Introduction to Ulcerative Colitis

The principal causes of Ulcerative colitis are complex, with a weakened epithelial (“gut”) barrier function-AKA “leaky gut” being the hallmark of this and other autoimmune diseases. Other important factors include an altered microbiome, genetic, and often toxic environmental factors such as mold and mycotoxins. Unfortunately, most of the roughly one million American suffering from U.C. receive Ulcerative colitis treatment from G.I. doctors, using toxic “biologics.”

Allopathic (versus functional medicine) U.C. typically starts with gut and brain-damaging corticosteroids. Next, sometimes 5-aminosalicylic acid products are used, but quite frankly, not as often as they should be, along with toxic immunomodulators such as methotrexate or Azathioprine. Sometimes, doctors simply skip to the most toxic drugs called “biologicals,” which are very potent suppressors of the entire immune system.

None of the drugs listed above can cure U.C. At best, about half of all patients become unresponsive to their current therapy and need to be “switched up” to another, more toxic drug. Surveys show that up to 40% of all Ulcerative colitis patients are switching to Functional Medicine care. We can use non-toxic peptides and other non-toxic therapies to give patients lasting remissions. We also all use a specific ulcerative colitis diet for all patients and wonder why on earth non-functionally trained doctors don’t connect the dots regarding diet and symptoms.

Here’s a synopsis of what you probably already know about symptoms and diagnosis if you are reading this article.

The symptoms of Ulcerative colitis symptoms will vary depending on the location of the colonic lesions and the severity of the inflammation. However, most people experience moderate symptoms, and some may even have long periods of remission. Here is a list of the typical symptoms.

  • Abdominal pain and cramping
  • Diarrhea, often with pus and blood
  • Rectal bleeding
  • Urgency to defecate
  • Rectal pain
  • Fatigue (due to mitochondrial involvement)
  • Weight loss
  • Fever
  • Failure to grow (in children)

Ulcerative colitis can lead to some severe health complications. These are far less likely to occur with functional care if you are in remission. They are as follows.

  • Significant dehydration and electrolyte imbalances
  • Severe bleeding
  • Mouth ulcers
  • Bone loss
  • An increased risk of colon cancer
  • Liver involvement
  • An increased risk of blood clots
  • Inflammation of the skin, joints, and eyes

Next, I’ll detail the five major factors that you can control regarding what causes Ulcerative colitis to occur and flare: the “root cause.”

The #1 Root Cause of Ulcerative Colitis: Leaky Gut

Traditional medicine teaches us that risk factors implicated with Ulcerative colitis include smoking cigarettes, eating a low fiber diet, having a negatively altered microbiome, and even (surprise!) having increased gut permeability. In addition, medications such as non-steroidal anti-inflammatory drugs are also linked to an increased risk of Ulcerative colitis. Each one of these items can cause gut hyper-permeability: leaky gut. Leaky gut is the root cause of all autoimmune diseases, including Rheumatoid arthritis, Hashimoto’s thyroiditis, and Ulcerative colitis. Here are the reasons most Americans have some degree of gut hyper-permeability syndrome.

Food for a Leaky Gut

The food you eat can be the direct cause of leaky gut. People who regularly consume the “standard American diet” with its seed oil-laden fast foods, highly-processed foods, and high sugar content put total health- not just their Gi tracts at high risk. As you are (hopefully) aware, GMO foods are proven to damage the gut lining and disturb the microbiome. These foods dominate the corn, wheat, and soy markets. In addition, GMO gluten is increasingly blamed for non-celiac gluten sensitivity and leaky gut. It’s not your imagination if you think that certain foods are causing symptoms. It’s estimated that 25-75% of Americans have some type of food sensitivity. This sensitivity is different from a food allergy that causes immediate allergic symptoms. The most frequent foods causing sensitivities are (in this order) wheat, dairy, eggs-usually the whites, and corn.

But there’s more! Consuming artificial sweeteners, GMO foods, additives, dyes, and hidden sugars such as high fructose corn syrup can also result in leaky gut. Add in non-sprouted grains and lectins (found in nightshade vegetables and beans), excessive caffeine and alcohol, soda, and even fruit juice for good measure. So I’m not surprised that close to 100% of my new patients come to me with gut issues and leaky gut, and yes, Ulcerative colitis, too.

Even those of you eating what you believe to be a healthy diet are likely to have a degree of leaky gut. I’ll explain why in the paragraphs below. Is what I’m about to tell you enough to trigger you to the other side of actually “getting” Ulcerative colitis? Do you actually want to find out the hard way? Surely, not. Suppose you have Ulcerative colitis and you “eat what you want” while taking a  harmful biologic drug. Are you willing to alter your eating habits for better overall health and a promise for a better chance of remission? Sure you are—and I’ll give you the exact Ulcerative colitis diet plan after I finish reviewing the other causes of leaky gut.

Environmental contaminants and toxins

Gastrointestinal toxins we absorb or consume can damage our gut lining and disorder our microbiome. For example, when we eat canned tuna, we are eating mercury. When we drink unfiltered water, we drink fluoride. When we drink through plastic straws, we consume traces of plastics. When we swim in chlorinated pools, we ( over time) absorb chlorine that damages our gut. We can accumulate toxins via skincare products and from taking showers with un-filtered water. We breathe polluted air if we live in or around an industrial or high-traffic city. In a dusty house, even dust mites can cause leaky gut.

Finally, an increasingly prevalent problem due to climate change is water-damaged buildings that grow toxic mold. Twenty-five percent of us cannot (genetically) clear our bodies of mold toxins, so they damage our gut and cause various symptoms and long-term medical problems; unless treated by a CIRSliterate functional doctor. If you have had mold in your home (50% of structures in the U.S.!), you probably have mycotoxins in your HVAC system. Yes, you breathe in the toxins, but the lungs are more resilient-they will damage the gut lining fairly rapidly. And yes, this alone may be what causes your leaky gut and your subsequent Ulcerative colitis.

