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The Role of Yeast in Digestive Function and Gut Health: Exploring the Gut Mycobiome

Key Topics: Digestive Health
September 16, 2023 • 3 min read
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The gut microbiome includes more than just bacteria. Yeast are a critical component of the gut microbiome, contributing to a healthy intestinal environment and aiding in digestion.

The gut is inhabited by far more than bacteria; it also contains viruses and fungi.1 While that may conjure up mental images of mushrooms or petri dishes, fungi are very important to the gastrointestinal (GI) system. More research studies are investigating the role of yeast as part of the gut mycobiome and the beneficial effects on human health, including digestive function and GI health. Together with bacteria, yeast promote healthy intestinal barrier function, influence host neurological function, modulate the immune system, and help regulate blood glucose levels.1

The gut mycobiome (a subpopulation of the gut microbiome that consists of fungi) is determined in part by environmental factors, including the diet.1 While research in this field is challenging, promoting a healthy gut environment through diet and lifestyle factors stimulates growth of beneficial microbes, both yeast and bacteria, which then further improves gut health.

“Biomes” in the Gut
Mycobiome Fungal species that live in the GI tract
Microbiome The genetic material of all the microbes in the gut


Understanding Yeast

Yeast that make up the gut mycobiome account for less than one percent of total gut microbes; however, they play an important role in gut health and the health of the entire body.1,2 There are about 140 different fungal genera although most belong to the Candida, Saccharomyces, and Cladosporium genera.2 Yeast species that reside in the gut either promote GI health or disturb it when dysbiosis occurs.2 Dysbiosis of yeast and other fungi in the gut has been related to several complex GI diseases, including inflammatory bowel disease and colorectal cancer.3-5  Many of these species contribute to gut health through several mechanisms, including facilitating nutrient extraction, assisting in digestion, training the immune system, and defending against harmful pathogens.6,7


Dysbiosis of yeast and other fungi in the gut has been related to several complex GI diseases, including inflammatory bowel disease and colorectal cancer.


The two most commonly studied yeasts for human health are Saccharomyces boulardii (S. boulardii) and Saccharomyces boulardii var. cerevisiae (S. cerevisiae). These two yeasts are members of the same species but have important differences related to their genetics, metabolism, and physiological effects.7 S. boulardii was first discovered in the 1920s and is extracted from lychee fruit.7,8 As a dietary supplement, S. boulardii concentrations typically reach a steady level in the gut within three days and are cleared from stool within two to five days after discontinuing, meaning the effects likely only last as long as it is being consumed.7

Yeast and Gut Health

Within the GI tract, yeast stimulate host immune defenses, neutralize bacterial toxins, and decrease bacterial adherence to intestinal epithelial cells, preventing translocation into circulation.7,9 They can also promote maintenance of the gut barrier membrane and decrease permeability to help inhibit pathogen translocation.7 Certain yeast species appear to interfere with pro-inflammatory cellular signaling pathways, decreasing inflammation by reducing the expression of inflammatory cytokines and blocking proteins involved in inflammation signaling (NF-κB and MAPK).7,9 Together, all of these actions result in significant protection from pathogenic invaders and inflammation within the gut.

Yeast of the mycobiome also play an important role in helping their host break down food. They enhance trophic factors including brush border membrane enzymes and nutrient transporters, which enables greater absorption of vital nutrients.7 This is especially important in GI conditions characterized by diarrhea due to its negative effects on microbiome composition and intestinal mucosa. Diarrhea can result in decreased intestinal enzymatic activity and transporter expression whereas certain yeast species, including S. boulardii, can help restore intestinal homeostasis.7,9,10 Many yeast species are also able to degrade phytate, helping to increase intestinal absorption of divalent minerals including iron, zinc, calcium, and magnesium.9

Diarrhea can result in decreased intestinal enzymatic activity and transporter expression whereas certain yeast species, including S. boulardii, can help restore intestinal homeostasis.


Other important gut functions of yeast include binding and degrading mycotoxins, secondary metabolites produced by other types of fungi that can lead to various diseases in both humans and animals.9 They can also increase short-chain fatty acid concentration in the gut, promoting water and electrolyte absorption.7 All of these functions can have a significant, positive impact on gut health.

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  1. Tian, Y., Gou, W., Ma, Y., Shuai, M., Liang, X., Fu, Y., Zheng, J.-S. (2023). The Short-Term Variation of Human Gut Mycobiome in Response to Dietary Intervention of Different Macronutrient Distributions. Nutrients, 15:2152.
  2. Shankar, J. (2021). Food Habit Associated Mycobiota Composition and Their Impact on Human Health. Front Nutr, 8:773577.
  3. Zhang, L., Zhan, H., Xu, W., Yan, S., Ng, S.C. (2021). The role of gut mycobiome in health and diseases. Ther Adv Gastroenterol, 14:1.
  4. Ott, S.J., Kühbacher, T., Musfeldt, M., Rosenstiel, P., Hellmig, S., Rehman, A., Drews, O., Weichert,W., Timmis, K.N., Schreiber, S. (2008). Fungi and inflammatory bowel diseases: Alterations of composition and diversity. Scand J Gastroenterol, 43:831.
  5. Luan, C., Xie, L., Yang, X., et al. (2015). Dysbiosis of fungal microbiota in the intestinal mucosa of patients with colorectal adenomas. Sci Rep, 5:7980.
  6. Schei, K., Avershina, E., Øien, T., Rudi, K., Follesad, T., Salamati, S., Ødegård, A. (2017). Early gut mycobiota and mother-offspring transfer. Microbiome, 5:107.
  7. Zanello, G., Meurens, F., Berri, M., Salmon, H. (2009). Saccharomyces boulardii effects on gastrointestinal disease. Curr Issues Mol Biol, 11:47.
  8. Gu, Y., Wang, C., Qin, X., Zhou, B., Liu, X., Liu, T., Xie, R., Liu, J., Wang, B., Cao, H. (2022). Saccharomyces boulardii, a yeast probiotic, inhibits gut motility through upregulating intestinal serotonin transporter and modulating gut microbiota. Pharmacol Res, 181:106291.
  9. Moslehi-Jenabian, S., Pedersen, L.L., Jespersen, L. (2010). Beneficial Effects of Probiotic and Food Borne Yeasts on Human Health. Nutrients, 2:449.
  10. Jahn, H.U., Ullrich, R., Schneider, T., Liehr, R.M., Schieferdecker, H.L., Holst, H., Zeitz, M. (1996). Immunological and trophical effects of Saccharomyces boulardii on the small intestine in healthy human volunteers. Digestion, 57:95.

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