Frontiers in Cellular and Infection Microbiology (Dec 2020)

A Metagenome-Wide Association Study of Gut Microbiome in Patients With Multiple Sclerosis Revealed Novel Disease Pathology

  • Toshihiro Kishikawa,
  • Toshihiro Kishikawa,
  • Kotaro Ogawa,
  • Kotaro Ogawa,
  • Daisuke Motooka,
  • Akiko Hosokawa,
  • Akiko Hosokawa,
  • Makoto Kinoshita,
  • Ken Suzuki,
  • Kenichi Yamamoto,
  • Kenichi Yamamoto,
  • Tatsuo Masuda,
  • Yuki Matsumoto,
  • Takuro Nii,
  • Takuro Nii,
  • Yuichi Maeda,
  • Yuichi Maeda,
  • Shota Nakamura,
  • Shota Nakamura,
  • Hidenori Inohara,
  • Hideki Mochizuki,
  • Tatsusada Okuno,
  • Yukinori Okada,
  • Yukinori Okada,
  • Yukinori Okada

DOI
https://doi.org/10.3389/fcimb.2020.585973
Journal volume & issue
Vol. 10

Abstract

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While microbiome plays key roles in the etiology of multiple sclerosis (MS), its mechanism remains elusive. Here, we conducted a comprehensive metagenome-wide association study (MWAS) of the relapsing-remitting MS gut microbiome (ncase = 26, ncontrol = 77) in the Japanese population, by using whole-genome shotgun sequencing. Our MWAS consisted of three major bioinformatic analytic pipelines (phylogenetic analysis, functional gene analysis, and pathway analysis). Phylogenetic case-control association tests showed discrepancies of eight clades, most of which were related to the immune system (false discovery rate [FDR] < 0.10; e.g., Erysipelatoclostridium_sp. and Gemella morbillorum). Gene association tests found an increased abundance of one putative dehydrogenase gene (Clo1100_2356) and one ABC transporter related gene (Mahau_1952) in the MS metagenome compared with controls (FDR < 0.1). Molecular pathway analysis of the microbiome gene case-control comparisons identified enrichment of multiple Gene Ontology terms, with the most significant enrichment on cell outer membrane (P = 1.5 × 10−7). Interaction between the metagenome and host genome was identified by comparing biological pathway enrichment between the MS MWAS and the MS genome-wide association study (GWAS) results (i.e., MWAS-GWAS interaction). No apparent discrepancies in alpha or beta diversities of metagenome were found between MS cases and controls. Our shotgun sequencing-based MWAS highlights novel characteristics of the MS gut microbiome and its interaction with host genome, which contributes to our understanding of the microbiome’s role in MS pathophysiology.

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