Gut microbiome of treatment-naïve MS patients of different ethnicities early in disease course
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Ventura RE, Iizumi T, Battaglia T, Liu M, Perez-Perez GI, Herbert J, Blaser MJ
Journal
Scientific reports
Year
2019
Although the intestinal microbiome has been increasingly implicated in autoimmune diseases, much is unknown about its roles in Multiple Sclerosis (MS). Our aim was to compare the microbiome between treatment-naïve MS subjects early in their disease course and controls, and between Caucasian (CA), Hispanic (HA), and African American (AA) MS subjects. From fecal samples, we performed 16S rRNA V4 sequencing and analysis from 45 MS subjects (15 CA, 16 HA, 14 AA) and 44 matched healthy controls, and whole metagenomic shotgun sequencing from 24 MS subjects (all newly diagnosed, treatment-naïve, and steroid-free) and 24 controls. In all three ethnic groups, there was an increased relative abundance of the same single genus, Clostridium, compared to ethnicity-matched controls. Analysis of microbiota networks showed significant changes in the network characteristics between combined MS cohorts and controls, suggesting global differences not restricted to individual taxa. Metagenomic analysis revealed significant enrichment of individual species within Clostridia as well as particular functional pathways in the MS subjects. The increased relative abundance of Clostridia in all three early MS cohorts compared to controls provides candidate taxa for further study as biomarkers or as etiologic agents in MS.
Experiment 1
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
- Caucasian Americans (CA)
- 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 Caucasian Americans
- 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
- 15
- 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 2D
Description: Differential abundance of taxa in Caucasian MS and control samples.
Abundance in Group 1: increased abundance in Caucasian Americans (CA)
| NCBI | Quality Control | Links |
|---|---|---|
| Verrucomicrobiales | ||
| Verrucomicrobiota | ||
| Verrucomicrobiaceae | ||
| Verrucomicrobiia | ||
| Clostridium | ||
| MogibacteriaceaeMogibacteriaceae | ||
| Akkermansia |
Revision editor(s): MyleeeA
Experiment 2
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-10-21
Differences from previous experiment shown
Subjects
- 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 1 sample size Number of subjects in the case (exposed) group
- 16
Lab analysis
Statistical Analysis
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
Experiment 3
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-10-21
Differences from previous experiment shown
Subjects
- 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
Lab analysis
Statistical Analysis
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
Experiment 4
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-10-21
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Multiple Sclerosis (MS)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- All treatment-naïve Multiple Sclerosis subjects who were diagnosed within 6 months of the specimen collection. They subjects included Caucasian American, Hispanic American and African American.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 24
- Group 1 sample size Number of subjects in the case (exposed) group
- 24
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Less than 3months
Lab analysis
- Sequencing type
- WMS
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
Statistical Analysis
- Matched on Factors on which subjects have been matched on in a case-control study
- ethnic group, age
Signature 1
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-10-21
Source: Figure 4
Description: Differential abundance of taxa in the Multiple Sclerosis and control subjects from Whole Genome Sequencing (WGS) analysis as determined by LDA effect size (LEfSe).
Abundance in Group 1: increased abundance in Multiple Sclerosis (MS)
Revision editor(s): MyleeeA
Signature 2
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-10-21
Source: Figure 4
Description: Differential abundance of taxa in the Multiple Sclerosis and control subjects from Whole Genome Sequencing (WGS) analysis as determined by LDA effect size (LEfSe).
Abundance in Group 1: decreased abundance in Multiple Sclerosis (MS)
| NCBI | Quality Control | Links |
|---|---|---|
| Burkholderiales bacterium 1_1_47 | ||
| Haemophilus parainfluenzae | ||
| Alistipes senegalensis | ||
| Bacteroides xylanisolvens | ||
| Odoribacter splanchnicus | ||
| Barnesiella intestinihominis |
Revision editor(s): MyleeeA
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