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Updated: Aug 5, 2026

Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing
Published on: October 15, 2019
Metagenomic Analysis of the Pediatric-Onset Multiple Sclerosis Gut Microbiome
Ali I Mirza1, Feng Zhu1, Natalie Knox1
1From the Department of Medicine (Neurology) (A.I.M., F.Z., Y.Z., H.T.), The University of British Columbia, Vancouver; National Microbiology Laboratory (N.K., G.V.D., M.G.), Public Health Agency of Canada; Department of Medical Microbiology and Infectious Diseases (N.K., G.V.D., M.G.), Department of Internal Medicine, Max Rady College of Medicine, Rady Faculty of Health Sciences (C.N.B., R.A.M.), and Inflammatory Bowel Disease Clinical and Research Centre (C.N.B.), University of Manitoba, Winnipeg; Roy Romanow Provincial Laboratory (J.D.F.), Regina; Department of Pathology and Laboratory Medicine (J.D.F.), College of Medicine, University of Saskatchewan, Saskatoon, Canada; Department of Neurology (J.H., E.W.), University of California San Francisco; Department of Pediatrics (Neurology) (E.A.Y., J.O.), The Hospital for Sick Children, Toronto; Department of Neurology and Neurosurgery (D.L.A.), Montreal Neurological Institute, McGill University, Montreal, Canada; Centre for Neuroinflammation and Experimental Therapeutics and Department of Neurology (A.B.-O.), University of Pennsylvania Perelman School of Medicine, Philadelphia; Faculty of Health Sciences (W.H.), Simon Fraser University, Burnaby, Canada; and The Children's Hospital of Philadelphia (B.B.), PA.
Insights
The gut microbiome in pediatric multiple sclerosis (MS) shows differences in function and bacteria compared to healthy children. Disease-modifying drug (DMD) use impacts the gut microbiome, suggesting a disturbed functional potential in pediatric MS.
Area of Science:
- Microbiology
- Immunology
- Pediatric Neurology
Background:
- The gut microbiome's role in pediatric-onset multiple sclerosis (MS) is largely unknown.
- Understanding these microbial differences is crucial for potential therapeutic targets.
Purpose of the Study:
- To investigate the functional potential and taxonomy of the gut microbiome in children with MS.
- To compare the gut microbiome of pediatric MS patients with healthy controls.
Main Methods:
- Metagenomic analysis of stool samples from 20 pediatric MS patients and 20 matched controls.
- Comparison of microbial taxonomy and functional pathways using statistical tests.
- Assessment of differences based on disease status and disease-modifying drug (DMD) exposure.
Main Results:
- Pediatric MS patients showed higher methanogenesis prevalence and increased *Methanobrevibacter* abundance compared to controls.
- A depletion in homolactic fermentation pathways was observed in individuals with MS.
- DMD exposure was linked to enrichment of butyrate-producing enzymes.
Conclusions:
- The gut microbiome's functional potential and taxonomy are altered in pediatric-onset MS.
- Specific microbial pathways and taxa differ between MS patients and controls.
- DMD treatment influences the gut microbiome composition in pediatric MS.
Background And Objectives:
Little is known of the functional potential of the gut microbiome in pediatric-onset multiple sclerosis (MS). We performed metagenomic analyses using stool samples from individuals with pediatric-onset MS and unaffected controls.
Methods:
Persons ≤21 years old enrolled in the Canadian Pediatric Demyelinating Disease Network providing a stool sample were eligible. Twenty patients with MS (McDonald criteria) with symptom onset <18 years were matched to 20 controls by sex, age (±3 years), stool consistency, and race. Microbial taxonomy and functional potentials were estimated from stool sample-derived metagenomic reads and compared by disease status (MS vs controls) and disease-modifying drug (DMD) exposure using alpha diversity, relative abundance, and prevalence using Wilcoxon rank sum, ALDEx2, and Fisher exact tests, respectively.
Results:
Individuals with MS were aged 13.6 years (mean) at symptom onset and 8 were DMD-naive. Mean ages at stool sample were 16.1 and 15.4 years for MS and control participants, respectively; 80% were girls. Alpha diversity of enzymes and proteins did not differ by disease or DMD status (p > 0.20), but metabolic pathways, gene annotations, and microbial taxonomy did. Individuals with MS (vs controls) exhibited higher methanogenesis prevalence (odds ratio 10, p = 0.044) and Methanobrevibacter abundance (log2 fold change [LFC] 1.7, p = 0.0014), but lower homolactic fermentation abundance (LFC -0.48, p = 0.039). Differences by DMD status included lower phosphate butyryl transferase for DMD-naive vs exposed patients with MS (LFC -1.0, p = 0.033).
Discussion:
The gut microbiome's functional potential and taxonomy differed between individuals with pediatric-onset MS vs controls, including higher prevalence of a methane-producing pathway from Archaea and depletion of the lactate fermentation pathway. DMD exposure was associated with butyrate-producing enzyme enrichment. Together these findings indicate that the gut microbiome of individuals with MS may have a disturbed functional potential.
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