Are we finally saluting the fungal kingdom as a co-ruler of GI health and disease?

March 11, 2015 By: Christen Rune Stensvold

Are we finally saluting the fungal kingdom as a co-ruler of GI health and disease?

The human body is host to myriads of fungal species—typically yeasts, moulds and dermatophytes. It has also long been known that Candida spp. present on the skin or mucosal surfaces can end up causing invasive mycotic disease in immunocompromised individuals, critical care patients and in those undergoing abdominal surgery, resulting in candidaemia or deep-seated candidiasis. Meanwhile, the impact of intestinal fungal colonisation and infection on gastrointestinal health and disease remains elusive. Thanks to advances in DNA detection technologies and mass spectrometry, the role of fungi in human gastrointestinal pathology, immunology and ecology is now finally—though slowly—being unravelled.

Over the past few years, communities of intestinal bacteria have been scrutinized meticulously in order to identify their role in human health and disease. This discipline is now commonly referred to as ‘gut microbiome research’, involving analysis of the structure and function of bacteria. Meanwhile, kingdoms of ubiquitous organisms in and on the human body have been more or less ignored;1,2 these kingdoms include fungi and parasitic protists.

If we acknowledge the fact that such organisms are common denizens of our gastrointestinal canal,3 why have they failed to catch our attention? Firstly, it’s not unusual to hear people saying that bacteria outnumber microbial eukaryotic organisms a zillion times or so, and that bacteria are therefore seemingly much more important to study. However, while the crude number of colonising eukaryote organisms may be several orders of magnitudes lower than the number of bacteria, we should remember that the genomes of such organisms are typically larger, and the expressed gene repertoire may be much more comprehensive and refined. Secondly, problems related to detection and identification are almost certainly one of the main reasons why we have failed to include eukaryotes in gut microbiome research. Finally, the potentially ‘bittersweet’ nature of fungal colonisation may blur the pathway to knowledge.

The bittersweet nature of fungal colonisation is highlighted in a talk given by Dr Gianluca Ianiro at EAGEN Gut Microbiota 2014: EAGAN Advances in Gut Microbiota and Fecal Microbiota Transplantation.4 Dr Ianiro also addresses the fundamental question of why we should bother about the fungal microbiome (the mycobiome) at all. He puts emphasis on the fact that a yeast such as Saccharomoyces cerevisiae var. boullardi is widely used as a probiotic (and possibly the only commercialised probiotic yeast), but that Saccharomyces is also a potential cause of fungaemia, suggesting that the virulence and/or host response to the yeast may vary dramatically.

“Nobody is fungus-free,” Huffnagle and Noverr claim in an article published in 2013.5 They go on, “Every individual’s microbiome contains thousands of different species of microbes, of which 99.9% of the total number of microbial cells belong to only a few species. The less abundant (< 0.1%), but more diverse, component of the microbiome has been termed the ‘rare biosphere’. The impact of this rare biosphere on human health is significant because it can act as a reservoir for blooms of pathogenic microbes when the host is compromised.”  Asymptomatic yeast colonisation of mucosal surfaces may develop into a yeast infection in cases where the microbial ecology is skewed, for example during and/or after the use of antibiotics. Although research into the gut mycobiome is still in its infancy, it is clear that species of Candida can coexist with the intestinal bacterial microbiome, bloom during dysbiosis due to use of antibiotics and colonise inflamed intestinal mucosal surfaces.

Very recently, Luan and colleagues6 analysed the fungal microbiota by deep sequencing the internal transcribed spacer 1 region (the marker commonly used for DNA-based fungal identification) of fungal DNA extracted directly from rinsed tissue biopsy samples from early-stage and advanced-stage colorectal adenomas as well as from adjacent (normal) tissue. The authors identified that core operational taxonomic units (OTU; taxonomic level of sampling when only DNA data are available) formed separate clusters for advanced and nonadvanced adenomas, for which the abundance of four OTU differed significantly. Both adenoma size and disease stage were associated with changes in the fungal microbiota. With no control material from healthy individuals available for analysis, the most important take-home message here may not be so much the findings, but the technical approach and the recognition that—similar to bacteria—intestinal eukaryotic communities may be significantly linked to disease processes, including that of colorectal cancer (CRC), in which case the microbiota represents not only a potential means of CRC detection (screening by biomarkers) but also intervention (microbiota manipulation).

