Gut microbiome of treatment-naïve MS patients of different ethnicities early in disease course/Experiment 3
From BugSigDB
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-10-21
Subjects
- Location of subjects
- United States of America
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Homo sapiens
- 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
- Relapsing-remitting multiple sclerosis Acute Relapsing Multiple Sclerosis,MS RELAPSING REMITTING,Multiple Sclerosis, Acute Relapsing,Multiple Sclerosis, Relapsing Remitting,Multiple Sclerosis, Relapsing-Remitting,Multiple Sclerosis, Remitting-Relapsing,Relapsing Remitting Multiple Sclerosis,Relapsing-remitting MS,relapsing-remitting multiple sclerosis,Remitting Relapsing Multiple Sclerosis,Remitting-Relapsing Multiple Sclerosis,RRMS,Relapsing-remitting multiple sclerosis
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy Controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- African Americans (AA)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Individuals diagnosed with relapsing-remitting multiple sclerosis (MS) who were African Americans by Ethnicity
- Group 0 sample size Number of subjects in the control (unexposed) group
- 14
- Group 1 sample size Number of subjects in the case (exposed) group
- 14
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Less than 3 months
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
- Matched on Factors on which subjects have been matched on in a case-control study
- ethnic group
Alpha Diversity
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-10-21
Source: Figure 2F
Description: Differential abundance of taxa's that were significantly enriched in African American MS and control samples using linear discriminant analysis (LDA) score of differences by LDA effect size (LEfSe)
Abundance in Group 1: increased abundance in African Americans (AA)
| NCBI | Quality Control | Links |
|---|---|---|
| Adlercreutzia | ||
| Butyricicoccus | ||
| Clostridium | ||
| Coriobacteriaceae | ||
| Coriobacteriales | ||
| Coriobacteriia |
Revision editor(s): MyleeeA