Here’s something else to keep in mind: the gut-brain barrier. Once the gut barrier is damaged, so too is the gut-brain barrier. That’s why leaky gut is often associated with symptoms such as brain fog, difficulting concentrating, and even mood issues.

As a “sidebar,” if you are my patient or simply purchase a one-time consultation, I can easily keep you safe from all of the contaminants listed above without much “hassle factor.” Now let’s discuss something that I find in most new patients, especially since “COVID times”: elevated stress and cortisol levels.

Chronic Stress

If you “feel stressed,” you are likely to have a high fasting cortisol level. High cortisol as a sole factor can cause the breakdown of your G.I. lining=leaky gut. It accomplishes this by slowing down both G.I. motility and the entire digestion process. When these things happen, some people experience heartburn or bloating after eating, while others have absolutely no symptoms. During this decreased digestive activity, blood flow decreases to all digestive organs, including the liver. The decrease in the liver’s detoxification activities results in a higher concentration of toxic metabolites, which chip away at your gut lining. Let’s talk a bit more about cortisol to get a handle on your stress if needed.


The only hormone that increases as we age is cortisol. It increases under acute stress, a short-term benefit for your body. However, chronic high cortisol levels can lead to increased plaquing on your coronary arteries, immune system dysfunction, impaired cognitive function, decreased mitochondrial biogenesis (causing fatigue) and put you at greater risk for cancer. In addition, it can cause insomnia- high cortisol levels interfere with regular sleep patterns.

High cortisol can be the root cause of your weight gain, as it is a driver of high leptin levels. High cortisol can also cause sugar cravings. It will impair your ability to lose fat and build muscle, as it is catabolic. It not only can decrease muscle mass but can also reduce bone mass. In addition, it can slow down your metabolic rate by reducing thyroid hormone output.

Therefore, we functional docs lower cortisol levels for people under stress and most individuals 55+ years of age. I often re-set the adrenals with adrenal adaptogens and adrenal glandulars. Sometimes I use integratives such as a magnolia bark derivative. Sometimes I use aromatherapy or liposomal GABA. You can find these products at a discounted rate right here. Finally, I’ll often turn to the intra-nasal peptide called Selank, a compounded prescription medication.

Selank: (Thr-Lys-Pro-Arg-Pro-Gly-Pro) 

Clinical studies show that Selank has strong anti-anxiety and neuroprotective effects. The physical effects of Selank are similar to those of anti-anxiety medications (e.g., Xanax), which enhance the activity of the GABA: the calming neurotransmitter. In addition, there is a similarity between the changes in the expression of 45 genes one hour after either GABA or Selank is given, which is practically identical. Now, let’s get back to the causes of leaky gut.


Americans tend to think of over-the-counter medications as entirely harmless. They often “pop” painkillers as if they’re candy. T.V. commercials feature actors who are proud of themselves when they take just one non-steroidal anti-inflammatory pain killer in the morning and not again until the end of the day. Unfortunately, Everything in the non-steroidal anti-inflammatory category (e.g., Motrin and Aleve) can breach your gut lining. The vast majority of people who take OTC pain relievers regularly have leaky gut.

And, speaking of OTC drugs, we now have a variety of proton pump inhibitors sold over-the-counter, thereby sky-rocketing their use. These drugs were not designed for more than short-term use. However, many people now use these PPIs (Protonix, Prevacid, and Nexium) for chronic heartburn and slowly dissolve the thin mucous lining of their G.I. tract.

Another category of gut-busters is antibiotics. I am constantly amazed by the number of antibiotics my new patients tell me they were prescribed for what sure sounded to me like viral infections. A little-known fact is that 75% of sinus infections clear with saline lavage, not requiring any antibiotics. Antibiotics not only notoriously cause leaky gut, but they also upset the microbiome.

Synthetic hormones such as birth control pills or cortisone-containing steroids (e.g., a Medrol dose-pack) can trigger the growth of excess candida (yeast), which also often damages the gut lining, with or without the existence of SIFO (small intestinal fungal overgrowth).

Gut Dysbiosis

Dysbiosis of the gut means that your G.I. microbiome is not balanced between “good bugs” and “bad bugs.” A correctly populated microbiome is crucial for optimal G.I. function, brain function, immune function, and the entire body’s proper function. Candida (yeast) overgrowth can invade the intestinal wall lining to cause SIFO, small intestinal fungal overgrowth; mentioned above. Toxic E. Coli species are common culprits in SIBO (small intestinal bacterial overgrowth) issues which I will discuss further in the next section.

Other organisms such as Helicobacter pylori (responsible for ulcers and cases of severe heartburn) or giardia (a parasite) can also eat away at the intestinal lining. Three common things can lead to decreased gut motility and therefore SIBO and SIFO: low progesterone levels, hypothyroidism, and low serotonin levels. The most common autoimmune disease (Hashimoto’s thyroiditis) sometimes accompanies the diagnosis of Ulcerative colitis, including gut dysbiosis, which doesn’t necessarily mean outright SIBO or SIFO-to make this distinction clear.

Let’s discuss how Hashimoto’s thyroiditis affects the gut. Many people have actual or functional hypothyroidism by the time they are diagnosed with Hashi’s. Since gut motility decreases when someone is hypothyroid, constipation is common. It’s reduced gut motility that causes this constipation. But then, constipation and the associated leaky gut often lead to small intestinal bacterial overgrowth. It’s estimated in numerous studies that a minimum of 50% of those with Hashimoto’s have untreated SIBO. Do you have SIBO or SIFO, you might be wondering? Let’s discuss.


SIBO and SIFO disrupt the gastrointestinal balance  (dysbiosis), often causing gas, bloating, and leaky gut. But it doesn’t happen out of the blue: we can generally follow up to find the culprit.

Any hormonal imbalances can cause chronic constipation, not just low progesterone or decreased thyroid hormone levels. In addition, all types of cancer chemotherapy agents can cause these gut issues.

