The overlooked mycobiota: Emerging evidence of fungi’s role in immune and gut health

A new review spotlights mycobiota, the often-overlooked part of the gut microbiome that includes various fungi. Although it makes up a small segment, it plays a crucial role in shaping immunity and affecting health and disease. Nutrition Insight talks to one of the researchers to learn about the mycobiota, which opens an underexplored challenge for developing new nutrition solutions. 

The review, published in Virulence, reflects optimism about emerging research surrounding the gut microbiome’s fungal component that may potentially improve scientists’ understanding and treatments of diseases, such as inflammatory bowel disease, asthma, and carcinogenesis. It could also play a role in cancer development through immune modulation and its interactions with tumor-associated microbiota.

“Although fungi make up only a small fraction of the gut microbiota, their larger cell structures, metabolic capacity, and unique components such as β-glucans, mannans, and chitin allow them to exert disproportionate effects on the immune system,” says Dr. Youqun Xiang, at the

Department of Colorectal and Anal Surgery, The First Affiliated Hospital of Wenzhou Medical University.

“Experimental studies suggest that fungi can act as powerful immunological ‘signalers,’ but most of these findings come from bacterial-depletion models. Translating those insights to intact microbial ecosystems remains an open challenge.”

The review notes that Candida typically dominates the intestinal fungal community in humans. Other key species include Saccharomyces, Malassezia, Penicillium, Cladosporium, Aspergillus, Debaryomyces, Pichia, Cladosporium, Galactomyces, and Trichosporon. 

“One of the central questions is whether fungal imbalances drive disease or whether disease states reshape the mycobiota,” notes Xiang, but “current evidence is inconclusive.” 

“Some fungal probiotics and antifungal interventions show potential in alleviating disease outcomes, but the mechanisms — specific strains, metabolites, or host interactions — are not yet fully defined. More mechanistic studies and clinical validation are essential before moving toward disease-specific claims.”

Probiotics modulating the mycobiota

The review spotlights probiotics’ potential as an alternative antifungal therapy, with emerging research proving they can suppress certain yeasts for treating health issues. 

The gut microbiome’s fungal component may improve treatments of diseases, such as inflammatory bowel disease, asthma, and carcinogenesis.It adds that while ulcerative colitis and Crohn’s disease have been linked to microbiome imbalances, patients have also been noted to experience mycobiota dysbiosis, experiencing fungal outgrowth.

“The probiotic field has focused overwhelmingly on bacteria, leaving the fungal dimension largely unexplored,” says Xiang. 

“Yet fungi are already part of everyday diets through fermented foods like bread, cheese, and wine. Their relative genetic stability and unique metabolic activities could make them particularly attractive candidates for safe and predictable probiotic development.”

For instance, Lactobacillus spp. and Bifidobacterium spp. demonstrated antifungal properties in vitro. 

“Oral administration of Escherichia coli strain Nissle 1917, Lactobacillus acidophilus, Bifidobacterium lactis, Bifidobacterium longum, and Bifidobacterium bifidum has been shown to inhibit the growth of pathogenic fungi like Candida albicans in the gastrointestinal tract,” details the paper. 

“Additionally, fungal species such as Saccharomyces cerevisiae and Saccharomyces boulardii are widely used probiotic yeasts for treating diarrhea.”

The researchers point out that these probiotics modulate the mycobiota through filamentation, adhesion, and biofilm.

Diets’ influence on mycobiota

The study notes that diet also plays a role in influencing the composition of gut microbiota and mycobiota. 

Dietary sources of SCFAs, generated by gut bacteria, can inhibit the growth of Candida spp.Studies have linked carbohydrate-rich and Western diets high in fat and sugar and low in vegetable fiber to Candida growth and a decrease in beneficial anaerobic bacteria populations, like Bifidobacterium.

“Dietary sources of short-chain fatty acids (SCFAs), generated by gut bacteria, can inhibit the growth of Candida spp. by regulating its metabolism, gene expression, and signalling pathways. Not only can the nutrients affect the gut mycobiota, but food is also an important source of gut fungi,” the paper details.

“Plant-based diets and animal-based diets are also correlated with Penicillium and Candida abundance, respectively.” This year, a study of 21,561 people found that plant-based diets shape healthier microbiomes and have better cardiometabolic outcomes.

Consuming bread and beer has been correlated with Saccharomyces cerevisiae levels in human stools.

“Saccharomyces boulardii has now been proved to be effective in the treatment of gastrointestinal infections caused by Helicobacter pylori, Salmonella, and Clostridium difficile,” the review adds.

Gut fungi have also been linked to regulating immune responses, such as asthma. The condition is triggered by inhalation of fungal species such as Aspergillus, Penicillium, and Alternaria.

The review points out that the mechanisms by which these fungi are detected by intestinal components, causing lung sensitivity to allergens, are not fully understood. Studies have found Wallemia mellicola, a species linked to asthma sensitization, in salt-fermented foods.

“Since the early wave of microbiome research has already consumed much of the market’s initial enthusiasm, future efforts should focus on uncovering the precise mechanisms of host–microbiota interactions,” Xiang suggests. 

“The probiotic field has focused overwhelmingly on bacteria, leaving the fungal dimension largely unexplored,” says Xiang.“To build credibility and advance the field, it will be essential to collaborate closely with clinical studies that can help disentangle causality from mere association.”

Microbiome mania

Research on the microbiome is booming. A recent study suggests that protein sources can significantly impact gut microbiota, which could have implications for human health and disease prevention. It suggests egg white protein may harm gut health by promoting mucin-degrading bacteria, while brown rice is less harmful and more compatible with maintaining microbial balance, and yeast falls somewhere in the middle, providing beneficial shifts but risking mucosal degradation.

Recently, scientists created a microbial map revealing how every actor in the food system should restore and protect shrinking microbiomes to boost human and planetary health. This alarming trend affects ecosystems at large and shows the interconnections between microbial diversity in soil, water, and the human gut.

Meanwhile, gut microbes, which were previously thought to feed on dietary fiber, may actually feed on glucose excreted by the host, according to research from Kobe University, Japan. The report suggests that as a result, these bacteria produce SCFA, which are essential to several body functions. The study authors suggest the symbiotic relationship is a precursor to new therapeutics.