Review article: fungal microbiota and digestive diseases

Aliment Pharmacol Ther. 2014 Apr;39(8):751-66. doi: 10.1111/apt.12665. Epub 2014 Feb 24.


Background: The role of the fungal microbiota in digestive diseases is poorly defined, but is becoming better understood due to advances in metagenomics.

Aim: To review the gastrointestinal fungal microbiota and its relationship with digestive diseases.

Methods: Search of the literature using PubMed and MEDLINE databases. Subject headings including 'fungal-bacterial interactions', 'mycotoxins', 'immunity to fungi', 'fungal infection', 'fungal microbiota', 'mycobiome' and 'digestive diseases' were used.

Results: The fungal microbiota is an integral part of the gastrointestinal microecosystem with up to 10(6) microorganisms per gram of faeces. Next-generation sequencing of the fungal 18S rRNA gene has allowed better characterisation of the gastrointestinal mycobiome. Numerous interactions between fungi and bacteria and the complex immune response to gastrointestinal commensal or pathogenic fungi all impact on the pathophysiology of inflammatory bowel disease and other gastrointestinal inflammatory entities such as peptic ulcers. Mycotoxins generated as fungal metabolites contribute to disturbances of gastrointestinal barrier and immune functions and are associated with chronic intestinal inflammatory conditions as well as hepatocellular and oesophagogastric cancer. Systemic and gastrointestinal disease can also lead to secondary fungal infections. Fungal genomic databases and methodologies need to be further developed and will allow a much better understanding of the diversity and function of the mycobiome in gastrointestinal inflammation, tumourigenesis, liver cirrhosis and transplantation, and its alteration as a consequence of antibiotic therapy and chemotherapy.

Conclusions: The fungal microbiota and its metabolites impact gastrointestinal function and contribute to the pathogenesis of digestive diseases. Further metagenomic analyses of the gastrointestinal mycobiome in health and disease is needed.

Publication types

  • Review

MeSH terms

  • Bacteria / isolation & purification
  • Feces / microbiology
  • Fungi / isolation & purification
  • Gastrointestinal Diseases / microbiology*
  • Gastrointestinal Diseases / physiopathology
  • Humans
  • Inflammation / microbiology*
  • Inflammation / physiopathology
  • Inflammatory Bowel Diseases / microbiology*
  • Inflammatory Bowel Diseases / physiopathology
  • Microbiota