The symptoms of small intestinal bacterial or fungal overgrowth are often confused with those of other G.I. disorders. The most common symptoms are flatulence and bloating as well as bloating after meals. Other symptoms include abdominal pain and constipation, but sometimes- diarrhea. These symptoms cause many patients to be labeled “IBS” (irritable bowel syndrome), never getting their symptoms addressed correctly. In addition, multiple food intolerances commonly develop as the situation goes untreated.

The lactulose hydrogen breath test (LHBT) is often utilized to diagnose SIBO. However, because these breath tests are neither sensitive nor specific (up to 60% false negatives), most Functional doctors will treat a patient when they exhibit classic symptoms. Meanwhile, SIFO is only diagnosed with an invasive small bowel aspiration, so ditto for treatment of that as well.

Treatment in the non-Functional G.I. world is typically a long course of an antibiotic called rifamixin. However, herbal therapies are actually more effective (per clinical studies) than rifaximin for curing small intestinal bacterial overgrowth. Some effective herbals include oregano oil,  barberry, berberine, olive leaf extract, and wormwood. This combination is effective for SIFO as well. Although you can purchase these herbals over the counter, I recommend seeking a good (functional) medical opinion first.

Now that we’ve covered all of the things that can cause a leaky gut let’s talk about how to fix that gut and the steps we take in functional medicine to put your Ulcerative colitis in permanent remission. Here’s what you’ll need to do.

Treat Underlying Gut Issues

Heal your Gut 

Getting you into remission from Ulcerative colitis begins with simply fixing your leaky gut. You will use (under medical care and by prescription, (not by yourself with black market products) gut-healing peptides (which will be discussed further on) and (if needed) fortifying supplements for leaky gut such as collagen powder and l-glutamine. Vitamin D levels need to be augmented in just about everyone, and then sporulating probiotics should be added when the symptoms start to subside. At this time, you’ll also add prebiotic fibrous carbohydrates (supplements or foods) to your diet. More about re-balancing your microbiome (the prebiotics and probiotics) is coming up. But first, let’s talk about fixing your cortisol levels and then- your eating habits.

Control Stress to Lower Cortisol

Stress is honestly just terrible for your health, as you learned earlier. We all seem to know this- but let’s review some of why this is. We know cortisol is a direct neurotoxin, a genuine risk factor for Alzheimer’s disease. We know it adds fat to our bodies while reducing our muscle mass. When we’re talking about Ulcerative colitis or any autoimmune disease, we see the direct effect of high cortisol on the gut. As discussed previously, sustained high cortisol might be someone’s only reason for developing a leaky gut.

Adrenal (herbal) adaptogens, glandulars, liposomal or topical (not oral) GABA, and specific aromatherapy blends that contain lavender can lower cortisol. In addition, stress-busting techniques such as “vagal breathing,” meditation, and yoga are relaxing and will lower cortisol. Finally, simply activating your hypoglossal nerve and the adjacent vagal nerve to tone down your sympathetic nervous system will help. All you need to do is sing, say “Lalalala,” or even just gargle! The fundamental lifestyle change that non-functional doctors ignore is a proper Ulcerative colitis diet.

Change your Diet

It’s necessary to eliminate foods from your diet that can cause leaky gut. This involves reviewing the list of “bad foods” discussed above or simply following the list of what to take out and include, which I’ll discuss below. If you have any food sensitivities, eliminate those foods if you haven’t done so already. It is easier to start with a basic diet and then reintroduce certain foods (e.g., seeds, nuts, eggs, etc.) when your symptoms are under control.

If you are eating a typical fast food-processed American diet, you’ll note that your modifications will cause you to shed some pounds, have more energy, and feel generally better. So the first thing you should do is clean out your pantry and make a list of “allowed foods.”

This AIP (autoimmune protocol) diet restricts the “typical gut offenders” such as gluten, eggs, dairy, sugar corn, processed foods, fast foods, nightshade vegetables, citrus, grains, legumes, as well as caffeine and alcohol. Yes, just like the Paleo diet! And yes, you’ll get your coffee, some specific alcohol, and other items back when you are in remission. My Ulcerative colitis diet restricts high FODMAP foods (such as coconut milk) if they cause G.I. distress. Yes, I know it-this diet is restrictive, but it will help get you well, and in a few months, you can reintroduce some food items. I learn what foods my patients “really miss,” so I let them know when they can introduce “what” and don’t use a dietician, while other doctors use dieticians regularly. If you use one, make sure they are familiar with the AIP diet plan.

The Ulcerative Colitis Diet

Let’s talk about what you eliminate

  • Fast foods and highly processed foods—obviously
  • Grains. One or two of these might come back.
  • Dairy products. High-fat A2 dairy will likely come back.
  • Eggs. But you can have duck eggs. Or quail eggs. And chicken eggs will likely come back.
  • Nightshade vegetable includes eggplant, potatoes, tomatoes, peppers, and okra.
  • Spices made from nightshades, like chili powder, paprika, cayenne, chipotle, and red pepper.
  • Alcohol. This will come back with specific selections.
  • Caffeinated teas: herbals are fine. This will come back.
  • Soy. But try Bragg’s aminos-it tastes just like soy sauce.
  • Legumes, such as beans, lentils, and peanuts.
  • Seed oils, such as vegetable and canola oil.
  • Refined sugars. In time, you can have some sugar back.
  • Nuts and seeds. Most of these will come back-and I mean in “re-intro foods” when I say “will come back.”
  • Herbs from seeds like coriander, cumin, and nutmeg.
  • Coffee. This will come back.
  • Chocolate. Dark chocolate will come back.
  • Dried fruits. These will return in small quantities.
  • Food additives, like gums and emulsifiers. These will return in small quantities.
  • Alternative sweeteners such as xylitol and mannitol with stevia are OK in small amounts.
Here are the basics of your eating plan
  • Except for the nightshades, all vegetables, and remember corn is a grain, technically. Most can re-intro corn.
  • Fish, shellfish, meats, and poultry.
  • Low sugar; small quantities of fruits (berries only at first) and then apples
  • Healthy non-seed oils (olive, avocado, MCT) and animal fats such as ghee. A2 butter will be a re-intro food.
  • Herbal Tea
  • Vinegar: Restrict to apple cider initially.
  • Small amounts of freshly squeezed lemon juice with olive oil for salads
  • Bone broth (or gelatin/collagen).

