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Our gut microbiomes are made of millions of tiny microbes, such as bacteria, fungi, and protists, which perform services like helping us digest food and protecting us against certain infections. If fungi and protists are microbes too, why have they largely been left out of gut microbiome research, which has focused instead almost solely on bacteria? Microbes interact in our gut environment in ways that we yet don’t fully understand. And the only way that we will begin to is by bringing fungi and protists into the research mix.

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Bacteria are single-celled organisms that are invisible to the naked eye and very abundant in our guts. They get a lot of attention because they cause disease and death. But focusing solely on this one facet of the microbiome contributes to the misconceptions that only bacteria inhabit our guts and that bacteria are exclusively what gut microbes should look like. Such fallacies are driving dangerous trends that aren’t backed up by science, like DIY fecal transplants. Ignoring that our guts are complex environments inhabited by a plethora of microbes in favor of quick home remedies can lead to serious life-threatening situations, like transplanting antibiotic resistant organisms and viruses, such as HIV and hepatitis.

Fungi and protists can be single-celled and microscopic too. They are also abundant in our guts, and cause a lot of diseases in humans, although they are rarely marked as health threats. Regardless, fungi, protists, and bacteria inhabit the same spaces in our guts and share and compete for resources. And even though studying all members of the microbiome is extremely challenging, it is the only way that we will begin to understand the complex interactions among them and do better science.

Understanding the dynamics of fungal and protist gut communities is key in figuring out what role our microbiomes play in disease onset and progression

By studying both fungi and bacteria in the gut microbiome of people with Crohn’s disease, for example, a chronic inflammation of the gastrointestinal tract, scientists found that people with Crohn’s had less bacteria and more fungi in their gut compared to people without the disease. In fact, there is evidence showing that Crohn’s disease flare ups, which is a sudden intensification of symptoms, are directly related to the increase of fungi in the gut. People with types 1 and 2 diabetes show similar trends, hosting more fungi in their gut compared to non-diabetic people.

But as of right now, it is unclear whether these changes between fungi and bacteria in the gut microbiome are simply the result of disease progression or if these changes actually play a crucial role in disease onset. The case of protists is even worse - they aren’t even considered yet in most gut microbiome studies. But understanding the dynamics of fungal and protist gut communities is key in figuring out what role our microbiomes play in disease onset and progression.

Right now, interpretations of gut microbiome studies should be taken with caution. We cannot make any major assumptions about the gut microbiome and its association to diseases, or how to treat them, until we have a better understanding of how every microbial group in the gut microbiome behaves individually and how they interact. Even though there are a lot of interesting health trends associated with the bacteriome, there are also potentially millions of fungi and protists that are being ignored. It's time to investigate them.