Updated 24th April 2024

Your mycobiome: The fungus among us

Share this article

  • Share on Facebook
  • Share on Twitter
  • Print this page
  • Email this page

The microorganisms that live in your gut play a role in your overall health. And as scientists look longer and harder, the importance of these organisms grows ever clearer.

Although most of the research into these microbes focuses on bacteria, they’re not the only organisms living within us.

Your gut also hosts viruses, protozoa, archaea, and the subject of this feature: fungi. 

Collectively referred to as the gut mycobiome, our gut fungi are much less numerous than our gut bacteria. Still, scientists estimate that each of us hosts around 1 billion of them.

Aided by recent developments in technology, researchers are slowly charting the role of your gut mycobiome in health and disease. 

Gut fungi still hold many secrets. But today, we’ll look at their possible links to inflammatory bowel disease (IBD), colon cancer, metabolic conditions, and other areas of health.

A ‘healthy’ mycobiome?

Experts are still figuring out what a healthy gut microbiome might look like. But over the last couple of decades, they’ve identified some species of gut bacteria that they class as “good” or “bad.” 

And it seems that a diverse gut microbiome is linked to better health.

With the mycobiome, though, the picture is much murkier.

Though scientists have identified a range of fungi in people’s guts, they haven't yet established a “normal” or “healthy” gut mycobiome.

The authors of a review explain that nearly half of all types of fungi reported “have only been found in one sample or one study.”

Also, they note, the gut mycobiome appears to be less diverse and less stable than the gut microbiome.

Imagine that you analyzed a person’s gut bacteria twice, a few months apart. If the person hadn’t radically changed their diet or taken antibiotics, you’d likely find a lot of the same species from the initial sample.

The gut mycobiome, on the other hand, doesn't seem to be so consistent.

One study looked at the gut mycobiomes of people 3–4 months apart. They found the same fungus in both samples less than 20% of the time.

Still, some species crop up more often than others.

A study analyzing 317 poop samples from 147 volunteers found that these species were particularly common:

  • Saccharomyces cerevisiae: This is also known as brewer’s or baker’s yeast.

  • Malassezia restricta: This is often found on the skin, and it's associated with dandruff.

  • Candida albicans: In some people, higher numbers of this fungi can cause infections.

So, if there’s not much fungi in your gut, and the population varies so much over time, is it likely to have much influence on your health? 

Scientists are still figuring this out. But some studies offer hints that gut fungi may indeed be important.

Bacterial and fungal interactions

One way that gut fungi may influence health is through their interactions with gut bacteria. There’s some evidence that they help keep the gut microbiome in balance.

As an example, one study used mice with a condition similar to IBD. When the mice received a drug that killed off their gut fungi, it caused an increase in “bad” bacteria and a decrease in “good” bacteria.

Some fungi also seem to fill in for “good” gut bacteria when these aren't around.

For instance, in another mouse study, scientists found that if they killed off “good” gut bacteria, gut fungi stepped in to protect the gut lining and prevent infection.

Bacteria and fungi have evolved together for millions of years. And they happily live side by side in dense biofilms

According to the authors of a review, “Clearly, there is a strong connection between fungal and bacteria cells.” Although we don’t know exactly what they’re saying to each other, they’re certainly in cahoots.

For instance, there’s evidence that the fungus C. albicans might make the bacteria Helicobacter pylori more likely to cause gut conditions.

Scientists now need to dive deeper to discover how these relationships work and how important they are for our health.

A fungal role in IBD?

IBD is a chronic condition that involves inflammation of the gut. The two main types are Crohn’s disease and ulcerative colitis. And experts are still working to understand what causes IBD.

Some believe that fungi might play a part. This theory was first discussed back in 1990. 

Researchers noted that people with Crohn’s disease had higher blood levels of antibodies to C. cerevisiae — one of the common gut fungi we mentioned earlier — than people with ulcerative colitis and healthy people.  

And later studies found that people with IBD had a more diverse range of fungi in their guts.

Another study in people with Crohn’s disease found that the diversity of gut fungi increased as their symptoms flared up.