You will follow this eating plan (along with the “meds” your Functional M.D. prescribes) until your stools become formed and the pus and bleeding stop. For most people, this occurs within 2-3 months. When you are given the “OK,” you can add a cup of brewed coffee with a splash of additive-free coconut or almond milk. Coconut milk is not included for most U.C. patients at first because it is a high FODMAP food in more than tiny amounts, meaning that it can cause G.I. symptoms. Reintroducing food is quite personalized, so don’t try to do this without medical or dietary guidance. Eating the wrong foods will provoke symptoms, even if you follow the correct medication regimen, which I’ll discuss later. Now let’s review the “meds” you can take if needed.


We’ve reviewed what you should not take- so what do you take instead? If you have pain, instead of NSAIDs, use Tylenol. But be sure to use the brand name Tylenol, which is made with gluten-free fillers, whereas generics often contain gluten. (I know!). You can also find safe brands of specific CBD1-CBD-A products for pain. For heartburn, try a white TUMS or Rolaid if you’re in a bind. Even better: find suitable digestive enzymes. Many herbals can substitute for antibiotics and antifungals, but please get some medical guidance. Finally, remain vigilant regarding what you put in your mouth and into your digestive tract, knowing that you can find soy and gluten fillers in vitamins and medications. Really!

Clear up the gut and other infections 

Most small-intestinal-bacterial-overgrowth (SIBO) cases occur when bacteria from the colon basically “backwashes” into the usually sterile jejunum. If you are a female with a history of vaginal yeast infections, you infect your gut, especially if you have some sort of gut motility issue, as mentioned previously. Recall that the most common yeast (SIFO) and SIBO symptoms are gas, bloating, and constipation. When in doubt, we treat since herbals-used for SIBO, SIFO, and even vaginal infections, are so benign and work better than their pharmaceutical counterparts.

Clear out Toxins 

Now that I’ve gotten you slightly paranoid about all the toxins you’re absorbing and consuming let’s focus on what commonly causes the problems. The toxins that routinely cause leaky gut are the mycotoxins in your home or office. The guiltiest heavy metal? Mercury. How do you know if mold is making you sick? If you have gut issues, fatigue, and a foggy brain, with a history of mold exposure, you should investigate this possibility to see if you have mold toxicity. And what about heavy metals like mercury? This depends on your environmental history (It’s an industrial pollutant), your diet, and even dental fillings. I’ll discuss this in more detail below. Lead poisoning is now directly related to drinking water pipes, so be aware of the quality of your community’s water pipes. Toxins cause illness in varying degrees in different people. Here’s why.

Toxins play more of a crucial role if you have “faulty genetics,” including misfires in your detoxification pathways. Many patients are eager to have dental work that they don’t need to have when they are sick with CIRS because they think mercury is making them sicker. The truth is that having a few mercury amalgam fillings isn’t enough to cause mercury toxicity and certainly not leaky gut. We generally say “having seven or eight fillings” is a problem that needs to be addressed (by a specialized Dentist) after getting the patient’s general health under control. However, be careful with your diet as a steady diet of tuna sushi or canned tuna fish is enough to cause methylmercury build-up with effects on the gut, brain, and other organs.

Re-Balance your Microbiome

You have more “bad bacteria” than “good bacteria” populating your G.I. tract when you have leaky gut.”  We use prebiotic fiber (foods or powders) to feed the good bacteria and (for non-CIRS patients) a little bit of “good yeast” to re-create a healthy gut microbiome. Regarding prebiotic fiber, start with asparagus, red onions, Jerusalem artichokes, and unripe bananas. Then, if you prefer powders or supplements, just add some daily psyllium fiber.

When the mucous layer of your gut lining heals up (3- 4 weeks “in”), you can add probiotics. Don’t purchase or make your own yogurt; you don’t yet have the “OK” for dairy-but you can do this “later.” Historically, we have recommended 50 to 100 billion probiotic CFUs daily regarding probiotics. A mixture of Lactobacillus species and Bifidobacterium species is standard, but there is increasingly more evidence supporting the use of sporulating probiotics for an even better and more diverse microbiome. A generic product, VSL3, has yielded positive remission studies, as have the probiotic strains Lactobacillus casei and Lactobacillus rhamnosus. However, I’m now usually first prescribing sporulating probiotics.

Current research supports the use of sporulating, also known as soil-based probiotics, to create a more diverse and thereby a more healthy microbiome. These probiotics are so potent that you have to be careful not to “overdose,” or you can experience cramping and diarrhea, which you might mistake for a U.C. flare. Start low at 5 billion CFUs and increase to about 25 billion CFUs daily. These sporulating probiotics are species of Bacillus with b. subtilis and b. coagulans being the most studied. If you are left with “gas” as your only symptom, studies look promising for using 10 billion CFUs of Lactobacillus Plantarum.

Re-balance Gut Motility  

As the smooth muscle of the gut lining becomes destroyed, some colon segments get “out of sync.” As the gut heals, it’s not always going to heal evenly. We, therefore, sometimes need to use products to bulk up the stool to improve the transport of “contents” with examples of good bulking agents being modified citrus pectin or a multi-fiber blend. Sometimes we need to also enhance G.I. transit at the smooth muscle level by increasing serotonin levels with 5-HTP. It’s a bit odd, I know, to posit that a disease that can produce “explosive” diarrhea can cause bloating, gas and constipation while healing occurs, but indeed, this is the case.

Balance your Hormones 

Your functional doctor should balance both male hormones and female hormones for optimal gut motility. You need to be “regular” to prevent “backwash” and, therefore, infections. The gut functions more efficiently, and the microbiome remains more helpful when your hormones are corrected. A complete discussion of all of your hormones is beyond the scope of this article. The information is, however, available in this blog. Be aware, however, that the decrease in estrogen during menopause causes a rise in cortisol, something that you now know can cause leaky gut. You are also aware that adequate progesterone is necessary for optimal gut motility, as is sufficient thyroid hormone.

