The Role That Gut Fungi, Yeast & Viruses—Along With Good Gut Bacteria—Play In Our Health

The Role That Gut Fungi, Yeast & Viruses—Along With Good Gut Bacteria—Play In Our Health

  • Probiotics 101

  • By Desiree Nielsen, Registered Dietitian

    As our awareness of the microbiome grows like, well, bacteria multiplying – one significant consideration is often overlooked. A healthy gut is a diverse ecosystem, containing more than just bacteria. Amongst the legions of bacteria, there are viruses, yeast and fungi that leave us with many unanswered questions. What is the optimal balance? How can we influence these populations? How do the different microorganisms interact with each other…and us??

    Our focus has mainly been on the bacteria that call us home. Research on the virome, or virus microbiome, is far less advanced than our understanding of their bacterial neighbours1-4. Yeasts and fungi, often associated with infections like candida, also contribute to the gut population in predominantly unknown ways. The mycobiome, or fungal microbiome, is thought to account for 0.1%2 of the total microbiome but has the potential for a much more significant impact on the health of its ecosystem, and you.


    Unravelling the Myco Mystery

    Neither plant nor animal, fungi are a group of organisms genetically distinct from bacteria; bacteria are single-celled organisms that lack a DNA-containing nucleus. Fungal cells (and human cells for that matter) are known as eukaryotic, meaning that they do have a DNA-containing nucleus along with other membrane-bound organelles. Within the Fungal Kingdom, you have single-celled yeasts and multi-cellular fungi.

    Fungi are relatively mysterious organisms; in our environment, many edible mushrooms (a type of fungi) are prized for their medicinal properties, such as Reishi, Chaga and Lion’s Mane. We use other fungi to ferment and transform our favourite food and beverages, such as bread, cheese, beer and kombucha3.

    In our bodies, the composition of our core gut mycobiome is still unclear; however, Candida and Saccharomyces are known to be dominant species found in multiple locations in and on the human body, including the colon3,4. Just as with bacteria, the vaginal tract is abundant with yeasts and contributes to our colonization at birth. Diet and environment can also dictate our mycobiome makeup3-5. Fungi common in fermented foods, such as Saccharomyces, are commonly identified in our feces although it is not known whether they are a transient or resident presence in our guts5.


    How The Mycobiome Interacts with Digestive Health

    How humans benefit from our fungal community is also still a question. So how can we be sure that fungi contribute meaningfully to human health? Our best understood fungal interactions are in fact with opportunistic pathogens, that can cause infection when our microbiome and immune systems are weakened4,5. Think of oral thrush, athlete’s foot or vaginal yeast infection. Certain fungi such as Aspergillus species produce mycotoxins that can contribute to inflammation, gut barrier dysfunction and human disease including cancers5.

    We now know that fungi are found throughout the digestive tract, and some, such as Candida albicans, can survive the acidic environment of the stomach5. Emerging research suggests that those with Crohn’s disease may have higher levels of resident fungi than those without4,5. Antifungal medications have been shown to improve gut-level inflammation and symptoms of the inflammatory bowel diseases in a few studies5. It is also hypothesized that fungi may be involved in the development of irritable bowel syndrome, although it’s still too early in the research to tell5.

    Another solid clue about the role fungi play in human health comes via the research on fungal strains that have been shown to have a probiotic effect on the human body, namely Saccharomyces cerevisiae, which is sold as a probiotic. As with our research on bacteria, it has been shown that S.cerevisiae can not only produce a therapeutic benefit to humans but also appears to have the ability to fight off pathogenic members of its own species and interact synergistically with gut bacteria4,5.


    Cultivating a Strong Microbial Relationship

    As with any ecosystem, a diverse microbiome (that includes bacteria, viruses, yeast and fungi) is a healthy microbiome. We know that diet plays a significant role in shaping this ecosystem – there is even emerging evidence that the same is true for fungi4. In its current state, the research suggests that we should be eating plenty of colourful, high fibre plant foods to feed beneficial bacteria and help to control inflammation in the gut that can drive the growth of opportunistic pathogens. Avoiding tobacco use, in addition to an excess of added sugars and refined flours, will also help control the growth of microbial species such as E.coli bacteria and Candida yeast3-5.

    We should also extend this diversity into our homes; when the weather permits, throwing open the windows improves the variety of ambient microbes indoors. Eliminating the use of antibacterial home cleaners in favour of pure soaps or natural cleaners made with vinegar, and essential oils also supports microbial diversity. We are surrounded by beneficial microbes that help to control more pathogenic strains; in attempting to eradicate the microbes that make us sick, we also eliminate more protective strains that keep us well.

    Bacteria and fungi, as competing members of our microbiome, are in constant interaction with each other5. It is thought that some strains of Lactobacillus bacteria can inhibit the growth of Candida albicans, and support the immune system in its moderating actions5. Ensuring a robust, diverse community of beneficial bacteria supported by the daily use of an effective and high-quality probiotic, such as Bio-K+, is an important step in maintaining harmonious relationships with all of the microbes.


    The human body is a vast universe that continues to reveal its mysteries. While we are learning more about the microbiome every single day, it is to be expected that many more surprises are in store. Our understanding of fungi, and of the true diversity of our microbiome in general, is just beginning to bloom. Mycobiome research will help us to understand our bodies better and how to foster better health. As we continue to learn, eating a healthful, plant-centred diet and encouraging greater microbial diversity within is our best bet for a stronger inner ecosystem.


    Do you have more questions on gut health? Let us know in comments below! For more healthy inspirations, join our community. Click here to find Bio-K+ closest point of sale. Contact us or find us on Facebook and Instagram.



    1. Zou, Shimian et al. “Research on the Human Virome: Where Are We and What Is next.” Microbiome4 (2016): 32. PMC. Web. 18 May 2018.
    2. Qin, Junjie, et al. "A human gut microbial gene catalogue established by metagenomic sequencing." nature464.7285 (2010): 59.
    3. Nash, Andrea K., et al. "The gut mycobiome of the Human Microbiome Project healthy cohort." Microbiome5.1 (2017): 153.
    4. Suhr, Mallory J., and Heather E. Hallen-Adams. "The human gut mycobiome: pitfalls and potentials—a mycologist’s perspective." Mycologia107.6 (2015): 1057-1073.
    5. Wang, Z. K., et al. "fungal microbiota and digestive diseases." Alimentary pharmacology & therapeutics39.8 (2014): 751-766. 

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    Desiree Nielsen Registered Dietitian
    About the author
    Desiree Nielsen is a registered dietitian, author and host of the vegetarian cooking sshow, The Urban Vegetarian. Desiree takes an evidence-based, integrative approach to her dietetics work, with a focus on anti-inflammatory, plant-centredcentered nutrition and digestive health.
    View all articles by Desiree Nielsen
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