision editor(s): AaishahM