Get on the RIght Treatment Regimen

Although the data exists, I am not aware of any other doctors who use my exact protocol to treat Ulcerative Colitis. I know that my protocol works, and also know that at first, it’s rather daunting to take patients who come to you with pancolitis, or in the hospital, or after being told that they need to have their entire colon removed. But I’ve taken on these patients and have gotten them all in remission to a person. Here’s how—and don’t try this at home.

Low Dose Naltrexone 

It’s a staggering number: about one-third of patients with Ulcerative colitis are resistant to all currently available pharmaceuticals, or they will relapse over time. Meanwhile, for many years now, scientists have studied the effects of low-dose naltrexone (LDN) on the gut epithelial barrier in treatment-resistant Ulcerative colitis patients.

An important clinical study enrolled close to 600 inflammatory bowel patients. There were many positive findings among the approximately 250 patients who became persistent LDN takers. The patients were able to reduce their toxic drugs by quite significant amounts. All previously consumed drugs were reduced by 12%, with intestinal corticosteroids markedly decreased by 32%. In addition, patients could lower intestinal anti-inflammatory agents by 17%, aminosalicylates were reduced by 17%, and other immunosuppressants were down by a whopping 29%! Of significant importance: this study did not manipulate diet or use any other gut-healing agents. No probiotics! No gluten removal! No peptides!

In another study, low-dose naltrexone was given to 47 patients who were followed prospectively for 12 weeks. Endoscopic data and tissue biopsies were collected. Researchers evaluated the effects of LDN on wound healing and tissue biopsies from endoscopic procedures. The results? Spectacular. Low dose naltrexone (again-alone!) resulted in “significant clinical improvement” in 75% of these patients, with complete remission noted in 25%.

The most recent clinical study assessing LDN in patients with inflammatory bowel disease involved 19 Ulcerative colitis patients and 28 patients affected by Crohn’s disease. Patients with an unresponsive and very active phase of their disease received a daily dose of LDN  in addition to standard treatment. Follow-up lasted for three months. Thirty-five patients (75%!) responded to therapy with decreased disease activity which lasted for at least a month. Six patients achieved complete clinical remission. Five of those six had a complete endoscopic remission. This data was emerging well before peptides became available on the compounding markets. I knew LDN couldn’t get the job done by itself but wondered why it wasn’t being added to traditional regimens. Could it be that it is inexpensive, with minimal profit margin, while biologics are quite profitable? Sadly, that’s what I think.

Imagine if the above patients had eaten my Ulcerative colitis diet, taken peptides (which you’ll read about shortly), had adequate vitamin D levels, and taken sporulating probiotics with good prebiotics, along with their LDN? Wow, right? I was determined to find out. My first patient was myself. And I eagerly learned all about peptides to do an excellent job for myself and, eventually, my patients. Here is what you need to know about peptides.


Peptides are protein molecules that are short chains of amino acids: typically composed of two to thirty amino acids. The peptides we use in functional medicine are isolated from human secretions and then re-purposed elsewhere in the body. Therefore, they are bioidentical because of their origins, meaning no side effects as we see from pharmaceuticals. Many peptides are utilized in functional and integrative medicine, but I have found three in particular that I use in various forms, combinations, and doses for Ulcerative colitis treatment. Let me take a moment to mention that buying black market peptides will not get you the results you desire. I don’t need to tell you why I hope.


KPV is a cleavage product of a melanocortin called α-Melanocyte-stimulating hormone (α-MSH). It has both protective and anti-inflammatory effects. The three amino acids mediate its anti-inflammatory activity at the end of what’s called the N terminal:lysine-proline-valine. Interestingly enough, the KPV peptide alone exerts an even more potent anti-inflammatory effect than the whole α-MSH peptide.

Oral administration of KPV will diminish the inflammatory responses of epithelial and immune cells in the colon. It also decreases the incidence of active colitis. KPV exerts its anti-inflammatory function inside colonic cells, which inactivates inflammatory pathways by reducing pro-inflammatory cytokine genetic expression. Unlike the drugs currently used for Ulcerative colitis treatment, KPV is a naturally derived tripeptide without side effects.


BPC-157 is a series of amino acids with remarkable healing properties. For the purposes of this article, note that the effects on the G.I. tract include anti-ulcer properties, cellular protection, and documented healing of leaky gut syndrome. In addition, this pentadecapeptide Gly-Glu-Pro-Pro-Pro-Gly-Lys-Pro-Ala-Asp-Asp-Ala-Gly-Leu-Val is very useful to help wean all patients off of toxic proton pump inhibitor (PPI) medication. Lastly, it helps counteract the development of peritonitis and heal intestinal lesions after injuries.

BPC-157 is stable in the acids of human gastric juice and is effective in both the lower and upper G.I. tract. It is remarkably free of side effects and drug interactions. BPC-157 is proven to be a part of an effective treatment for Ulcerative colitis and Crohn’s disease. It interacts with the protective nitric oxide generation system, raising NO levels, providing endothelium protection, and healing Ulcerative colitis lesions.


This peptide modulates and increases copper uptake into cells. For this reason, if you take this peptide, you must ingest an adequate daily dosage of zinc. The human peptide GHK-Cu (glycyl-l-histidyl-l-lysine) has multiple positive biological actions. First, it increases collagen, elastin, and glycosaminoglycan synthesis. Secondly, it stimulates blood vessel and nerve growth and improves tissue repair. Finally, it decreases ulcers and infections in bone, liver, lung connective tissue, skin, and the stomach lining. For these reasons, we believe that it has reparative value for the entirety of the gut.

Another peptide with promise:

LL-37 is an antimicrobial peptide involved with our innate immune system of defense against microbial invasion and decreases gut permeability via improved tight junctions (claudin, occludins). It appears to help treat Crohn’s and Ulcerative Colitis in animal studies. With approximately 3000 peptides isolated and in the process of being studied, I’m sure that there will be variations to my Ulcerative colitis treatment regimen. For right now, however, this is the best we’ve got.