Once the people had received treatment and their symptoms had improved, the diversity went back down.

Join our mailing list

Sign up for fresh insights into our scientific discoveries and the latest nutrition updates. No spam, just science.

Links between gut fungi and IBD seem increasingly likely, but we still don’t know precisely how the relationship works. Or how much it matters.

It could be that changes in gut bacteria are driving the changes in gut fungi. Or perhaps the inflammation that comes with IBD impacts fungal diversity. We don’t know. 

But some researchers hope that, in the future, altering gut fungi with dietary changes, probiotics, or antifungals might be useful. And we sorely need better treatments for these conditions.

Gut fungi and cancer

Scientists have already spotted links between changes in gut bacteria and colon cancer. And more recent research suggests that the same might be true for your gut fungi.

For instance, one study looked at a type of tumor called an adenoma. They found distinct differences in the fungi present in the tumors, compared with healthy tissue. 

And the changes in fungi were related to the stage of the tumor — how large it was and how far the cancer had spread.

According to the authors of a review, scientists have also seen changes in gut fungi in colon cancer and cancer associated with ulcerative colitis. 

At this stage, we don’t know whether fungi play a part in cancer development.

However, the authors suggest that differences in gut fungi might one day be a noninvasive way to determine the stage of cancer.

Gut fungi and metabolic health

Obesity and diabetes are metabolic health conditions. And some early research suggests that gut fungi might be linked to metabolic health.

For instance, scientists have identified differences in the gut mycobiomes of people with type 1 and type 2 diabetes, compared with people who have neither condition. 

Some studies also point to differences in the gut mycobiomes of people with obesity, which seem to have less diversity.

Still, overall, there's been very little research into links between the gut mycobiome and metabolic health.

Building links

So far, we’ve taken a brief look at the current associations between gut fungi and IBD, cancer, and metabolic health. But these aren't the only conditions that scientists have investigated.

Here's a glimpse into other areas of health that researchers are looking into:

  • Alcoholic liver disease: Scientists found a “lower fungal diversity with an overgrowth of Candida.” 

  • COVID-19: A study found differences between the gut mycobiomes of people with a SARS-CoV-2 infection and those without one.

  • Hepatitis B: Researchers identified differences in gut fungi diversity among people with different stages of the disease and healthy people.

  • Multiple sclerosis (MS): Scientists have noted differences between the gut mycobiomes of people with MS and those without it.

  • Cognitive health: Researchers have found differences between the gut mycobiomes of people with mild cognitive impairment and Alzheimer’s disease.

A huge gap to cross

While identifying links between health outcomes and gut fungi is important, it’s just the first step. As it stands, there are more questions than answers.

We don’t know which way the relationship runs: Do changes in your gut fungi cause health conditions? Or do the changes associated with health conditions cause the changes to your gut mycobiome?

Also, dietary factors can increase the risk of many diseases. So, maybe your diet drives the differences in gut fungi — but perhaps those changes don’t make any difference to your health.

The authors of a review pose a number of questions to show how far we are from understanding our resident fungi, including, “What are they doing in a healthy host, and would their absence be detrimental?” 

In other words, we still don’t know whether gut fungi are vital in the same way that gut bacteria are. 

However, many scientists are confident that gut fungi truly are important. The authors of another review write, “It is clear that gut mycobiome has an indisputable role in host homeostasis and disease development.”

The authors of a different review are a little more cautious. They note that while “Studies performed so far have shown potential links of mycobiome in health and diseases, it is important to demonstrate the causation rather than association.”

As ever, only more research will get to the truth. And as the information slowly accumulates, it promises to provide fascinating insights.


