Your mycobiome: The fungus among us

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. 

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.

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.

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.

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.  

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.

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.

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. 

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.

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?” 

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.