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. 2022 Mar 8;98(10):e1050-e1063.
doi: 10.1212/WNL.0000000000013245. Epub 2021 Dec 22.

Metagenomic Analysis of the Pediatric-Onset Multiple Sclerosis Gut Microbiome

Ali I Mirza  1 , Feng Zhu  1 , Natalie Knox  1 , Jessica D Forbes  1 , Gary Van Domselaar  1 , Charles N Bernstein  1 , Morag Graham  1 , Ruth Ann Marrie  1 , Janace Hart  1 , E Ann Yeh  1 , Douglas L Arnold  1 , Amit Bar-Or  1 , Julia O'Mahony  1 , Yinshan Zhao  1 , William Hsiao  1 , Brenda Banwell  1 , Emmanuelle Waubant  1 , Helen Tremlett  2
Affiliations

Metagenomic Analysis of the Pediatric-Onset Multiple Sclerosis Gut Microbiome

Ali I Mirza et al. Neurology. .

Abstract

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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Figures

Figure 1
Figure 1. Alpha Diversity of the Gut Microbiota Enzymes and Proteins for the Individuals With Pediatric-Onset Multiple Sclerosis and Controls, Including by Disease-Modifying Drug Exposure Status
Differences in alpha diversity of Kyoto Encyclopedia of Genes and Genomes (KEGG) Orthologs (KOs), enzyme commissions (ECs), and microbial species relative abundance were assessed by disease status (multiple sclerosis [MS] and controls) and by disease-modifying drug (DMD) exposure. Diversity measures includes observed number (richness) and inverse Simpson (true diversity). None of the comparisons was statistically significant (p > 0.05, Wilcoxon rank sum test and Dunn test). (A, B) ECs alpha diversity comparing individuals with MS and controls and by DMD exposure, respectively. (C, D) KO alpha diversity comparing individuals with MS and controls and by DMD exposure, respectively.
Figure 2
Figure 2. Gut Microbiome Metabolic Pathway Relative Abundance and Prevalence for the Individuals With Pediatric-Onset Multiple Sclerosis and Controls, Including by Disease-Modifying Drug Exposure Status
Relative abundance of metabolic pathways (pathways from the MetaCyc database) were estimated for 40 participants: 20 controls and 20 individuals with multiple sclerosis (MS) (of whom 8 were disease-modifying drug [DMD]–naive and 12 DMD-exposed MS). All groups were compared pairwise by differences in relative abundance (A) and prevalence of the pathways (B). Pathways that were significantly different between individuals with MS and controls were assessed further for differences by DMD exposure. (A) Differences in the median log ratio transformed abundances between each pairwise group comparison. In total, 1 pathway was significantly higher and 4 significantly lower in individuals with MS compared to controls. (B) Prevalence of significantly different pathways (3 total) among participants within each group and subgroup, represented as bars. The odds of MS onset given presence of the pathway compared to absence of the pathway is reported under the asterisk. *p < 0.05; **p < 0.01; Inf = infinite because this genus was not found among controls.
Figure 3
Figure 3. Gene Functional Annotations Relative Abundance for the Individuals With Pediatric-Onset Multiple Sclerosis and Controls, Including by Disease-Modifying Drug Exposure Status
Abundance of gene function annotations among 3 independent domains of the Gene Ontology knowledgebase—biological process (BP), cellular component (CC), and molecular function (MF)—were estimated for all participants. Gene annotations were grouped into higher order biological functions. All groups were compared pairwise by differences in relative abundance of the gene annotations. Gene annotations that were significantly different between individuals with multiple sclerosis (MS) and controls were further assessed for differences by disease-modifying drug (DMD) exposure. Differences in the median log ratio transformed abundances between each pairwise comparison. The relative abundance of 68 total gene annotations were significantly different between individuals with MS and controls, of which 60 informative gene annotations are displayed in the heatmap. *p < 0.05; **p < 0.01; ***p < 0.005.
Figure 4
Figure 4. Genus-Level Gut Microbial Taxonomy Relative Abundance for the Individuals With Pediatric-Onset Multiple Sclerosis and Controls, Including by Disease-Modifying Drug Exposure Status
Genera relative abundance of bacteria, archaea, and virus were estimated for all 40 participants. All groups were compared pairwise by differences in relative abundance of genera. Differences in the median log-ratio transformed abundances between each pairwise comparison. In total, 27 bacterial (black text), 4 archaeal (green text), and 1 viral (blue font) genera significantly different between individuals with multiple sclerosis (MS) and controls are displayed in the heatmap. Genera were indicated for higher (red shading) or lower (blue shading) median relative abundance of the 1st group compared to the 2nd group, respectively. *p < 0.05; **p < 0.01; ***p < 0.005. DMD = disease-modifying drug.
Figure 5
Figure 5. Microbial Species Relative Abundance for the Individuals With Pediatric-Onset Multiple Sclerosis and Controls, Including by Disease-Modifying Drug Exposure Status
Species relative abundance of bacteria, archaea, and a virus species were estimated for all 40 participants. All groups were compared pairwise by differences in relative abundance. In total, 40 bacterial (black font) and 3 archaeal (green text) and 1 viral (blue text) species differed significantly between individuals with MS and controls are displayed in the heatmap. Red shading indicates a higher and blue a lower median relative abundance of the 1st group (e.g., multiple sclerosis [MS]) compared to the 2nd group (e.g., controls). *p < 0.05; **p < 0.01; ***p < 0.005. DMD = disease-modifying drug.
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References

    1. Thompson AJ, Baranzini SE, Geurts J, Hemmer B, Ciccarelli O. Multiple sclerosis. Lancet. 2018;391(10130):1622-1636. - PubMed
    1. Fan Y, Pedersen O. Gut microbiota in human metabolic health and disease. Nat Rev Microbiol. 2021;19(1):55-71. - PubMed
    1. Tremlett H, Bauer KC, Appel-Cresswell S, Finlay BB, Waubant E. The gut microbiome in human neurological disease: a review. Ann Neurol. 2017;81(3):369-382. - PubMed
    1. Sun L, Xie C, Wang G, et al. . Gut microbiota and intestinal FXR mediate the clinical benefits of metformin. Nat Med. 2018;24(12):1919-1929. - PMC - PubMed
    1. Waubant E, Lucas R, Mowry E, et al. . Environmental and genetic risk factors for MS: an integrated review. Ann Clin Transl Neurol. 2019;6(9):1905-1922. - PMC - PubMed

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