Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis/Experiment 1
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-latent period(post-EAE induction): 3 days post immunization(3 DPI)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Post-Experimental Autoimmune Encephalomyelitis induction-latent period(post-EAE induction): 3 days post immunization(3 DPI), refers to fecal samples collected three days after immunization. Mice were immunized with Myelin oligodendrocyte glycoprotein(MOG) for EAE induction. EAE was induced by injecting 8- to 10-week-old female C57BL/6J mice with 150 mg MOG35–55 peptide (Genemed Synthesis) emulsified in complete Freund’s adjuvant (CFA) (BD Difco) per mouse subcutaneously in the flanks, followed by intraperitoneal administration of 150 ng pertussis toxin (List Biological Laboratories, Inc.) per mouse on days 0 and 2.
- 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 3 days post immunization(3 DPI) and 0 day post immunization(0 DPI)
Abundance in Group 1: increased abundance in Post-Experimental Autoimmune Encephalomyelitis induction-latent period(post-EAE induction): 3 days post immunization(3 DPI)
| NCBI | Quality Control | Links |
|---|---|---|
| Thomasclavelia cocleata | ||
| Ruminococcus flavefaciens | ||
| Clostridium ruminantium |
Revision editor(s): KateRasheed
Signature 2
Needs review
Source: Fig. 1F
Description: Differentially abundant taxa between 3 days post immunization(3 DPI) and 0 day post immunization(0 DPI)
Abundance in Group 1: decreased abundance in Post-Experimental Autoimmune Encephalomyelitis induction-latent period(post-EAE induction): 3 days post immunization(3 DPI)
| NCBI | Quality Control | Links |
|---|---|---|
| Dorea formicigenerans | ||
| Lacrimispora indolis | ||
| Lactobacillus taiwanensis | ||
| [Clostridium] viride | ||
| Lactobacillus gasseri | ||
| Lactobacillus johnsonii | ||
| Lactobacillus hominis |
Revision editor(s): KateRasheed
