Gut microbiome of treatment-naïve MS patients of different ethnicities early in disease course/Experiment 2
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
- Hispanic Americans (HA)
- 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 Hispanic Americans by Ethnicity
- Group 0 sample size Number of subjects in the control (unexposed) group
- 15
- Group 1 sample size Number of subjects in the case (exposed) group
- 16
- 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 2E
Description: Differential abundance of taxa's that were significantly enriched in Hispanic MS and control samples using linear discriminant analysis (LDA) score of differences by LDA effect size (LEfSe)
Abundance in Group 1: increased abundance in Hispanic Americans (HA)
| NCBI | Quality Control | Links |
|---|---|---|
| Blautia | ||
| Clostridium | ||
| Bacilli | ||
| Dorea | ||
| Holdemania | ||
| Adlercreutzia |
Revision editor(s): MyleeeA
Signature 2
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-10-21
Source: Figure 2E
Description: Differential abundance of taxa's that were significantly enriched in Hispanic MS and control samples using linear discriminant analysis (LDA) score of differences by LDA effect size (LEfSe)
Abundance in Group 1: decreased abundance in Hispanic Americans (HA)
| NCBI | Quality Control | Links |
|---|---|---|
| Dialister | ||
| Lachnospira | ||
| Prevotella | ||
| Prevotellaceae | ||
| Slackia | ||
| ParaprevotellaceaeParaprevotellaceae | ||
| Muribaculaceae |
Revision editor(s): MyleeeA