Is a Keto Diet Plan the Best Way to Lose Weight?

If you’re able to alter the way you eat and stick to the keto diet plan, this definitely does “deliver.”  Perhaps, you’re a “dieting” veteran, but still, that doesn’t mean you are versed in how to get ketotic, stay ketotic, and know exactly what to eat and when to eat it. You are also likely unaware of how long you can safely “do” ketosis, how to prevent side effects, and so on. Don’t fret—I’ve done all of the heavy lifting for you. In future articles, I’ll get into the health benefits of “going keto” such as control of Type 2 Diabetes, the role in the treatment of cancer, the prominent role in treating some types of cognitive impairment, epilepsy, diseases of female hormones such as polycystic ovarian syndrome and even Parkinson’s disease. Note: the verdict isn’t in regarding the long-term use of this keto diet plan, so my advice would be to use it when you need it and then eat an anti-inflammatory diet when you don’t. This particular article will focus on how and why to use the keto diet plan for weight loss.

Here’s a significant caveat: If you are using the keto diet plan to self-medicate a disease (which I never recommend, by the way), be careful that you don’t drop weight you don’t plan on dropping.

The new way to “do ketosis” is similar to the Atkins diet, which boosts the body’s fat-burning abilities by eating only low-carb foods and getting rid of foods high in carbs and sugar. Removing glucose and fructose from “carb foods” will allow the body to burn fat for energy instead of glucose. The major differences between the standard keto diet and the Atkins diet are the use of only healthy fats, less overall protein, and no bacon or other processed or seared meat. As an aside, I hope you know to never sear or burn your meat. High temperatures produce toxic, carcinogenic fats. Here is what I’ll cover in this article.

  • What’s in the Standard Keto Diet Plan?
  • Does Ketosis Suppress your Appetite?
  • Your metabolism and (therefore) calorie count in ketosis
  • Is the keto diet plan safe?
  • Protecting your Microbiome During Ketosis
  • What foods should you simply get out of your house?
  • Step by step: the beginner’s guide to doing a safe keto diet plan
  • What about the “Keto Flu”?
  • What are all of the Specific foods, beverages, condiments I can have?
  • How to calculate how much protein you need per day
  • How many carbs?
  • How much fat?
  • What should your week and day look like?
  • Your ketotic day at a glance

The Standard Keto Diet Plan

There are several ketogenic diets “out there” for people with mitochondrial dysfunction, athletes, and so on. However, for weight loss, we use the standard ketogenic diet. The guidelines are 70-80% healthy fats, 10-20% protein, and 5% carbohydrates. I’ll later translate this into a menu of what you should be eating. Also, remember there is actually no absolute limit to fat intake because energy requirements vary from person to person.

If you are already following my anti-inflammatory diet plan, you will notice the foods are quite similar. However, the noticeable difference is a significant increase in your intake of healthy fats. The key to this eating plan is that you will not feel hungry. Let me explain why.

Using Ketosis to Suppress Appetite

Ketosis is one of the best natural appetite suppressants. If you are eating a typical high-carb American diet, you are experiencing blood sugar swings that cause you to have bouts of intense hunger- sometimes within two hours of eating a meal.  When you start burning fat for fuel (ketosis) rather than using glucose for fuel (“regular eating”), your blood sugar will stabilize at a lower, healthier level, and the ketones made by your liver will suppress your hunger via two major mechanisms.

When it comes to the bulk of hunger pangs, we’re talking about ghrelin. Ghrelin increases appetite. When you eat a meal, ghrelin levels drop, but less so if you are overweight. When you lose weight, your body senses starvation, and ghrelin levels increase, but they do not increase if you are in ketosis. And then there’s leptin.

Leptin gets a lot of publicity as the “hunger hormone, ” but it’s really more of a “fat-storage hormone.” Ketosis doesn’t suppress leptin when you first start this diet. So at first, you might get a little hungry and even have some cravings. It’s not super common, but it’s possible via a couple of complex biochemical changes, including an increase in the relaxation brain chemical called GABA. If this happens, just “power through it” if you don’t have a Functional doctor like me, it won’t last long.

Anyway-back to leptin because this hormone is rather complex. If you are stressed, your cortisol level is up, which then raises your leptin level. Consuming a lot of grains and fruits (fructose) will raise leptin. Having an undiagnosed mold and mycotoxin illness will always raise your leptin. Doing this keto diet plan will help lower your leptin, allowing your fat cells to stop clinging to every calorie you eat. And then there’s the satiety hormone, CCK.

Ketones and CCK—the feel full hormone

CCK is a hormone released by your intestines after you eat. It seems to be a pretty intense regulator of food intake. In clinical studies, CCK injections make people stop eating. The normal decrease in CCK secretion with weight loss is circumvented when you eat a ketotic diet. So, another benefit of a keto diet plan for weight loss is that you won’t experience those annoying plateaus that occur with regular diets.

Your metabolism in Ketosis

You’ll be happy to learn that you don’t have to count calories. You. Just. Don’t! Eat until you are full and don’t snack. Ketosis is a natural metabolic booster, so don’t be afraid of the “fat calories.” You’ll convert the fat to brain-healthy ketones and use them for fuel, with the excess being excreted in your urine. Be careful not to add excess carbs, which could throw you out of ketosis. More about the number of fats, carbs, and protein you can eat coming up later in this article.

Is this diet safe?

Ketosis is safe if you are a healthy adult. If you have Type 1 diabetes, check with your doctor. If you have any lower GI issues such as Chrohn’s disease or leaky gut, you need to be very careful of food choices and length of time in ketosis. I always advise patients with “gut issues” to take the right supplements to heal the most common gut symptoms such as post-meal bloating, watch for flares and add a good fiber supplement to their regimen that serves as prebiotic fiber. Details about this coming up. During the first two weeks of your diet, it’s common to have some fatigue and brain fog.

