Yeast, Candida, and the mycobiome

The human digestive tract contains more microorganisms than there are cells in our entire body. Estimates show we have roughly 100,000 organisms with 500-1000 species that constitute the microbiome. Some of those critters are yeasts and that will be the focus of this article. Don’t panic–all of us have yeast in our gut. In fact, some of these fungi play a protective role by stimulating the immune system to be wary of more dangerous pathogens. The question is, what role are these yeasts playing in our individual overall health? 

Yeasts are part of the larger category of fungus, an entire biological kingdom. Fungi are complex and differ from other kingdoms in complex ways. Here’s how:  

“Unlike animals, they have cell walls, not membranes; unlike plants, they cannot make their own food; unlike bacteria, they hold their DNA within a nucleus and pack cells with organelles—features that make them, at the cellular level, weirdly similar to us. Fungi break rocks, nourish plants, seed clouds, cloak our skin and pack our guts, a mostly hidden and unrecorded world living alongside us and within us.”

the mycobiome (fungal microbiome)

The part of your microbiome which contains these yeasts is called the mycobiome. There are relatively few species of fungus that can colonize our gut but in some cases they can have a great impact on our health. Candida albicans is the most commonly encountered fungal pathogen of humans, and is frequently found on the mucosal surfaces of the body. It is the host response to these microorganisms which is so variable. This brings me to a very important bit of clinical experience–you don’t always want to treat yeast and if you do treat, you may not want to engage in a purely “kill everything” approach.

Diet and environmental factors play a role in the mycobiome and overall the mycobiome is less stable than the bacterial levels in the gut. Meaning, your daily intake of foods can shift the levels of yeast or fungus in your gut pretty quickly. Dietary sources of fungus come mainly from fresh fruits and vegetables. I’m not about to tell you to stop eating those! 

Candida species have these little “feet”, if you will, called hyphae. Hyphae can stomp little holes in the intestinal wall lining, increasing the permeability of this barrier and leading to what is commonly called “leaky gut.” If you have a leaky gut, particles of food and other environmental exposures can translocate to the lymphatic system and even reach your bloodstream in some cases. This is why leaky gut is so significant, it means there will be effects across your whole body. 

Leaky gut has been correlated with numerous systemic conditions–allergies, fatigue, brain fog, general lymphatic sluggishness and more detrimental conditions related to oxidative stress/inflammation that may be destructive to healthy nerve tissues. In my experience, one of the most common reasons for a person to develop “leaky gut” is an overgrowth, or colonization, of fungus in the digestive tract. 

So how does one know if they have fungal colonization in the gut? First, there are a set of questions I always ask my patients and many of them point to a yeast overgrowth issue. Since I am also steeped in blood type physiology science, it’s also interesting to note that Blood Type O individuals have a higher level of what is called “Candida carriage.” The Blood Type O antigen that is expressed all along our digestive tracts, is made up of fucose–a preferred food source for many Candida species. 

Common symptoms of a yeast overgrowth issue include:

  • Fatigue 
  • Rashes and skin irritations, especially the classic redness that many yeasty rashes produce 
  • Persistent itching anywhere on the body, but especially rectal itching after a bowel movement 
  • Chronic vaginal yeast including discharge, burning and discomfort 
  • Chronic toe or fingernail fungus 
  • Gas and bloating in the abdomen with a lot of dietary triggers 
  • Variability in stool quality–alternating constipation and diarrhea (much like small intestinal bacterial overgrowth (SIBO) in this case it’s fungal overgrowth, or SIFO. 
  • Foggy thinking, or “brain fog”–a very common symptom many don’t realize is associated with fungal overgrowth 

The interesting thing is that these signs and symptoms may not be present, even in people where yeast is playing a detrimental role in overall health. I’ve seen many female patients who have had a microscopic exam done at the gynecologist and no yeast is present. Yet the body is still reacting to yeast in ways that are producing discomfort. Conversely, some women are told they have a “yeast infection” even though they were not symptomatic at all. 

One’s sensitivity to yeast is what is really crucial. This is why I love using the Yeast mix of low dose immunotherapy (LDI) for some individuals. It’s not matter of the gross amount of yeast present but how sensitive any given individual is to its presence. In fact, this is the case for many of the antigens/pathogens that I use LDI for. 

Having said that, testing for fungal overgrowth can be an important part of evaluation but also tricky. Candida albicans can form biofilms, tightly packed communities of organisms that can evade immune detection. These biofilms can also colonize mucosal surfaces and make it more difficult to get positive findings in cultures. 

The gold standard for testing is organic acid testing through urine. In particular, the marker for arabinose is associated with yeast colonization in the gut. I routinely use organic acid testing that measures multiple markers for fungal overgrowth. There are two labs that offer comprehensive testing that I rely on for objective data about the current state of your digestive system–and much more like neurotransmitter levels and nutritional status for a number of things that are not easy to measure through a blood draw. They are Great Plains and US Biotek

Treating Candida

As mentioned above, dietary changes can have some effect on fungal levels in the gut. The main areas I focus on are the removal of refined sugars and increasing healthy fibers, both of which support a healthy microbiome overall. 

If a person has longer-standing issues, it is often necessary to treat them with a number of approaches. Anti-fungal foods, herbs and nutritional supplements can be the mainstay of my approach with certain patients. With others we need to do more biofilm disruptors for those that have deeper-seated colonization and for others it’s more of an immune tolerance approach using complex homeopathics and potentially LDI

One must exercise caution when attempting to eradicate yeast in their digestive tracts. As the organisms die off they can release mycotoxins that can create an acute inflammatory state in the body, what I call an “aggravation.” It’s always prudent to have a plan in place for this possibility. 

Using binders and being careful with dosing are just two simple things that can reduce the symptoms during an aggravation, or sidestepping one altogether. I’ve got lots of other tricks up my sleeve as well after many years in practice, many of them relate to a healthy functioning lymphatic system as well. As always, individualized care is the cornerstone of my work in naturopathic medicine. There simply are no protocols for complex chronic illnesses like yeast overgrowth and the havoc it can wreak on a person’s body.