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The microbiome in rheumatology: Where are we and where should we go?
  1. Julia Manasson,
  2. Rebecca B Blank,
  3. Jose U Scher
  1. Division of Rheumatology, Department of Medicine, New York University Grossman School of Medicine, New York, New York, USA
  1. Correspondence to Dr Jose U Scher, Division of Rheumatology, Department of Medicine, New York University Grossman School of Medicine, New York, NY 10016, USA; jose.scher{at}


From birth, humans coexist and coevolve with trillions of micro-organisms inhabiting most body surfaces and cavities, referred to as the human microbiome. Advances in sequencing technologies and computational methods have propelled the exploration of the microbiome’s contribution to human health and disease, spearheaded by massive efforts such as the Human Microbiome Project and the Europe-based MetaHit Consortium. Yet, despite the accumulated body of literature and a growing awareness among patients, microbiome research in rheumatology has not had a key impact on clinical practice. Herein, we describe some of the landmark microbiome studies in autoimmunity and rheumatology, the challenges and opportunities of microbiome research and how to navigate them, advances in related fields that have overcome these pitfalls, and future directions of harnessing the microbiome for diagnostic and therapeutic purposes.

  • autoimmune diseases
  • microbiome
  • methods
  • study design
  • best practices
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  • Handling editor Josef S Smolen

  • Contributors 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 JUS is funded by NIH/NIAMS R01AR074500, the National Psoriasis Foundation, the Colton Center for Autoimmunity, the Riley Family Foundation and the Snyder Family Foundation.

  • Competing interests JUS has been granted USPTO patent no. 10011883 ('Causative agents and diagnostic methods relating to rheumatoid arthritis'). JUS has consulted for UCB, Janssen, Novartis 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.

  • Patient consent for publication Not required.

  • Provenance and peer review Commissioned; externally peer reviewed.

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