Allergies, Candida, Gut Flora and Disease—The Connection

Our microbiome is the key to our immune system and the overall health of our inner ecosystem
June 15, 2020 Updated: June 15, 2020

Our body has an ecosystem of bacteria and fungi living in it and on it that is critical to our immune system and overall health. This microbiome helps us break down food, produces hormones, and plays many other roles.

Unfortunately, this ecosystem can get out of wack and one little fungus, Candida, can be particularly problematic.

Allergies have been closely linked to the health of the microbiome, several studies have found, including a review of more than 100 studies published in Frontiers in Immunology in 2018.

Allergies are symptoms of an overwhelmed immune system trying frantically to defend itself from any and all possible threats. Allergy medications suppress symptoms, but symptom suppression doesn’t resolve the problem the body is reacting to. Worse, these drugs, and symptom suppression, can lead to disease. Food allergies, seasonal allergies, and other allergies can be significantly impacted by resolving problems in the microbiome, research has found.

The catch is that the microbiome is affected by our behaviors, particularly food and medication use. While suppressing allergies can be as easy as taking a pill, resolving the actual issue requires more effort—and information.

Your body’s microbiome, or gut flora, primarily consists of bacteria and fungi. Candida is one kind of fungus present in the gut. A healthy gut contains a ratio of about 1000 bacteria to 1 Candida yeast cell. The fungi that like our body best is Candida albicans, a kind of yeast that proliferates in a host who consumes a poor diet or otherwise disrupts their gut flora.

Thrush in the mouth or vaginal yeast infections are the more familiar forms of illness that result from Candia overgrowth, but several other diseases, including irritable bowel syndrome, are linked to the fungus.

There are several causes of this imbalance in our gut flora. Some of the more common include taking antibiotics or ingesting them from our food. Refined foods that feed the wrong flora, too much sugar, and other toxins, drugs, or contaminants can also damage beneficial bacteria.

Candida Are Opportunists

Candida isn’t all bad; it has its job to do, just like every other microbe, but when it’s not kept in check, things get messy. So what happens when you kill the good bacteria? Candida takes over. That’s partly because Candida spores can survive just about anything and they are just waiting for the room to grow.

When our gut has a diverse mix of beneficial gut bacteria, it can crowd out potential pathogens and keep Candida in check.

The most beneficial gut bacteria love to dine on the most beneficial foods we can eat—vegetables and whole grains. The more produce you eat, the healthier your gut flora will be.

But when you drink alcohol, eat sugary foods, take antibiotics, or do anything else that disturbs the gut flora, you kill beneficial bacteria and leave behind Candida spores. These spores will hatch and flourish when they discover the coast is clear. Ideally, when this imbalance happens, our appendix squirts out some bacteria it had saved up for just such an occasion. Unfortunately, our modern sugary, chemically laden diets and lifestyles can clear cut our gut flora and leave Candida so much space that the appendix’s bacteria can’t compete.

At this point, there’s a very inhospitable environment in the gut. Candida doesn’t seem to mind neighbors, so once the gut is overrun by Candida, the whole ecosystem of the gut becomes distorted. Some of the gut flora that may have been beneficial now adapt to this new environment in unhealthy ways.

Microbes mutate.

E-coli, for instance, is a perfectly fine bacteria to have in our gut under natural circumstances. But if a diet is too acidic, or there are too many antibiotics, the bacteria become hardier and more dangerous. This is seen in cows as well. There is now a global problem of antifungal drugs, which can treat Candida, becoming less effective as the fungus hardens.

A Causal Agent of Other Infections

Speaking of adapting, once that Candida is feeling crowded and has outgrown its home in the gut, Candida can grow out of its single-cell yeast form and into a filamentous fungal form that grows root-like tentacles (hyphae) that drill deep into the mucosal lining of the gut, poking “holes” into already an irritated and inflamed, gut lining, resulting in a leaky gut.

Leaky gut, or intestinal permeability, happens when our food and digestive waste is able to leak out the cell walls of the gastrointestinal tract.

When this happens, Candida and other waste can leak into the bloodstream and travel throughout the body. Candida can then infect every organ of the body and repeat the hyphal hole-making process in all of its new homes. When it takes the pseudohyphal and hyphal fungal forms, it creates a toxic biofilm that protects itself against things that would normally kill it, such as antibiotics and antifungal medications.

Candida is the key that unleashes a barrage of other infectious microbes and partially digested food from our gut into the bloodstream. Now the body is in a constant battle with Candida and other invaders that continue to try to rip it apart. There is a back and forth with the gut’s permeability, as the body is constantly repairing the gut and fighting off infection while Candida, waste, and pathogens undermine this effort.

Candida, parasites, infectious bacteria, other fungi, and all kinds of microbes that escape the gut will set up their colonies where they can hide and find food. Infectious microbes generally eat simple sugars and decaying cells. Pathogens like to congregate in cavities and around old injuries (this is why old injuries ache and become inflamed). The mere presence of these microbes irritates their surroundings, causing damage to cells that die and then end up feeding the pathogens.

This is partly why the body will crave sugar. Every time you feed the pathogens, there’s a feeling of relief within the body. It feels good because the pathogens are eating the sugar rather than the body. Unfortunately, the next thing they do is multiply. Then, they turn on you when they’re out of sugar to eat.

Candida can feed a variety of vicious cycles and release toxins that cause more as Candida dies. Two of the most prominent toxins produced are acetaldehyde and gliotoxin.

Acetaldehyde, which is a metabolic byproduct of Candida that is similar to carbon dioxide that we exhale, leads to oxidative stress and inflammation. Too much acetaldehyde in the body is the equivalent of alcohol poisoning. Gliotoxin, another major toxin created by this yeast, suppresses the immune system and kills key immune cells, liver cells, and impairs the liver’s ability to detoxify the body.

Is Candida the Problem?

Both of the aforementioned toxins can be linked to almost every autoimmune disease or symptom there is, but once Candida permeates the gut, it’s not just Candida causing the problems. The body is susceptible to anything and everything at this point.

All kinds of undigested food particles and microbes flood the bloodstream off and on as the gut walls deteriorate and heal—all while the immune system is completely overtaxed. To make matters worse, what Candida does to the intestinal wall when it goes fungal, it will do in other areas of the body as well, which wreaks havoc on the immune system.

The typical human in modern society is dealing with so many different kinds of infections and other toxins at one time that the body reacts to anything and everything that doesn’t belong. The more inflamed the body becomes, the more the immune system becomes overburdened and confused.

It’s a painful cycle linked to allergies and autoimmune diseases. Aches and pains from old injuries and allergies can be some of the first signs of an unbalanced, unhealthy gut that is currently, or has been, seeping toxins and microbes into the body.

Once the gut allows an infection into the body, Candida may or may not still play a factor in disease, but it’s almost always an underlying cause. Fixing this problem isn’t as easy as taking a pill. This is why a holistic approach is imperative to getting well.

Natural Gut Healing Protocol

Signs of Candida overgrowth can range from allergies to itchy feet. The impact can unsettle normal hormone production in the gut and have wide-ranging impacts on mood, contributing to depression or anxiety. It can be difficult to test for Candida overgrowth since the fungus can grow or decline with diet and other issues.

Fortunately, most people can resolve this issue if they have all of their body parts, and the tonsils, appendix, or other organs once deemed unnecessary haven’t been hastily removed.

Things get tricky when parts are missing, but most of us can get completely well with just the right diet alone. Supplements can speed up the process but aren’t usually a necessity. With the wrong diet, supplements aren’t going to be nearly as effective.

Here’s a protocol to rid the body of infectious microbes, heal the gut, and balance the flora.

Drink Lots of Cranberry Lemonade

As a way of a medical precaution, before considering the treatment below, be aware: If you are susceptible to kidney stones, be careful of cranberry juice and consult a doctor. You should also be wary if you are on warfarin (Coumadin), a drug used to slow blood clotting since there is a mild interaction. Cranberry juice can also affect how quickly the liver breaks down some medications.

For most others, drink between a half a gallon and a gallon of cranberry lemonade a day to flush the liver and kidneys of toxins, and help rejuvenate the endocrine system, which will help keep the blood clean and reduce “die-off symptoms” commonly associated with killing Candida. And don’t confuse cranberry juice with sugary cranberry drinks.

Cranberry Lemonade Recipe

  • Glass gallon jar
  • Safe, clean, spring water or distilled water
  • 1 cup of unsweetened, organic cranberry juice, not from concentrate
  • 3 organic fresh lemons
  • A citrus juicer
  • Liquid stevia
  • Liquid cayenne

Fill the jar to about 85 percent capacity with water, preferable spring or distilled water free of chlorine or other additives. Squeeze the lemons and pour the juice into the water. Add cranberry juice. Add stevia to taste and then add cayenne to taste. The amount of cayenne used is up to you, but the more the better.

Eat Right

Produce detoxifies. Fresh, whole, organic vegetables, herbs, and fruits are the best way to pull toxins from the body as they repopulate healthy, beneficial gut bacteria and give the body the nutrients it needs, including enzymes and other phytonutrients that are almost non-existent in many modern diets.

Try to eat a huge salad every day with lots of greens, plenty of other colors, garlic, cilantro, ginger, and more.

Eat whole foods; avoid refined foods. Brown rice is good; white rice is out. Avoid any wheat; artificial colors, flavors, preservatives, or sweeteners; trans fats; and MSG. Avoid carbonated beverages. Avoid GMOs. Don’t go crazy with fruit, and besides stevia, avoid or limit sweeteners.

Our modern diet almost always includes too much-refined sugar. You may be thinking honey is a good alternative, but that’s only true when the gut is healed, the body is relatively free of infection, and the immune system functions properly. Otherwise, even with its antimicrobial properties, honey can feed infection as it goes through the digestion process.

The above methods should be enough for most people with the right diet, but for really prominent fungal issues, there are plenty of supplements aimed at helping address microbiome issues or Candida overgrowth problems.


Candida is a hot topic of debate within both the naturopathic community and conventional medicine, with views ranging from Candida being the root of everything that’s wrong with the body to it being a very rare issue that is completely overblown.

Fortunately, the best solution to a Candida overgrowth problem is a healthy diet that will be good for anybody and just about any health issue. And being mindful of the health of your gut flora is a great way to improve your overall well being.

Michael Edwards is the founder, owner, and editor-in-chief for Organic Lifestyle Magazine. This article was originally published on