Alteration of fungal microbiota after 5-ASA treatment in UC patients. IBD. (2020). https://academic.oup.com/ibdjournal/article/26/3/380/5637359 

Alterations in fecal fungal microbiome of patients with COVID-19 during time of hospitalization until discharge. Gastroenterology. (2020). https://www.sciencedirect.com/science/article/pii/S0016508520348526 

Alterations of the gut mycobiome in patients with MS. eBioMedicine. (2021). https://www.sciencedirect.com/science/article/pii/S2352396421003509 

Analysis of the gut mycobiome in adult patients with type 1 and type 2 diabetes using next-generation sequencing (NGS) with increased sensitivity — pilot study. Nutrients. (2021). https://www.mdpi.com/2072-6643/13/4/1066 

Antibody to selected strains of Saccharomyces cerevisiae (baker's and brewer's yeast) and Candida albicans in Crohn's disease. Gut. (1990). https://pubmed.ncbi.nlm.nih.gov/2190866/ 

Changes in the composition of intestinal fungi and their role in mice with dextran sulfate sodium-induced colitis. Scientific Reports. (2015). https://www.nature.com/articles/srep10416 

Commensal fungi recapitulate the protective benefits of intestinal bacteria. Cell Host and Microbe. (2017). https://www.cell.com/cell-host-microbe/fulltext/S1931-3128(17)30448-1 

Cooperative evolutionary strategy between the bacteriome and mycobiome. mBio. (2016). https://journals.asm.org/doi/10.1128/mBio.01951-16 

Correlation between gastrointestinal fungi and varying degrees of chronic hepatitis B virus infection. Diagnostic Microbiology and Infectious Disease. (2011). https://www.sciencedirect.com/science/article/pii/S0732889310001288 

Dysbiosis of fungal microbiota in the intestinal mucosa of patients with colorectal adenomas. Scientific Reports. (2015). https://pubmed.ncbi.nlm.nih.gov/25613490/ 

Fungi and inflammatory bowel diseases: Alterations of composition and diversity. Scandinavian Journal of Gastroenterology. (2008). https://pubmed.ncbi.nlm.nih.gov/18584522/ 

Fungi inhabiting the healthy human gastrointestinal tract: A diverse and dynamic community. Fungal Ecology. (2015). https://www.sciencedirect.com/science/article/pii/S1754504815000070 

Fungi in the healthy human. Virulence. (2016). https://www.tandfonline.com/doi/full/10.1080/21505594.2016.1247140 

Gut mycobiome and its interaction with diet, gut bacteria and Alzheimer's disease markers in subjects with mild cognitive impairment: A pilot study. eBioMedicine. (2020). https://www.sciencedirect.com/science/article/pii/S2352396420303261 

Identification and characterization of lipases from Malassezia restricta, a causative agent of dandruff. FEMS Yeast Research. (2015). https://academic.oup.com/femsyr/article/15/7/fov078/641800 

Intestinal fungal dysbiosis and systemic immune response to fungi in patients with alcoholic hepatitis. Hepatology. (2020). https://journals.lww.com/hep/Abstract/2020/02000/Intestinal_Fungal_Dysbiosis_and_Systemic_Immune.12.aspx 

Investigating colonization of the healthy adult gastrointestinal tract by fungi. mSphere. (2018). https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5874442/ 

Mycobiome in the gut: A multiperspective review. Mediators of Inflammation. (2020). https://www.hindawi.com/journals/mi/2020/9560684/ 

Obesity changes the human gut mycobiome. Scientific Reports. (2015). https://www.nature.com/articles/srep14600 

The cross-kingdom interaction between Helicobacter pylori and Candida albicans. PLOS Pathogens. (2021). https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8101746/ 

The gut microbiota, bacterial metabolites and colorectal cancer. Nature Reviews Microbiology. (2014). https://pubmed.ncbi.nlm.nih.gov/25198138/ 

The gut mycobiome in health, disease, and clinical applications in association with the gut bacterial microbiome assembly. The Lancet Microbe. (2022). https://www.sciencedirect.com/science/article/pii/S2666524722002038 

The role of gut mycobiome in health and diseases. Therapeutic Advances in Gastroenterology. (2021). https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8474302/ 

Treatment of inflammatory bowel disease: A comprehensive review. Frontiers in Medicine. (2021). https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8720971/ 

What is inflammatory bowel disease (IBD)? (2022). https://www.cdc.gov/ibd/what-is-IBD.htm

Share this article

  • Share on Facebook
  • Share on Twitter
  • Print this page
  • Email this page