Some people also develop dry eyes and sinuses. In addition, there is evidence that ketosis might disrupt mucous production in the gut, predisposing you to a possible leaky gut. It also might disrupt the microbiome.  I’ll therefore give you my recommendations on how to protect your gut below when I also discuss prebiotics and probiotics. Meanwhile, if the level of ketosis is too much for you, just adjust your level as I’ll instruct you to do further in the article.

Protecting your Microbiome During Ketosis

To maintain a healthy gut during the keto diet plan, use gut lining reinforcing products such as l-glutamine, colostrum, or even the peptide BPC-157. Also, eat or use prebiotics and probiotics: let me explain exactly how to do this.

Prebiotics are nondigestible carbohydrate compounds found in fibrous foods which assist in the growth of healthy bacteria in the gut. One mechanism of action: good prebiotics often create short-chain fatty acids such as the very healthy-bacteria-friendly short-chain fatty acid called butyrate. Good sources of prebiotics include unripe bananas, raw leeks, raw or cooked onions, raw dandelion greens, Jerusalem artichokes, chicory, asparagus, raw garlic. You can also purchase prebiotic fiber blends and put them in smoothies or shakes.

Probiotics are live bacteria that are ingested, multiply in the gut, and have beneficial effects. One benefit you’ll love is that they increase your metabolism. Sources of probiotics are dairy or coconut kefir or yogurt and fermented foods such as kimchi and sauerkraut. A complete list is below.

  • Yogurt (sugar-free), including non-dairy coconut yogurt (Homemade from starter cultures is best.)
  • Cheese made from raw (unpasteurized) milk with the latest research showing that A2 dairy is the healthiest choice
  • Kefir (fermented milk or coconut drink)
  • Pickles (refrigerated, nonpasteurized)
  • Olives (organic, no additives)
  • Kimchi (spicy Korean condiment)
  • Sauerkraut and other fermented vegetables (refrigerated, nonpasteurized)
  • Kombucha (sugar-free, effervescent cultured drink)

Since you have to make a daily effort to eat sufficient probiotics, many people use probiotic supplements instead. State-of-the-art supplementation combines Lactobacillus and Bifidobacterium species plus sporulating probiotics (Bacillus species) to create more gut diversity and even some healthy yeast (Saccharomyces) if you do not have mold mycotoxins in your environment, making you sick.

In addition to the dietary additions above, there are modifications to typical keto diet plan foods, which are suggested by functional doctors who want to protect your gut. Multiple clinical studies show that plant-derived protein is far more beneficial for your microbiome (and your metabolism) than animal-based protein. A way to augment this effect is to take omega-3 fish oil supplements to offset the high amount of omega-6 fatty acids you consume when eating meat. Lastly, let me remind you how harmful to the gut processed foods and most artificial sweeteners are.  And while I’m discussing harmful foods, let’s segway right into what foods to get out of your house before you get started on your keto diet plan.

Get rid of these foods

Those of you reading this are coming from many different food worlds. Some of you are already trying to follow a healthy diet. Unfortunately, commercial diet plans may have hoodwinked others and now eat many processed (just like junk) foods from the diet plan. Still, others might be eating what they think are healthy foods such as whole-grain bread. So what’s wrong with whole-grain bread, you ask? Sadly, whole-grain bread cranks up blood sugar more than eating sugar!

Lastly, there may be some of you who are still eating a typical American diet filled with processed and fast foods, sugar, and starchy, processed carbohydrates. No matter what food world you are coming from, you need to clear your pantry and your life from a host of unhealthy and decidedly weight-gainer foods so you can lose the pounds once and for all. Please clean out the sugars, starches, packaged and processed foods from your pantry and freezer. You are going to eat whole, fresh, real food. Guess what? You will feel satisfied, and you’ll love it!

Other no-nos include eliminating most (but not all) dairy products (high in the sugar: galactose) and all grains. Recall you will only consume “healthy fats,” so hydrogenated vegetable oils (cottonseed, canola, sunflower, etc.), peanut butter, and soy products need to go. Don’t worry about the peanut butter because you can have healthy (raw, sprouted) cashew butter and some almond butter.

The beginner’s guide to using ketosis for weight loss (how-to’s):

  1. Throw out (or donate) the unwanted foods and get psyched.
  2. Get a ketosis meter or urine strips that measure ketones. Check morning and evening: .5-3.0 mmol/l is the range you’ll want to be in. I’ll discuss where “you should be” when discussing the keto flu in the next section.
  3. Get a scale and weigh yourself in the morning before consuming anything.
  4. Make a grocery list, health food store list, and online purchase list for the products and foods you will need for success. Find out local sources of organic, non-GMO vegetables, grass-fed meats, wild-caught seafood, grass-fed butter, and pastured organic eggs. Source out good, guar gum and carrageenan-free coconut milk. Source out natural shredded coconut and raw non-pasteurized nuts and nut butter. If you will get fancy and start baking, you will need to source out nut flours. You can get some of these things in health food stores, including MCT oil and a delicious casein-free butter called ghee. I love ghee. It adds a depth of buttery flavor to vegetables and even eggs.
  5. Secure your healthy fats and the one type of fat that will get you into ketosis faster than any fat, MCT oil. Coconut oil has a fair amount of medium-chain triglycerides, but for best results, you’ll need some MCT oil.
  6. Consider purchasing some “exogenous ketones,” which are supplements or supplement powders containing beta-hydroxybutyrate salts if you need a “ketone boost” in the situations described below.

You should not stay in ketosis for more than 2 weeks in a row for best results and overall health. Recall I discussed changes in GI mucous above. When GI mucous is disrupted, so is the microbiome, or gut bacterial protection. We don’t know the long-term ramifications of prolonged uninterrupted ketosis, but studies suggest possible leaky gut. In addition, studies show that one day of very low protein is likely a great health practice for everyone to do weekly. Some people notice drying out of mucous membranes, which isn’t good for prolonged periods, either. For most people, this results in dry eyes, easily relieved with lubricant eye drops.

