Implications of gut microbiota dysbiosis and metabolic changes in prion disease/Experiment 1
From BugSigDB
Needs review
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
- Prion disease prion disease,prion disease pathway,prion induced disorder,prion protein disease,spongiform encephalopathy,Prion disease
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy Control
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Prion-infected mice
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Prion-infected mice
- Group 0 sample size Number of subjects in the control (unexposed) group
- 25
- Group 1 sample size Number of subjects in the case (exposed) group
- 12
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
- Random Forest Analysis
- Welch's T-Test
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 3
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Richness Number of species
- decreased
Signature 1
Needs review
Source: Fig. 2B
Description: Cladogram made by LEfSe reflecting differentially abundance of bacterial taxa.
Abundance in Group 1: decreased abundance in Prion-infected mice
| NCBI | Quality Control | Links |
|---|---|---|
| Alloprevotella | ||
| Candidatus Saccharibacteria | ||
| Candidatus Saccharimonas | ||
| Oscillospiraceae | ||
| Prevotellaceae | ||
| Rikenellaceae RC9 gut groupRikenellaceae RC9 gut group |
Revision editor(s): Ikehdarlington
Signature 2
Needs review
Source: Fig. 2B
Description: Cladogram made by LEfSe reflecting differentially abundance of bacterial taxa.
Abundance in Group 1: increased abundance in Prion-infected mice
| NCBI | Quality Control | Links |
|---|---|---|
| Bacilli | ||
| Campylobacterales | ||
| Epsilonproteobacteria | ||
| Helicobacter | ||
| Helicobacteraceae | ||
| Lactobacillaceae | ||
| Lactobacillales | ||
| Lactobacillus | ||
| Pseudomonadota |
Revision editor(s): Ikehdarlington
