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Updated: Dec 8, 2025
Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing
Published on: October 15, 2019
Experimental autoimmune encephalomyelitis is associated with changes of the microbiota composition in the
David M Johanson1,2, Jennifer E Goertz1,2,3, Ioana A Marin1,2,4
1Center for Brain Immunology and Glia, University of Virginia, Charlottesville, VA, 22908, USA.
Abstract:
The gut microbiome is known to be sensitive to changes in the immune system, especially during autoimmune diseases such as Multiple Sclerosis (MS). Our study examines the changes to the gut microbiome that occur during experimental autoimmune encephalomyelitis (EAE), an animal model for MS. We collected fecal samples at key stages of EAE progression and quantified microbial abundances with 16S V3-V4 amplicon sequencing. Our analysis of the data suggests that the abundance of commensal Lactobacillaceae decreases during EAE while other commensal populations belonging to the Clostridiaceae, Ruminococcaceae, and Peptostreptococcaceae families expand. Community analysis with microbial co-occurrence networks points to these three expanding taxa as potential mediators of gut microbiome dysbiosis. We also employed PICRUSt2 to impute MetaCyc Enzyme Consortium (EC) pathway abundances from the original microbial abundance data. From this analysis, we found that a number of imputed EC pathways responsible for the production of immunomodulatory compounds appear to be enriched in mice undergoing EAE. Our analysis and interpretation of results provides a detailed picture of the changes to the gut microbiome that are occurring throughout the course of EAE disease progression and helps to evaluate EAE as a viable model for gut dysbiosis in MS patients.
Insights
Gut microbiome alterations occur during experimental autoimmune encephalomyelitis (EAE), an animal model for Multiple Sclerosis (MS). Key bacterial families shift, potentially mediating gut dysbiosis and impacting immunomodulatory pathways relevant to MS.
Area of Science:
- Microbiology
- Immunology
- Neuroscience
Background:
- The gut microbiome is sensitive to immune system changes, particularly in autoimmune diseases like Multiple Sclerosis (MS).
- Experimental Autoimmune Encephalomyelitis (EAE) serves as a crucial animal model for studying MS pathogenesis.
Purpose of the Study:
- To investigate gut microbiome composition and function changes during EAE progression.
- To assess the relevance of EAE as a model for gut dysbiosis observed in MS patients.
Main Methods:
- Fecal sample collection at key EAE stages.
- 16S V3-V4 amplicon sequencing for microbial abundance quantification.
- PICRUSt2 for imputation of MetaCyc Enzyme Consortium (EC) pathway abundances.
Main Results:
- Decreased abundance of Lactobacillaceae and increased abundance of Clostridiaceae, Ruminococcaceae, and Peptostreptococcaceae during EAE.
- Microbial co-occurrence networks identified expanding taxa as potential mediators of dysbiosis.
- Enrichment of imputed EC pathways involved in immunomodulatory compound production in EAE mice.
Conclusions:
- EAE exhibits significant gut microbiome dysbiosis, characterized by specific bacterial taxa shifts.
- These shifts and associated functional pathways may contribute to EAE pathogenesis.
- The study supports EAE as a relevant model for exploring gut dysbiosis in Multiple Sclerosis.
