The educational content in this post, elaborated in collaboration with Lesaffre, was independently developed and approved by the GMFH publishing team and editorial board.

Fungi are a small but important component of your gut microbiome

While bacteria are the main component of your gut microbiome, other key microorganisms are also present. They include archaea (similar to bacteria in shape and size), viruses, phages (viruses that selectively kill bacteria), fungi (including yeasts and molds), and all influence not only other gut microbes, but your health and quality of life.

Bacteria and archaea account for more than 99% of the overall mass of the entire gut microbiome. And even though fungi represent a small part of the gut microbiota, they are bigger cells than bacteria and their genes can codify for up to 15,000 fermentative functions (compared with the 1,500 to 2,000 genes encoded by gut bacteria belonging to the Lactobacillus and Bifidobacterium genera).

It is important to remember that fungi are not the enemies of bacteria, as they live together and both are involved in digestive and immune functions that are important for health. For instance, the alteration of the gut mycobiota has been associated with various diseases including inflammatory bowel disease, irritable bowel syndrome, coeliac disease and some cancers.

Mathias L. Richard from the Micalis Institute at France’s National Research Institute for Agriculture, Food and Environment (INRAE) explained in a video interview with GMFH editors that, despite their relevance to our health, the gut mycobiota has been largely overlooked until recently, mainly due to its presence in the gut in smaller amounts than bacteria and the smaller scientific community focused on characterizing and examining them in detail.


Diet is the factor that has the greatest influence on gut mycobiota

Candida and Saccharomyces are among the most abundant fungi present in the human gut. The mother’s mycobiota, found in the gut, skin and breast milk, is thought to be the first contact a baby has with fungi. In childhood, the first fungi colonizers, such as Debaryomyces species, are replaced by the strains identified in adults, consisting mainly of 10 common genera (Candida, Saccharomyces, Penicillium, Aspergillus, Cryptococcus, Malassezia, Cladosporium, Galactomyces, Debaryomyces and Trichosporon) and additional fungi whose composition is largely influenced by diet.

As with gut bacteria, lifestyle and diet have a huge influence on the composition and functions of gut mycobiota. For instance, the abundance of Candida species has been related to a high consumption of carbohydrate-rich foods and living in urban areas favors the presence of Saccharomyces cerevisiae.

Mathias L. Richard explains that “The vast majority [of gut fungi] was provided by food intake, from the fungi used for food production but also from fungi present in the fruit and vegetables we eat. As very few fungi provided by our food have the capacity to persist for more than 24 hours in the gut, it is likely that the mycobiota will change more than the bacterial microbiota and be less resilient.”


Which factors can alter your gut mycobiota and what can you do to look after it?

Gut mycobiota research is of importance for health, which is supported by the observation of an altered composition and/or functional diversity of fungi in diverse diseases. For instance, gut mycobiome composition emerges as a potential target in the management of inflammatory bowel diseases and colon and pancreatic cancers, with Malassezia being the most abundant fungal genus in both types of cancer.

A wide range of factors can determine or alter your gut mycobiota, including delivery method, gestational age, environment, season, diet, gender, antibiotic exposure, and chronic diseases that are not necessarily linked to the gut, such as obesity. Some of those factors have a direct influence, including what you eat every day, which has the greatest effect.

The availability of protein, fat and sugars in your diet can also influence your fungal microbiota, as happens with gut bacteria. The community of bacteria that live in close contact also communicate constantly with fungi through their metabolites and both can compete with the nutrients available in the gut or collaborate for mutual development. That means that any alterations in the balance of gut bacteria can affect the fungal microbiota and the reverse is also observed.

Beyond diet and gut bacteria, host genetics, age, sex and drugs can also affect the gut mycobiota. In particular, the health of your immune system is an important determinant of the composition of your gut mycobiota. For instance, individuals with a weakened immune system resulting from diabetes, HIV infection or the use of drugs that suppress the immune system (e.g., corticosteroids) are more likely to suffer an overgrowth of Candida species and infection of mucous membranes and moist areas of the skin, compared to healthy adults.

It is also important to note that the gut fungal community can influence host immunity to protect against bacterial and fungal infections. The link between the gut mycobiota and immune system is reflected by the impact of an altered gut mycobiota composition and the course of some immune-related diseases such as inflammatory bowel diseases.

Due to the emerging scientific interest in harnessing the gut mycobiota for health benefits, some strategies suggested for modifying the gut mycobiome with a documented alteration of the gut fungi community include fecal microbiota transfer, antifungal drugs for eliminating deleterious fungi and dietary interventions. However, most research in the gut mycobiota comes from animal models and it is too early to recommend a specific “recipe” to take care of it.

However, none of these methods have been validated for specific human diseases yet, caution is needed when seeking a one-size-fits all approach for taking care of your gut mycobiome. When it comes to what is the best dietary advice for taking care of your gut fungi, Mathias L. Richard acknowledges that “Since the definition of a good fungal gut microbiota is not yet known, we do not know what are the best ways of taking care of your gut mycobiota yet.”



Take-home messages

  • Fungi are a small component of the gut microbiome, but emerging studies highlight their crucial role for digestive and immune health.
  • The food you eat daily is the most important factor that shapes your gut fungi.
  • Fungi and bacteria in the gut work as a team and any alterations in the balance of one affect the other.
  • Strategies of potential interest for modifying the gut mycobiota for health benefits include diet, yeast probiotics, fecal microbiota transfers and antifungal drugs.



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