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Microbiome research in autoimmune and immune-mediated inflammatory diseases: lessons, advances and unmet needs
  1. Jose U Scher1,
  2. Renuka Nayak2,3,
  3. Jose C Clemente4
  1. 1Department of Medicine, NYU Psoriatic Arthritis Center, and NYU Colton Center for Autoimmunity, New York University School of Medicine, New York, New York, USA
  2. 2University of California San Francisco, San Francisco, California, USA
  3. 3San Francisco VA Medical Center, San Francisco, California, USA
  4. 4Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
  1. Correspondence to Dr Jose U Scher; jose.scher{at}nyulangone.org

Abstract

The increasing prevalence of autoimmune and immune-mediated diseases (AIMDs) underscores the need to understand environmental factors that contribute to their pathogenesis, with the microbiome emerging as a key player. Despite significant advancements in understanding how the microbiome influences physiological and inflammatory responses, translating these findings into clinical practice remains challenging. This viewpoint reviews the progress and obstacles in microbiome research related to AIMDs, examining molecular techniques that enhance our understanding of microbial contributions to disease. We discuss significant discoveries linking specific taxa and metabolites to diseases such as rheumatoid arthritis, systemic lupus erythematosus and spondyloarthritis, highlighting the role of gut dysbiosis and host–microbiome interactions. Furthermore, we explore the potential of microbiome-based therapeutics, including faecal microbiota transplantation and pharmacomicrobiomics, while addressing the challenges of identifying robust microbial targets. We advocate for integrative, transdisease studies and emphasise the need for diverse cohort research to generalise findings across populations. Understanding the microbiome’s role in AIMDs will pave the way for personalised medicine and innovative therapeutic strategies.

  • Arthritis
  • Autoimmune Diseases
  • Therapeutics

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Footnotes

  • Handling editor Josef S Smolen

  • X @RNayakMD

  • Contributors JUS is guarantor. All authors have contributed to the conception of the work, drafting and revising the work, and final approval of the version to be published.

  • Funding NIH NIH/NIAMS UC2 AR081034 (Scher, Clemente); NIH/NIAMS R01AR074500 (JUS, RN, JCC); National Psoriasis Foundation, The Colton Center for Autoimmunity, The Riley Family Foundation and The Snyder Family Foundation (JUS)

  • Competing interests JCC and RN have no conflicts to declare. JUS has served as a consultant for Janssen, Pfizer, Sanofi, UCB and BMS; and has received funding for investigator-initiated studies from Janssen and Pfizer.

  • Patient and public involvement Patients and/or the public were not involved in the design, or conduct, or reporting, or dissemination plans of this research.

  • Provenance and peer review Commissioned; externally peer reviewed.