Clinical Journal of Gastroenterology

, Volume 11, Issue 6, pp 449–456 | Cite as

The evidence for fungus in Crohn’s disease pathogenesis

  • Jun Miyoshi
  • Mark Anthony Sofia
  • Joseph Francis PierreEmail author
Clinical Review


Current evidence suggests the etiology of inflammatory bowel diseases (IBD) involves the confluence of host genetic, environmental, and microbial factors that lead to chronic, and often refractory, disease in susceptible individuals. The involvement of microbial triggers in IBD, including Crohn’s disease (CD), is increasingly evident with supporting data provided with advancements in metagenomic sequencing that have identified perturbations in microbial structure and function—broadly termed dysbiosis—in CD patients compared with healthy subjects. This concept is supported by the finding germ-free animals with CD genetic susceptibility fail to develop disease; demonstrating microorganisms are necessary but not sufficient for CD. The vast majority of CD microbiome research has focused on the complex bacterial communities and microbiome dysbiosis in the gut with 16S metagenomic sequencing. However, emerging data capturing eukaryotes suggest fungal opportunistic pathogens are also associated with IBD pathogenesis and chronicity. This hypothesis is further supported by historical observations that CD patient populations display elevated antibodies against fungal targets, even evident before disease diagnosis. This review discusses the current findings in the field, followed by historical and metagenomic evidence for fungal pathogens in the development and recurrence of CD in adult and pediatric populations.


Inflammatory bowel diseases Microbiome Mycobiome Fungal pathogens Crohn’s disease 


Compliance with ethical standards

Conflict of interest

The authors declare no conflicts of interest.


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Copyright information

© Japanese Society of Gastroenterology 2018

Authors and Affiliations

  • Jun Miyoshi
    • 1
  • Mark Anthony Sofia
    • 1
  • Joseph Francis Pierre
    • 2
    Email author
  1. 1.Section of Gastroenterology, Hepatology, and Nutrition, Department of MedicineThe University of ChicagoChicagoUSA
  2. 2.Department of PediatricsThe University of Tennessee Health Science CenterMemphisUSA

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