Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis/Experiment 17
From BugSigDB
Needs review
Subjects
- Location of subjects
- United States of America
- 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
- Treatment outcome measurement Treatment outcome measurement,treatment outcome measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Single-treatment housed control mice - 3 DPI
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Single-treatment housed vancomycin mice - 3 DPI
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Single-treatment housed vancomycin mice refers to conventionally raised mice with multiple sclerosis, who were treated with vancomycin. Mice were fed 200 μL of the vancomycin cecal slurry by oral gavage once for 2 weeks. This was done 4 weeks before EAE induction. These vancomycin-treated mice were housed with the same treatment group (single treatment) at 3 days post immunization(3 DPI).
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- 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
- Spearman Correlation
- 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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Richness Number of species
- decreased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- decreased
Signature 1
Needs review
Source: Fig. 5A
Description: Differentially abundant taxa between single-treatment housed untreated mice (control) and single-treatment housed vancomycin mice (vancomycin) at 3 days post immunization(3 DPI) using spearman correlation matrix.
Abundance in Group 1: increased abundance in Single-treatment housed vancomycin mice - 3 DPI
| NCBI | Quality Control | Links |
|---|---|---|
| Enterococcus | ||
| Clostridium XVIIIClostridium XVIII | ||
| Turicibacter | ||
| Akkermansia |
Revision editor(s): KateRasheed
Signature 2
Needs review
Source: Fig. 5A
Description: Differentially abundant taxa between single-treatment housed untreated mice (control) and single-treatment housed vancomycin mice (vancomycin) at 3 days post immunization(3 DPI) using spearman correlation matrix.
Abundance in Group 1: decreased abundance in Single-treatment housed vancomycin mice - 3 DPI
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerosporobacter | ||
| Roseburia | ||
| Ruminococcus | ||
| Clostridium IIIClostridium III | ||
| Holdemania | ||
| Anaeroplasma |
Revision editor(s): KateRasheed
