Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis/Experiment 3
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
- Multiple sclerosis Disseminated Sclerosis,generalized multiple sclerosis,insular sclerosis,MS,MS (Multiple Sclerosis),multiple sclerosis,MULTIPLE SCLEROSIS ACUTE FULMINATING,Multiple Sclerosis, Acute Fulminating,Sclerosis, Disseminated,Sclerosis, Multiple,Multiple sclerosis
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Pre-Experimental Autoimmune Encephalomyelitis induction(pre-EAE induction/Day 0): 0 day post immunization(0 DPI)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Post-Experimental Autoimmune Encephalomyelitis induction-peak disease(post-EAE induction): 15 days post immunization(15 DPI)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Post-Experimental Autoimmune Encephalomyelitis induction-peak disease(post-EAE induction): 15 days post immunization(15 DPI), refers to the timepoint for fecal sample collection(fifteen days after immunization). This was also the peak of multiple sclerosis disease.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 11
- Group 1 sample size Number of subjects in the case (exposed) group
- 11
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
- unchanged
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Needs review
Source: Fig. 1F
Description: Differentially abundant taxa between 15 days post immunization(15 DPI) and 0 day post immunization(0 DPI)
Abundance in Group 1: increased abundance in Post-Experimental Autoimmune Encephalomyelitis induction-peak disease(post-EAE induction): 15 days post immunization(15 DPI)
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia muciniphila | ||
| Ruminococcus flavefaciens | ||
| Clostridium ruminantium | ||
| [Clostridium] scindens |
Revision editor(s): KateRasheed
Signature 2
Needs review
Source: Fig. 1F
Description: Differentially abundant taxa between 15 days post immunization(15 DPI) and 0 day post immunization(0 DPI)
Abundance in Group 1: decreased abundance in Post-Experimental Autoimmune Encephalomyelitis induction-peak disease(post-EAE induction): 15 days post immunization(15 DPI)
Revision editor(s): KateRasheed
