Microbial Ecology

, Volume 75, Issue 4, pp 821–829 | Cite as

Fungi in Gastrointestinal Tracts of Human and Mice: from Community to Functions

  • Jiayan Li
  • Daiwen Chen
  • Bing Yu
  • Jun He
  • Ping Zheng
  • Xiangbing Mao
  • Jie Yu
  • Junqiu Luo
  • Gang Tian
  • Zhiqing Huang
  • Yuheng Luo


Fungi are often ignored in studies on gut microbes because of their low level of presence (making up only 0.1% of the total microorganisms) in the gastrointestinal tract (GIT) of monogastric animals. Recent studies using novel technologies such as next generation sequencing have expanded our understanding on the importance of intestinal fungi in humans and animals. Here, we provide a comprehensive review on the fungal community, the so-called mycobiome, and their functions from recent studies in humans and mice. In the GIT of humans, fungi belonging to the phyla Ascomycota, Basidiomycota and Chytridiomycota are predominant. The murine intestines harbor a more diverse assemblage of fungi. Diet is one of the major factors influencing colonization of fungi in the GIT. Presence of the genus Candida is positively associated with dietary carbohydrates, but are negatively correlated with dietary amino acids, proteins, and fatty acids. However, the relationship between diet and the fungal community (and functions), as well as the underlying mechanisms remains unclear. Dysbiosis of intestinal fungi can cause invasive infections and inflammatory bowel diseases (IBD). However, it is not clear whether dysbiosis of the mycobiome is a cause, or a result of IBD. Compared to non-inflamed intestinal mucosa, the abundance and diversity of fungi is significantly increased in the inflamed mucosa. The commonly observed commensal fungal species Candida albicans might contribute to occurrence and development of IBD. Limited studies show that Candida albicans might interact with immune cells of the host intestines through the pathways associated with Dectin-1, Toll-like receptor 2 (TLR2), and TLR4. This review is expected to provide new thoughts for future studies on intestinal fungi and for new therapies to fungal infections in the GIT of human and animals.


Commensal fungi Community Diet Intestinal immune Candida albicans IBD 



The authors thank Prof. André-Denis G. Wright from The University of Arizona and Prof. Weihuan Fang from Zhejiang University for revising the manuscript.

Author Contributions

Jiayan Li wrote the paper; Daiwen Chen, Bing Yu, and Jun He helped to write the paper; Ping Zheng Xiangbing Mao, Jie Yu, Junqiu Luo, and Gang Tian collected the references; Zhiqing Huang and Yuheng Luo helped to collect the references and revised the paper; Yuheng Luo had primary responsibility for final content. All authors read and approved the final manuscript.

Compliance with Ethical Standards

Conflict of Interest

The authors declare that they have no conflict of interest.

Ethical Approval

This article does not contain any studies with human participants or animals performed by any of the authors.


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Copyright information

© Springer Science+Business Media, LLC 2017

Authors and Affiliations

  • Jiayan Li
    • 1
  • Daiwen Chen
    • 1
  • Bing Yu
    • 1
  • Jun He
    • 1
  • Ping Zheng
    • 1
  • Xiangbing Mao
    • 1
  • Jie Yu
    • 1
  • Junqiu Luo
    • 1
  • Gang Tian
    • 1
  • Zhiqing Huang
    • 1
  • Yuheng Luo
    • 1
  1. 1.Key Laboratory for Animal Disease-Resistance Nutrition of China, Ministry of Education, Animal Nutrition InstituteSichuan Agricultural UniversityChengduChina

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