Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis/Experiment 7
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 - 15 DPI
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Single-treatment housed vancomycin mice - 15 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 15 days post immunization(15 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
- unchanged
- 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 15 days post immunization(15 DPI) using LEfSe
Abundance in Group 1: increased abundance in Single-treatment housed vancomycin mice - 15 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 15 days post immunization(15 DPI) using LEfSe
Abundance in Group 1: decreased abundance in Single-treatment housed vancomycin mice - 15 DPI
Revision editor(s): KateRasheed
