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Updated: Oct 25, 2025

Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing
Published on: October 15, 2019
HLA Class II Polymorphisms Modulate Gut Microbiota and Experimental Autoimmune Encephalomyelitis Phenotype
Shailesh K Shahi1, Soham Ali1,2, Camille M Jaime1
1Department of Pathology, University of Iowa, Iowa City, IA.
Genetic factors like HLA class II genes influence gut microbiota composition, impacting multiple sclerosis (MS) risk and severity in a mouse model. This highlights the interplay between genes and gut bacteria in MS pathogenesis.
Area of Science:
- Neuroimmunology
- Microbiome Research
- Genetics of Autoimmune Diseases
Background:
- Multiple sclerosis (MS) is a central nervous system (CNS) autoimmune disease influenced by genetic and environmental factors.
- Gut microbiota is a potential missing environmental factor in MS pathogenesis.
- The interaction between genetic factors (e.g., HLA class II genes) and gut microbiota in MS is not well understood.
Purpose of the Study:
- To investigate if HLA class II genes, known to influence MS susceptibility, also affect gut microbiota composition.
- To explore the role of specific HLA class II genes (HLA-DR3 and HLA-DQ8) in modulating gut microbiota and experimental autoimmune encephalomyelitis (EAE) severity.
Main Methods:
- Utilized HLA-DR3 and HLA-DQ8 transgenic mouse models, including double transgenic and knockout mice (AE-KO).
- Induced EAE, an animal model of MS, using myelin proteolipid protein (PLP) peptide.
- Analyzed gut microbiota composition in different transgenic mouse lines using sequencing techniques.
Main Results:
- HLA-DR3 transgenic mice were susceptible to EAE, while HLA-DQ8 transgenic mice were resistant.
- HLA-DR3.DQ8 double transgenic mice exhibited increased EAE prevalence and severity compared to HLA-DR3 mice.
- Gut microbiota composition differed significantly between AE-KO mice and HLA class II transgenic mice, with DQ8 mice microbiota being more similar to double transgenic mice.
Conclusions:
- HLA class II genes (HLA-DR3 and HLA-DQ8) significantly influence gut microbiota composition.
- The presence of HLA-DQ8 on an HLA-DR3 background exacerbates EAE severity, suggesting a role for DQ8-specific microbiota.
- Specific HLA genes interacting with distinct gut microbiota profiles contribute to EAE susceptibility and resistance in this MS animal model.
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