Review article: fungal microbiota and digestive diseases

Abstract

Summary 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 106 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.

Intestinal fungi contribute to development of alcoholic liver disease

“…The predominant commensal fungal species in the human intestine are Candida species, Saccharomyces cerevisiae, and Malassezia species (9). Like commensal bacteria in the intestine, fungi interact with their host.…”

Fungi in the healthy human gastrointestinal tract

“…Specifically, whole-body perspectives of the human mycobiome are provided by Cui and colleagues, 10 Huffnagle and Noverr, 11 Seed, 12 and Underhill and Iliev, 13 while the gut mycobiota is reviewed by Ianiro and colleagues, 14 Kirschner and colleagues, 15 and Suhr and Hallen-Adams. 16 The role of the gut mycobiota in disease is reviewed by Moyes and Naglik, 17 Wang and colleagues, 18 Gouba and Drancourt, 19 Mukherjee and colleagues, 20 and Richard and colleagues. 21 In this paper, we focus on the gut mycobiome of healthy humans, with a particular emphasis on the relatively few fungi that are widely distributed in human gut samples.…”

Fungal Signature in the Gut Microbiota of Pediatric Patients With Inflammatory Bowel Disease

“…Innate immune receptor activation by fungi may augment the development of colitis. The main pattern recognition receptors for fungi include Dectin-1, Dectin-2, DC-SIGN, mannose receptor, and mannose-binding lectin (29). Dectin-1 is a C-type lectin receptor, which recognizes β-glucans in the fungal cell wall.…”