Effects of Intestinal Fungi and Viruses on Immune Responses and Inflammatory Bowel Diseases

Gastroenterology. 2020 Dec 18;S0016-5085(20)35564-5.doi: 10.1053/j.gastro.2020.06.100. Online ahead of print.

Iliyan D Iliev 1, Ken Cadwell 2


Author information

  • 1Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA; The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA; Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA. Electronic address: iliev@med.cornell.edu.
  • 2Kimmel Center for Biology and Medicine, Skirball Institute, New York University Grossman School of Medicine, New York, NY, 10016, USA; Department of Microbiology, New York University Grossman School of Medicine, New York, NY, 10016, USA; Division of Gastroenterology and Hepatology, Department of Medicine, New York University Langone Health, New York, NY, 10016, USA. Electronic address: ken.cadwell@med.nyu.edu.


The intestinal microbiota comprises diverse fungal and viral components, in addition to bacteria. These microbes interact with the immune system and affect human physiology. Advances in metagenomics have associated inflammatory and autoimmune diseases with alterations in fungal and viral species in the gut. Studies of animal models have found that commensal fungi and viruses can activate host-protective immune pathways related to epithelial barrier integrity, but can also induce reactions that contribute to events associated with inflammatory bowel disease. Changes in our environment associated with modernization and the COVID-19 pandemic have exposed humans to new fungi and viruses, with unknown consequences. We review the lessons learned from studies of animal viruses and fungi commonly detected in the human gut and how these might affect health and intestinal disease.

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