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Metagenome-wide association study of gut microbiome revealed novel aetiology of rheumatoid arthritis in the Japanese population
  1. Toshihiro Kishikawa1,2,
  2. Yuichi Maeda3,4,
  3. Takuro Nii3,4,
  4. Daisuke Motooka5,
  5. Yuki Matsumoto5,
  6. Masato Matsushita6,7,
  7. Hidetoshi Matsuoka7,
  8. Maiko Yoshimura7,
  9. Shoji Kawada8,
  10. Satoru Teshigawara7,
  11. Eri Oguro3,7,
  12. Yasutaka Okita7,
  13. Keisuke Kawamoto8,
  14. Shinji Higa8,
  15. Toru Hirano3,
  16. Masashi Narazaki3,
  17. Atsushi Ogata8,
  18. Yukihiko Saeki7,9,
  19. Shota Nakamura5,
  20. Hidenori Inohara2,
  21. Atsushi Kumanogoh3,10,
  22. Kiyoshi Takeda4,11,
  23. Yukinori Okada1,12,13
  1. 1 Department of Statistical Genetics, Osaka University School of Medicine Graduate School of Medicine, Suita, Japan
  2. 2 Department of Otorhinolaryngology - Head and Neck Surgery, Osaka University Graduate School of Medicine, Suita, Japan
  3. 3 Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Japan
  4. 4 Laboratory of Immune Regulation, Department of Microbiology and Immunology, Osaka University Graduate School of Medicine, Suita, Japan
  5. 5 Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
  6. 6 Department of Rheumatology and Allergology, Saiseikai Senri Hospital, Suita, Japan
  7. 7 Rheumatology and Allergology, NHO Osaka Minami Medical Center, Kawachinagano, Japan
  8. 8 Division of Rheumatology, Department of Internal Medicine, Daini Osaka Police Hospital, Tennoji-ku, Japan
  9. 9 Clinical Research, NHO Osaka Minami Medical Center, Kawachinagano, Japan
  10. 10 Department of Immunopathology, Immunology Frontier Research Center, Osaka University, Suita, Japan
  11. 11 WPI Immunology Frontier Research Center, Osaka University, Suita, Japan
  12. 12 Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
  13. 13 Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
  1. Correspondence to Dr Yukinori Okada, Department of Statistical Genetics, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, Japan; yokada{at}


Objective The causality and pathogenic mechanism of microbiome composition remain elusive in many diseases, including autoimmune diseases such as rheumatoid arthritis (RA). This study aimed to elucidate gut microbiome’s role in RA pathology by a comprehensive metagenome-wide association study (MWAS).

Methods We conducted MWAS of the RA gut microbiome in the Japanese population (n case=82, n control=42) by using whole-genome shotgun sequencing of high depth (average 13 Gb per sample). Our MWAS consisted of three major bioinformatic analytic pipelines (phylogenetic analysis, functional gene analysis and pathway analysis).

Results Phylogenetic case–control association tests showed high abundance of multiple species belonging to the genus Prevotella (e.g., Prevotella denticola) in the RA case metagenome. The non-linear machine learning method efficiently deconvoluted the case–control phylogenetic discrepancy. Gene functional assessments showed that the abundance of one redox reaction-related gene (R6FCZ7) was significantly decreased in the RA metagenome compared with controls. A variety of biological pathways including those related to metabolism (e.g., fatty acid biosynthesis and glycosaminoglycan degradation) were enriched in the case–control comparison. A population-specific link between the metagenome and host genome was identified by comparing biological pathway enrichment between the RA metagenome and the RA genome-wide association study results. No apparent discrepancy in alpha or beta diversities of metagenome was found between RA cases and controls.

Conclusion Our shotgun sequencing-based MWAS highlights a novel link among the gut microbiome, host genome and pathology of RA, which contributes to our understanding of the microbiome’s role in RA aetiology.

  • rheumatoid arthritis
  • autoimmune diseases
  • gene polymorphism

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  • Handling editor Josef S Smolen

  • Contributors TK and YuO designed the study, conducted the data analysis and wrote the manuscript. YMae, TN, DM, YMat and SN conducted the experiments. YMae, TN, MM, HM, MY, SK, ST, EO, YaO, KK, SH, TH, MN, AO and YS collected the samples. HI, AK, KT and YuO supervised the study.

  • Funding This research was supported by the Japan Society for the Promotion of Science (JSPS) KAKENHI (15H05911, 19H01021), the Japan Agency for Medical Research and Development (AMED; 19gm6010001h0004, 19ek0410041h0003, 19ek0109413h0001, 19km0405211h0001), Takeda Science Foundation, Bioinformatics Initiative of Osaka University Graduate School of Medicine, and Grant Program for Next Generation Principal Investigators at Immunology Frontier Research Center (WPI-IFReC), Osaka University.

  • Competing interests None declared.

  • Patient consent for publication Not required.

  • Provenance and peer review Not commissioned; externally peer reviewed.

  • Data availability statement The whole-genome shotgun sequencing data are deposited in National Bioscience Database Center (NBDC) Human Database ( with the accession number of hum0197. The data are available upon reasonable request.

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