In a very recent review, Mukherjee and co-workers conclude that fungi may contribute to aggravating inflammatory responses, leading to increased disease severity.7 This process may involve multiple steps and components, including interactions between host immune cells with specific pattern-recognition receptors (e.g. dectin-1—a natural-killer-cell-receptor-like C-type lectin possibly involved in innate immune responses to fungal pathogens through recognition of β-glucan8) and pathogen-associated molecular patterns, including fungal cell wall moieties, such as mannan, glucan and chitin. Intriguing observations published in 2012 in Science by Iliev and co-workers9 suggest that certain polymorphisms in CLEC7A, the gene encoding dectin-1, are associated with medically refractory ulcerative colitis.

The presence of live fungi in stools is also interesting from the faecal microbiota transplantation (FMT) perspective. Which organisms—which potential pathogens—are screened for when manufacturing FMT products? This is one of several topics that will be addressed at the UEG-endorsed practice course ‘The Fecal Microbiota Transplantation’, which is taking place in Rome in April. 

And while we’re at it, how should we screen for fungi in stool samples? There are probably many opinions on that! Gouba and Drancourt have suggested the use of ‘culturomics’, which involves the use of several different culture media and incubation conditions to increase the efficiency of detection of organisms by culture, later identified by MALDI-TOF-MS to expand the repertoire of species and safeguard comprehensive detection.10 Whether this approach has advantages over metagenomics remains to be revealed.

Novel technologies and increased availability of genome data enable precise and sensitive detection and identification of fungal and other microeukaryotic organisms in the gastrointestinal tract and how they interact with each other and the host. Efforts to map differences in fungal diversity in various cohorts are essential to generating hypotheses on the role of fungi in disease. Such studies are often cross-sectional; however, longitudinal studies of the intestinal mycobiota and mycobiome in healthy and diseased cohorts are critical if we are to obtain a more detailed and accurate understanding of exactly how fungi govern our health.


  1. Anderson LO, Nielsen HV and Stensvold CR. Waiting for the human intestinal Eukaryotome. ISME J 2013; 7: 1253–1255.
  2. Norman JM, Handley SA and Virgin HW. Kingdom-agnostic metagenomics and the importance of complete characterization of enteric microbial communities. Gastroenterology 2014; 146: 1459–1469. 
  3. Scanlan PD and Marchesi JR. Micro-eukaryotic diversity of the human distal gut microbiota: qualitative assessment using culture-dependent and -independent analysis of faeces. ISME J 2008: 2: 1183–1193.
  4. Ianiro G. Gut Mycome. Presentation at the EAGEN Gut Microbiota 2014: EAGEN Advances on Gut Microbiota and Fecal Microbiota Transplantation. 
  5. Huffnagle GB and Noverr MC. The emerging world of the fungal microbiome. Trends Microbiol 2013; 21: 334–341. 
  6. Luan C, Xie L, Yang X, et al. Dysbiosis of fungal microbiota in the intestinal mucosa of patients with colorectal adenomas. Sci Rep 2015; 5:7980. doi: 10.1038/srep07980.
  7. Mukherjee PK, Sendid B, Hoarau G, et al. Mycobiota in gastrointestinal disease. Nat Rev Gastroenterol Hepatol 2015; 12: 77–87.
  8. Brown GD. Dectin-1: a signaling non-TLR pattern-recognition receptor. Nat Reviews Immunol 2006; 6: 33–43. 
  9. Iliev ID, Funari VA, Taylor KD, et al. Interactions between commensal fungi and the C-type lectin receptor Dectin-1 influence colitis. Science 2012; 336: 1314–1317.
  10. Gouba N and Drancourt M. Digestive tract mycobiota: A source of infection. Med Mal Infect 2015; 45: 9–16. 


Additional Information 

The photograph of Candida albicans grown on CHROM agar, in which a few hyphae are visible at 40x magnification, is provided courtesy of Rasmus Hare Jensen.

About the author

Dr Christen Rune Stensvold is a Senior Scientist and Public Health Microbiologist with specialty in parasitology. He has a Bachelor degree in Medical Sciences, an MSc in Parasitology, and a PhD in Health Sciences. He has been based at Statens Serum Institut, Copenhagen, since 2004. Since 2006, he has authored/co-authored more than 80 articles in international, peer-reviewed scientific journals. In 2013, he was awarded the Fritz Kauffmann Prize for his contribution to clinical microbiology in Denmark. For many years, he has been pursuing the role of common intestinal micro-eukaryotes in human health and disease. Follow Rune on Twitter @Eukaryotes.



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