Recent studies suggest that in addition to bacteria and viruses, mammalian gut is a home of diverse fungal community (mycobiota). Similar to bacteria, fungi might be involved in shaping the host mucosal immunity, but also provide a pool of potentially infectious organisms. Although commensal mycobiota do not lead to pathologies in healthy individuals, fungal infections are increasing in prevalence owing to more people living with suppressed immune systems, such as HIV, cancer and other immunosuppressed patients. However, the role of mycobiota during immunosuppression has not been explored yet. This is partially due to lack of standardized approaches, databases and experimental models to support the mycobiome studies. Immunosuppression therapy is a standard-of-care for many patients with autoimmune and chronic inflammatory conditions including Inflammatory Bowel Disease (IBD). These patient populations are frequently receiving immunomodulatory therapy and provide a pool of individuals, where gut mycobiota can be investigated under such conditions. Our preliminary studies identified fungal taxa associated with Ulcerative Colitis (a form of IBD) and specific opportunistic fungi (including Candida albicans and Aspergillus sydowii) that expand in patients treated with immunosuppressive drugs. In a mouse model of colitis, we determined that upon immunosuppression, fungi can overgrow and that mice colonized with C. albicans, develop severe colitis soon after treatment withdrawal (modeling corticosteroid tapering in patients with inflammatory conditions). In this proposal, we will explore the hypothesis that immunosuppression therapy can affect the intestinal mycobiota composition leading to the overgrowth of potentially harmful fungi that may contribute to disease in patients with IBD and other inflammatory conditions. Employing a custom developed mycobiome bioinformatics pipeline and mouse models of colitis and immunosuppression, we will test our hypothesis in two specific aims.
In Specific Aim 1, we will evaluate the mycobiota composition in patients with IBD (UC and Crohn's disease) during treatment with Corticosteroids, 6MP/AZA and Anti-TNF. We will further use a mouse model of colitis therapy, to differentiate between disease-related inflammation and immunosuppression as two potentially independent factors affecting the gut mycobiota.
In Specific Aim 2, we will explore whether intestinal colonization with specific fungi (C. albicans and A. sydowii) that expand during immunosuppression aggravate intestinal disease. We will also assess whether anti-fungal treatment can ameliorate colitis and be used as a potential co-therapy. The results of this study will provide a map of mycobiota profiles associated with IBD, with the use of immunosuppression, as well as the in vivo effect of specific fungi during colitis therapy. This will be a step further in the identificaion of fungal taxa to be used as biomarkers to define subgroups of immunosuppressed patients, at a higher risk of fungal overgrowth, which might benefit from anti-fungal co- therapy.

Public Health Relevance

The intestines are home to a community of bacteria, but also fungi, which include organisms known as 'opportunistic pathogens', meaning that under circumstances where the immune system is suppressed, they have the capacity to cause disease. Nowadays, increasing number of people are diagnosed with autoimmune and inflammatory diseases including Inflammatory Bowel Disease (IBD) where the main treatment entails prolonged use of immunosuppression drugs. In this project we will identify fungi that expand in the intestines of IBD patients during immunosuppression therapy, will use mouse model to test whether these fungi can aggravate intestinal disease, and will evaluate whether anti-fungal medication can be used as a possible co- treatment option in IBD.

National Institute of Health (NIH)
National Institute of Allergy and Infectious Diseases (NIAID)
Exploratory/Developmental Grants (R21)
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Immunity and Host Defense (IHD)
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Rothermel, Annette L
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Weill Medical College of Cornell University
Internal Medicine/Medicine
Schools of Medicine
New York
United States
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Leonardi, Irina; Li, Xin; Semon, Alexa et al. (2018) CX3CR1+ mononuclear phagocytes control immunity to intestinal fungi. Science 359:232-236
Iliev, Iliyan D; Leonardi, Irina (2017) Fungal dysbiosis: immunity and interactions at mucosal barriers. Nat Rev Immunol 17:635-646
Li, Xin; Leonardi, Irina; Iliev, Iliyan D (2017) Candidalysin sets off the innate alarm. Sci Immunol 2:
Blander, J Magarian; Longman, Randy S; Iliev, Iliyan D et al. (2017) Regulation of inflammation by microbiota interactions with the host. Nat Immunol 18:851-860
Lionakis, Michail S; Iliev, Iliyan D; Hohl, Tobias M (2017) Immunity against fungi. JCI Insight 2: