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This stuff is seriously nasty
A hidden fungus may be making you ill. A 35-year-old recently walked into my office suffering from a whole list of health problems (which is why I often call myself a "whole-listic doctor"). She had chronic fatigue, recurrent yeast vaginal infections, itchy ears, dandruff, patchy itchy skin rashes, irritable bowel syndrome, muscle twitching, acne rosacea, malabsorption, headaches, and more.

These symptoms can have multiple causes, but in her case all of these problems were related. They were symptoms of an overgrowth of yeast in and on her body. This patient had such a fungus problem that she was practically a walking mushroom!

The cause was clear. She had taken many, many courses of antibiotic over the years. She had been diagnosed with a mostly benign condition called mitral valve prolapse-a problem I believe is over diagnosed and over treated-and "needed" antibiotics every time she went to the dentist. In addition, she had many urinary tract infections for which she took many more courses of antibiotics.

Frequent use of antibiotics disrupts the normal balance between healthy bugs in the gut (lactobacillus, bifidobacter, e. coli) and other potentially dangerous bugs, including yeasts, bacteria, and occasionally parasites. These bad bugs are usually present in small numbers in the digestive system. But when the good bugs are killed by antibiotics (i) or not fed with adequate fiber, or the bad guys are fueled with too much sugar, or the gut's delicate ecosystem (ii) is damaged by too much stress, then yeasts and other noxious agents take over.

This can result in many chronic illnesses and symptoms including allergies, chronic inflammation, joint problems, mood and brain disorders, digestive symptoms, and more.

In today's problem I will explain why yeast overgrowth is such a common problem, why conventional medicine tends to overlook it, and provide you with a comprehensive plan to reduce and remove yeast and rebalance your gut's delicate ecosystem, which sits at the center of your health.

Yeast: A Common But Often Unrecognized Problem

Yeast overgrowth is quite common, but many people don't know they have it and conventional doctors tend to ignore it. In medical school, we are taught that you either have a disease or you don't. It's black and white. However, our bodies weren't designed with an "on" or "off" switch for disease. All diseases occur in shades of gray along a continuum of imbalance along spectrum of disease.
Many tests we use for diagnosis of yeast problems are not definitive or foolproof. Some can be helpful if they come out positive but don't rule yeast out if they're negative.
Medical students learn about fungal and yeast problems, but only in a limited way. They know that AIDS patients have severe yeast and fungal infections and need long-term anti-fungal treatment. People with diabetes tend to grow yeast because yeast likes sugar. Babies get thrush and need antifungal treatment. Women get vaginal Candida yeast infections. All of these are well-accepted and treatable problems. Unfortunately more subtle problems related to yeast are usually ignored and not linked to patient's complaints. If a subject is not taught in medical school, it is assumed not to be real. Medical history proves this is a dangerous assumption.

On the other hand, many alternative practitioners over diagnose yeast problems. However, there are many people who do have yeast problems, and most of them don't know it.

There is not enough research on this topic. But the collective intelligence of many doctors working in this field for decades with thousands of patients has helped us learn how to appropriately diagnose and treat this often misdiagnosed problem.

We know that yeast overgrowth can be triggered by a number of things. These include a high-sugar, high-fat, low-fiber diet, impaired immunity, use of drugs like antibiotics, birth control pills, estrogen, and steroids like prednisone, and psychological stress.

Although symptoms of yeast overgrowth are similar to those of many other conditions, you may have a yeast problem if you have these problems (iii):

General Symptoms
  • Chronic fatigue
  • Loss of energy
  • General malaise
  • Decreased libido
Gastrointestinal Symptoms
  • Thrush
  • Bloating and gas
  • Intestinal cramps
  • Rectal itching
  • Altered bowel function such as diarrhea (iv) or constipation
Genitourinary Symptoms
  • Yeast infections
  • Frequent bladder infections
  • Interstitial cystitis (irritable bladder)
Hormonal Complaints
  • Menstrual irregularities like pain, bleeding, etc.
  • Premenstrual syndrome
  • Thyroid dysfunction
Nervous System Complaints
  • Depression
  • Irritability
  • Inability to concentrate
Immune System Complaints
  • Allergies
  • Chemical sensitivities
  • Low immune function
Past History
  • Chronic yeast infections
  • Chronic antibiotic use for infections or acne
  • Oral birth control pill usage
  • Oral steroid hormone usage
Associated Conditions
  • Sensitivity to foods, chemicals, or other allergens
  • Eczema
  • Psoriasis
  • Irritable bowel syndrome
  • Craving for foods rich in carbohydrates or yeast
  • Toenail fungus
Many tests we use for diagnosis of yeast problems are not definitive or foolproof. It is often a diagnosis that must be made from a patient's story, symptoms, and physical findings on examination. Blood antibody levels for yeasts, stool tests, and organic acid urine tests (v) for yeast metabolites can be helpful if they come out positive but don't rule yeast out if they're negative.

The best method for diagnosis is a good history for risk factors like antibiotic use and symptoms of chronic yeast problems. The symptoms of yeast overgrowth vary from person to person and the response to treatments will vary. Some people may need aggressive treatment, while others many need only simple changes to make a significant difference in their health.

I recommend a systematic approach to yeast overgrowth. Taking the following steps can help overcome this common but under diagnosed ailment.

Overcoming Yeast Overgrowth

1. Address predisposing factors. Don't take antibiotics, steroids, or hormones unless absolutely medically necessary.
2. Eat a diet that doesn't feed yeast in the gut (low sugar and refined carbohydrates, and low mold and yeast in food (see below).

Comment: There is some difference in opinion about the role carbohydrates play when a person has a fungal overgrowth. Generally speaking, diets high in carbohydrates feed a fungal overgrowth, since fungus typically feeds off carbs. However, according to Paul Jaminet, author of Perfect Health Diet, switching to a very low carb or zero carb ketogenic diet may not fix the problem due to fungus being able to also feed off of ketones. From and interview between Chris Kresser and Paul Jaminet:
Chris: Right, so how can somebody, the second part of that question is how can someone distinguish between, what are the symptoms of infection first and then how can someone distinguish between the different types of infection fungal, bacterial, parasitic?

Paul: Yeah well this is one place I think diet can really help, is in diagnosis. Medicine is still in a primitive state it's not very good for diagnosing these infections much less treating them. But a lot of these pathogens respond very differently to different diets. So one of the key differences is in how they respond to a ketogenic diet for instance. So pathogens that have mitochondria like fungi and protozoa can metabolize ketones for energy. Bacteria and viruses can't, and so if you go on a ketogenic diet you'll starve bacteria and viruses but you'll feed fungi and protozoa. And so a simple thing to do is go on a ketogenic diet for a while, do your symptoms get worse or better. And that can tell you which class of pathogen you have, one with mitochondria or one that doesn't have mitochondria. And those kinds of tests can be a big help, and I think part of the reason medicine doesn't succeed against all these diseases is that nobody varies their diet, they're always eating the same diet. It's always 50% carbs with lots of wheat and sugar, plenty of vegetable oils, if you tell people to change their diet and eat healthy they look around and find other sources of the same nutrients, certainly never sample a ketogenic diet. So our basic diet, the perfect health diet, aims to be pretty much balanced, it aims to supply in food the amounts of nutrients that your body needs. And we tweak it in various ways so we tend to be very slightly low carb, but for therapeutic purposes and certain diseases we might go to more extreme diets like a ketogenic diet that's more low carb or there's a few diseases that may benefit from going higher carb. But also even apart from treatment the diet is a good diagnostic tool. And it's also helpful for gut infections to vary the types of food you eat, different foods get digested in different places in the digestive tract. Different things are accessible to different kinds of pathogens, the time scales in which things happen have diagnostic value. So fungi tend to do everything slower than bacteria, they multiply a lot slower, so fungal infections tend to be relatively stable whereas bacterial infections can be much more variable. There's a lot of ways you can manipulate diet and help understand your own disease and that can guide you to good treatments.

Chris: What's interesting is, as you're probably aware in the alternative health world there's a lot of different perceptions about how to deal with fungal infections and the word candida is thrown around a lot, which I think obviously that candida infection is real but I also, in my experience see it kind of slapped on as a diagnosis of exclusion, meaning we can't figure out what else it is so we'll just call it candida. But I'm really interested in what you were saying, I read your article when you talked about how fungi can utilize ketones and tend to progress on ketogenic diets because one of the interesting things about how the candida diet is typically administered is people remove fruit, they remove carbohydrates, starchy tubers and grains and I think they end up being on a very low carbohydrate diet in a lot of cases and perhaps not completely ketogenic or not strongly ketogenic but maybe mildly ketogenic and I see a lot of patients who just get worse and worse on those diets so I wonder if it has something to do with this mechanism that you're talking about.

Paul: Yeah I think it's very likely. It's not bad to go low carb by standard American diet standards, I think probably optimal for candida might be 600-800 carb calories a day, the average American gets maybe 1700 so cutting carbs in half for the average American is a good move. But going too low carb definitely risks systemic invasion so the very low carb approach, it's not bad for a fungal gut infection but it's not that good either. It doesn't do that much to promote good bacteria taking over the gut. A lot of plant foods can really help suppress fungi in the gut and promote bacteria. So they can help give you a better gut flora and I think a lot of people who go extremely low carb can end up with a gut dysbiosis of some kind after years on these extreme low carb diets.

Chris: Yeah I agree with that and I've definitely seen that to be true in my practice. And what about brain infections Paul, this is something you've talked a lot about are the nerves in the brain susceptible to the same pathogens?

Paul: Yeah they are. The brain seems to be more vulnerable to bacteria especially and a little less vulnerable to fungi. There are some protozoa that can live well in the brain, some viruses flourish there. The thing about the brain is it's pretty rich in glucose which bacteria like. Or glucose products like pyruvate or lactate which they can metabolize. So it's kind of a paradise for bacteria and so it's very important to maintain the integrity of the blood-brain barrier and try to help keep them out. But just like people get leaky guts they get a leaky blood-brain barrier. Also it's not uncommon if people get some kind of trauma to the head, they get some kind of brain injury involving bleeding, that breaches the blood-brain barrier and very commonly people get brain infections that develop after some kind of head trauma. They're not uncommon and bacteria do well in the brain, and fortunately ketogenic diets can be very helpful. Bacteria can't metabolize ketones, when you're on a ketogenic diet glucose levels decrease, so you're starving the bacteria. And ketogenic diets also promote autophagy which is part of the immune response. And you can also promote that even more with a low protein diet and so in that process the cell basically has its own self digestion machinery, little digestive vesicles called lysosomes that go around and look for junk that the cell doesn't need and they destroy it, digest it, and among the things they'll find when they're looking for junk are bacteria and viruses. So keeping autophagy going very frequently by occasional fasting or occasional ketogenic dieting or low protein dieting either intermittently or regularly, all of those things will help promote brain health and help keep your brain free of infections. And I think brain infections are responsible for a lot of late life degenerative diseases like Alzheimer's, Parkinson's, and probably others too. The brain is kind of a special place, it's a little sheltered in terms of its nutritional status, it doesn't vary as much with diet as the rest of the body. It has its own kind of immune functions, it's own kind of needs, so the symptoms are a little different. So I would say in general the three places to look for different kinds of, classes of symptoms would be the gut, brain, and the body. And each one has it's own characteristic symptoms and pathologies.

3. Use probiotics to repopulate the gut with healthy bacteria
4. Take antifungal herbs and medications when indicated
5. Identify potential environmental toxic fungi and molds in your home or workplace
6. Reduce stress.

The Yeast Control Eating Program

A simple five-day elimination of yeast and molds in your diet, followed by a challenge or binge of yeasty foods will often relieve and then trigger your symptoms. This can be a good diagnostic tool to see if a long-term yeast control diet would be helpful for you. Remember, different people with different sensitivities may require varying degrees of dietary restrictions. Often, the process of healing requires listening to your body and its signals and sensitivities. Nowhere is this better illustrated than in the management of yeast problems. Follow these guidelines as the first step to assess your yeast problem:
  • Eliminate all yeast promoting or yeasty and moldy substances from your diet.
  • Try to be totally strict during this time to get the best results.
  • Keep a food diary and track what you are eating. You should try to vary your meals and make sure you are not eating a lot of any one food.
  • Avoid the test foods for five full days.
  • On the sixth day, eat large amounts of the foods you have been avoiding and monitor your reaction. If you get a recurrence of symptoms, you have identified your problem. If not, then yeast may not be a problem.
  • Remember that sometimes a dietary change may not reduce the yeast overgrowth enough to resolve your symptoms. Then you may need to proceed to the next steps — medication or non-prescription treatments.
  • If you feel great off the yeasty foods, you might not want to do the challenge. It could make you feel very ill. Continue to follow a yeast control eating program for at least 3 months and continue with the other recommendations here.
Additional Steps You Can Take to Reduce or Control Yeast Overgrowth

Often, I find that patients need extra help and should take antifungal herbs, medications, and probiotics.


Take at least 10 to 20 billion live organisms a day of lactobacillus and bifidobacter species. (vi) A special "yeast against yeast" probiotic called saccharomyces boulardii (vii) can be very safe and effective in controlling yeast.

Non-prescription Anti-fungals

Using antifungal therapies such as herbs and other naturally occurring compounds can be very helpful in controlling yeast. The dose for all of the following herbal remedies is generally two pills with meals, three times a day for two to three months. You might need less or more based on your response and symptoms. Sometimes these remedies can be combined for better effect. To find the right combinations and doses for you and identify quality products, consult with a qualified practitioner trained in functional medicine ( Some of the best antifungal compounds include the following:
  • Oregano — Oil of oregano has many antibacterial and antifungal properties.
  • Garlic — Fresh, crushed garlic is a potent antimicrobial and immune booster.
  • Citrus seed extract — The phytochemicals in citrus seeds have been found to have potent antimicrobial properties.
  • Berberine — This potent yellow plant extract comes from goldenseal and barberry
  • Tannins — These are the astringent compounds found in tea and the bark of trees.
  • Undecylenate — This chemical compound is a potent antifungal.
  • Isatis tinctoria — This Chinese herb can be a useful adjunct to treating intestinal imbalances.
  • Caprylic acid — This is another useful compound for treating yeast.

Antifungal Medications

Sometimes, nutrition and supplements just aren't enough to clear up stubborn yeast overgrowth. That's where prescription medications can help. (viii) They're often needed to treat more resistant cases of yeast for either the short or long term — and in some cases can be miraculous in their results.

Nystatin is the most common antifungal drug and is often used to treat thrush in babies. It is not absorbed by the intestinal tract and has no systemic effects. Unfortunately, many fungal organisms are resistant to nystatin and you may need stronger medications. I say "unfortunately" because these drugs are generally processed by the liver and occasionally can cause reversible elevation of liver function tests. They also may have serious interactions with other medications.

People with liver or heart diseases often cannot take these drugs. If you do take Diflucan, Sporonox or Lamasil, you have to have your liver function checked every six weeks. For all of these reasons, you should only take prescription antifungals under the supervision of an experienced and qualified practitioner. These medications can often be life-saving treatments for many conditions unresponsive to conventional treatments.

Killing off yeast is a good thing. However you should be aware that in some people the dead yeast release enough byproducts to cause a "die off" reaction that may make you feel worse before you feel better. This reaction goes away may take up to a week to completely resolve. You can minimize its effects by following the yeast control eating program for a week or so before you start taking any antifungal preparations.

I also recommend taking two to three activated charcoal capsules every four to six hours during the day. Taking a soluble fiber supplement that contains guar gum, alginates, psyllium seed, or pectin to bind to yeast toxins before bed can also be helpful in reducing the "die off" reaction.

Now you know that fungi, yeasts, and mold can make you sick — but there's good news, too. You can treat the problem. I hope you'll use the tools I've given you in this blog to start getting well and feeling healthy now.

Now I'd like to hear from you...

Do you suffer from the symptoms described here? Have you been diagnosed with yeast overgrowth?

How do certain foods seem to affect your symptoms?

Are you seeing a doctor for yeast problems?

What's been your experience in dealing with and treating yeast?

Please let me know your thoughts by leaving a comment below.

  • (i) Kourbeti, I.S., Alegakis, D.E., Maraki, S., and G. Samonis. (2010). Impact of prolonged treatment with high-dose ciprofloxacin on human gut flora: A case report. J Med Case Reports. 4: 111.
  • (ii) Hawrelak, J.A. and S.P. Myers. (2004). The causes of intestinal dysbiosis: A review. Altern Med Rev. 9(2): 180-97. Review.
  • (iii) Pizzorno and Murray. 1999. Textbook of Natural Medicine. Churchill Livingstone.
  • (iv) Krause, R., Schwab, E., Bachhiesl, D., et al.(2001). Role of Candida in antibiotic-associated diarrhea. J Infect Dis. 184(8): 1065-9.
  • (v) Tana, C., Umesaki, Y., Imaoka, A., et al. (2010). Altered profiles of intestinal microbiota and organic acids may be the origin of symptoms in irritable bowel syndrome. Neurogastroenterol Motil. 22(5): 512-9.
  • (vi) Hatakka, K., Ahola, A.J., Yli-Knuuttila, H., et al. (2007). Probiotics reduce the prevalence of oral candida in the elderly - a randomized controlled trial. J Dent Res. 86(2): 125-30.
  • (vii) Pothoulakis, C. (2009). Review article: anti-inflammatory mechanisms of action of Saccharomyces boulardii. Aliment Pharmacol Ther. 30(8): 826-33. Epub 2008 Jul 23. Review.
  • (viii) Rimek, D., Redetzke, K., and R. Kappe. (2006). Impact of antifungal prophylaxis on the gastrointestinal yeast colonisation in patients with haematological malignancies. Mycoses. 49 Suppl (2):18-23.