Dysbiosis of gut fungal microbiota is associated with mucosal inflammation in Crohn's disease

J Clin Gastroenterol. 2014 Jul;48(6):513-23. doi: 10.1097/MCG.0000000000000035.


Goals: We aim to characterize the fungal microbiota in the intestinal mucosa and feces in patients with Crohn's disease (CD).

Background: Fungi represent a diverse microbial community in the human intestine and might play a role in the pathogenesis of CD; however, little is known about the structure and composition of the fungal microbiota especially adhering to the intestinal mucosa in CD patient.

Study: Nineteen patients with active CD and 7 healthy individuals were recruited in this study. The mucosa-associated and fecal fungal microbiotas in CD patients were analyzed using culture-independent community fingerprint techniques.

Results: The fungal richness and diversity were significantly elevated in the inflamed mucosa compared with the noninflamed mucosa. The predominant fungal composition in the inflamed mucosa was strikingly altered, mainly characterized by expansion in the proportions of Candida spp., Gibberella moniliformis, Alternaria brassicicola, and Cryptococcus neoformans. The fecal fungal community was perturbed in CD patients as accompanied by increased fungal diversity and prevalence in Candida albicans, Aspergillus clavatus, and C. neoformans. The species richness and diversity of the mucosal fungal community were associated with the expression of TNF-α, IFN-γ, or IL-10 (P<0.05). The diversity of the fecal fungal microbiota positively correlated with serum C-reactive protein and CD activity index (P<0.05).

Conclusions: This study first demonstrates that the fungal microbiota in the inflamed mucosa is distinguishable from that of the noninflamed area. Shifts of gut fungal microbiota composition may be associated with mucosal inflammation and disease activity of CD. Our data would provide novel insights into understanding the potential of gut fungal microbiota in the pathogenesis of CD.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adolescent
  • Adult
  • Aged
  • C-Reactive Protein / metabolism
  • Case-Control Studies
  • Crohn Disease / microbiology
  • Crohn Disease / pathology*
  • Dysbiosis / microbiology*
  • Feces / microbiology
  • Female
  • Fungi / isolation & purification*
  • Humans
  • Interferon-gamma / metabolism
  • Interleukin-10 / metabolism
  • Intestinal Mucosa / microbiology
  • Intestinal Mucosa / pathology*
  • Male
  • Microbiota
  • Middle Aged
  • Tumor Necrosis Factor-alpha / metabolism
  • Young Adult


  • Tumor Necrosis Factor-alpha
  • Interleukin-10
  • Interferon-gamma
  • C-Reactive Protein