Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis/Experiment 5
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 - 3 DPI 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
- 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
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. S4A
Description: Differentially abundant taxa between single-treatment housed vancomycin mice and single-treatment housed control mice at 3 days post immunization(3 DPI) using LEfSe
Abundance in Group 1: decreased abundance in Single-treatment housed vancomycin mice - 3 DPI
Revision editor(s): KateRasheed
Signature 2
Needs review
Source: Fig. S4A
Description: Differentially abundant taxa between single-treatment housed vancomycin mice and single-treatment housed control mice at 3 days post immunization(3 DPI) using LEfSe
Abundance in Group 1: increased abundance in Single-treatment housed vancomycin mice - 3 DPI
Revision editor(s): KateRasheed
