Inflammatory bowel disease (IBD), a family of relapsing and remitting autoimmune diseases of the gut that afflicts approximately 3 million Americans, has set scientists on the decades-long hunt to understand which microbes (if any in particular) are responsible for launching the immune system into overdrive, where it attacks intestinal tissues.

However, most microbiome research thus far has focused on what science had the best tools to study: bacteria. To be sure, bacteria are a plentiful and diverse component of the gut ecology, comprising trillions of organisms. The research suggests a critical role for bacteria in both the protection of a balanced gut and the descent into disease. But bacteria are not the only microbes that inhabit the gut. Newer research is illuminating a more mysterious player on the IBD field, and one that could change the game: fungi.

Inflammatory Bowel Disease at the Confluence of Genetics and Environment

IBD is a complex disease, with both genetic and environmental factors implicated in its development. Scientists believe IBD results from inappropriate immune responses to the microbial milieu in the intestine, and yet the exact communication breakdown between host and microbiome is still under investigation, and likely varies according to individual susceptibility and environmental factors. The 2 main types of IBD are Crohn's disease and ulcerative colitis, both of which damage the intestine through immune hyperactivation, but manifest with unique sequelae in different regions of the gut. Crohn's disease overtakes the entire thickness of the intestinal wall in the places it strikes and can appear anywhere in the gastrointestinal tract from mouth to anus. Symptoms include severe abdominal pain, weight loss, diarrhea and more serious complications, such as strictures and fistulae. Ulcerative colitis inflames the rectum and distal colon with fiery ulcers on the surface of the intestinal epithelium, leading to pain and bloody diarrhea. Both forms of IBD appear to require microbes for the development of disease.

As many as 240 genomic variants have been found that increase the likelihood of developing IBD, most of which are related to different aspects of the immune system's relationship to microbes, or to the intestinal barrier that keeps them both at a healthy distance. Twin studies support a heritable component of IBD, with higher concordance among monozygotic (identical) twins compared to dizygotic (fraternal) twins. And yet, genetic susceptibility is often not enough to precipitate disease by itself. The epidemiology shows strong environmental risk factors, such as diet, antibiotic exposure, rural vs. urban living and smoking, and epigenetic studies show a role for gene-environment interactions. Immigrant studies are particularly relevant for environmental factors, as they show that the disease risk for people immigrating from low-risk to high-risk regions of the world can equilibrate within a single generation.

Thus, the thirst to understand the environmental factors that drive susceptibility to disease, and in particular the role of the microbiota. The advent of new technologies to probe the microbiota has led to a dramatic increase in knowledge about its role in translating our environment into our physiology, but as recently as 2017, only an estimated 0.4% of "microbiota" studies specifically included fungi. This has left the field with plentiful but incomplete knowledge about the role of the microbiota as it relates to diseases like IBD, for which microbes are central players.

Fungi in Inflammatory Bowel Disease

To be fair, technical barriers have made studying fungi more difficult relative to bacteria. Many of the current sequencing tools for fungi emulate those used for bacteria, but have added complications that hamper their effectiveness. Both sample type and DNA extraction method strongly influence the type of diversity seen in a sample, leaving potential biases and underrepresentation of specific fungi. Moreover, reference databases used to identify sequences are still fledgling, meaning that the bioinformatic ability to trust a taxonomic identity is still imperfect.

However, limitations in technology are not for lack of curiosity. Fungi have long been of interest to scientists studying IBD. Like bacteria, they are ubiquitous in the environment, present in the body (including the gut) and sensitive to environmental factors, such as diet. Recent work shows that they take part in the assembly of the bacterial microbiome and influence immunological development in young mice. Early studies have shown that like bacteria, there is a fungal dysbiosis (or an imbalance in the community compared to healthy subjects) during IBD. Patients with Crohn's disease have elevated circulating antifungal antibodies, and certain fungal species, such as Candida albicans, actively worsen inflammatory colitis in mouse models. By contrast, other fungi, such as Saccharomyces boulardii, are therapeutic for the gut. Notably, many susceptibility genes are part of the interleukin-23 (IL-23) pathway, which helps regulate the body's response to outside pathogens like fungi. Thus, there is a promising role for fungi in the broader picture of IBD and its pathogenesis.

Fungi also influence the bacterial dynamics observed in the gut, partnering with them for cooperative and, occasionally, nefarious ends. Like other kinds of microbes, they have potentially been behind the scenes in many of the previous bacterial studies, a sort of dark matter pulling the strings. For instance, bacterial biofilms are known to be affiliated with IBD, including biofilms formed by adherent-invasive Escherichia coli. Interkingdom research shows that the yeast Candida tropicalis can team up with E. coli and Serratia marcescens bacteria to create a monstrous biofilm larger than any formed by just 1 or 2 of the species alone, and that this biofilm induces expression of fungal hyphae, which can be a marker for pathogenicity. These 3 species are abundant in patients with Crohn's disease compared to their healthy relatives, suggesting a camaraderie in their virulence.

Moreover, the inherent competition between fungi and bacteria for habitat and nutrients within the gut means that courses of antibiotics commonly given during intestinal disease disrupt more than just bacterial communities. Rather, since antibiotics selectively eliminate bacteria while leaving fungi undisturbed, antibiotics can dramatically tip the interkingdom balance and give fungi stronger prominence in the gut than they otherwise would have. Notably, antibiotics are a risk factor for the development of new IBD.

New research from Jain et al. suggests that this kind of disruption is not benign. Normally, wound healing in the gut is a cooperative process with commensal microbes, such as Akkermansia muciniphila bacteria, that help induce immune responses necessary to repair mucosal tissues. Yet, Jain et al. show that the fungus Debaryomyces hansenii is not only enriched in tissue from Crohn's patients, but actively disrupts the intestine's ability to repair itself. Thus, it's feasible that a simple course of antibiotics could interfere with the ancestral and symbiotic process of self-repair, through both bacterial and fungal means.

Interestingly, D. hansenii is also a microbial player in the food industry, where its high tolerance for salinity and pH variations make it ideal for curing and processing all kinds of meats and cheeses. Notably, meat intake has been associated with a higher rate of relapse for ulcerative colitis. A potential picture emerges in which dietary exposure and medical practice converge on a susceptible individual to invite IBD pathology. It's a picture seen with sharper resolution in light of the fungal members of the intestinal microbiota, and could surely be improved even further by the continued inclusion of other kinds of microbes in IBD microbiota studies as well.

As sequencing and culture technologies improve, future studies should continue to investigate the role of fungi in the gut, in both health and disease. Current knowledge about the bacterial microbiome is truly fascinating and paradigm-shifting, but little is known about other microbial players. For example, viruses farm gut bacterial populations and archaea and protozoa that have thus far remained in relative anonymity. These investigations will prove interesting and relevant and may hold some of the elusive answers the field has been itching for.