For all of these reasons, you will “do ketosis” for 2 weeks, and then each week, you’ll pick a day when you’ll go very low-protein (less than 10 grams) and high-carb (up to 200-300 grams-but only with “allowed foods”). To follow, the next morning, you’ll get back into ketosis with your MCT oil or your ketone supplements. If you are having trouble with this diet on weight training days, you can do a high carb day 2-3x per week and still lose weight. Obviously, the high-carb days would be your “lifting days.”

Will I Get the “Keto Flu”?

The ketogenic diet will change your metabolism by putting you into ketosis and turning you into someone who uses fat for fuel rather than sugar for fuel. As a result, you’ll notice some (hopefully) minor issues in the first two weeks. The following symptoms have been named the keto flu.

Keto flu symptoms can include having difficulty sleeping, feeling lethargic, getting constipated, being moody, losing sex drive, getting foggy-headed, and having bad breath. Fortunately, these side effects don’t affect everyone and usually only last for 1-2 weeks. Symptoms will abate as your body adjusts to being in ketosis. Remedies include reducing your levels of ketosis and finding a balance of hunger control and symptom relief. Note that the ingestion of ketone pills makes keto flu worse. Here’s what helps.

Melatonin helps sleep—fiber and water help constipation. Lastly, “cold-shocks” (see mitochondria article referenced earlier) help brain fog and energy levels, and so does the supplement, nicotinamide mononucleotide (NMN).

Specific foods

Healthy Fats

Healthy fats include saturated fats such as grass-fed butter, ghee, MCT-containing coconut oils, and sustainably produced palm oils. Even gross-sounding things such as lard, chicken fat, and duck fat are allowed. Monounsaturated fats such as olive oil and avocado oil are also quite healthy fats, but olive oil should not be used for cooking. MCT oil can be used for cooking and can be taken on a spoon or added to drinks. If MCT oil gives you intestinal cramps or diarrhea, just take the ketone supplements when you need a ketone boost. I’ll go into this more in-depth in a moment. Omega-3 fatty acids are very healthy and should be supplemented if healthy seafood is not plentiful.

All fat should be used liberally except for omega-6 fatty acids found in animal products. You should consume more omega-3s than omega-6s. If you supplement with DHA/EPA omega-3 supplements, you don’t have to “watch everything” you eat regarding the recommended 2:1 ratio of omega-6 to omega-3 fats. Introduce MCT oil slowly, or it will upset your stomach. Start with a daily teaspoon. Your goal is 1-2 or 3 TBSPs of MCT in the mornings to help power your ketosis throughout the day. You don’t have to “eat fatty foods” specifically, as doing so would lead you to a lot of animal protein, specifically beef and pork, which I’m decidedly not recommending for health, and environmental reasons. I won’t “pound this concept,” but I would again like to urge you to source your animal protein products from small farms and avoid factory-farmed meat.


Animal proteins contain few carbs but can be used by the body to make glucose, so don’t overdo it on these foods. This particular diet isn’t an “open bar” regarding meats as you might be used to if you have followed the Atkins diet in the past. However, with all the hunger-suppressing fats you will be consuming, you shouldn’t have to worry about the amount, especially during the first two critical weeks of this diet.

High omega-3 fish include sockeye salmon and sardines (in water) as the best choices. Beware of other fish unless you are sure it’s not farmed. Wild bass, mackerel, flounder, mahi-mahi, dolphin (no-not Flipper–the fish!), and anchovies are all healthy choices.

  • All meats which are grass-fed, organic, and certified to be such are acceptable.
  • Grass-fed organic meats are higher in omega-3s are just plain healthier for you.
  • Organ meats are technically permitted, but I’m not crazy about recommending parts of the body such as a liver or a kidney because they are the toxin-filtering organs of the body.
  • Cage-free “pastured” eggs are full of healthy cholesterol, and consumption of these products is no longer restricted. Poultry is the “least reliable organic” meat, but everything from chicken to quail, duck, goose, pheasant, and turkey is permitted. As always, source these products from family farms.

I allow all nuts other than peanuts. Other keto diets restrict nuts and seeds due to the amount of protein people eat when consuming nuts. However, you are all adults and can budget for the protein of walnuts, pecans, macadamia nuts, hazelnuts, and even high-protein almonds. Coconut can be consumed liberally and is encouraged.

Yes, I did say that dairy was a no-go, but you can absolutely budget some raw cheese and yogurt into your diet after the first 2 weeks.

Non-Starchy and Starchy Vegetables

During your first two weeks, you want to limit your veggie consumption to the very low carb group, with some of the low carb group carefully included. Then, after week 2, add in the moderate and high-moderate carb groups of foods and use the high carb veggies for your high carb day(s). Here are the groupings of your veggies.

Very low carb: Fresh herbs—close to 0 grams net carbs per 1-2 tablespoons. All leafy greens include romaine lettuce, endive, escarole, radicchio, spinach, collards, turnip greens, chicory, fennel, chard, and kale are most of the veggies in this group.

Low carb: Cucumber, zucchini, leeks, and chives, as well as onions and (my fave-on everything!) scallions, make up this flavorful group.

Moderate carb: Healthy and tasty cruciferous vegetables such as cabbage, cauliflower, broccoli, and brussels sprouts.

High-moderate carb: Asparagus, bell peppers, radishes, jicama, green beans, wax beans, water chestnuts, bean sprouts, bamboo shoots, and wax beans. Eggplant, bell peppers, and tomatoes are at the high end of the carbs and sometimes questioned as to their consumption during ketosis as the highest lectin-containing  “nightshade vegetables.” (Those with leaky gut or autoimmune disease should not consume nightshade vegetables, and so this question is “out there” as to whether or not they should be consumed in ketosis. I choose not to, personally).

High carb: All types of squashes, sweet potatoes, carrots, turnips, beets, parsnips, and rutabagas.


You can consume berries, apples, and citrus in small amounts, starting after the first two weeks, as they are lowest in fructose. You should know by now to exclude fruit juices if you have been following my anti-inflammatory diet. If not, now you know! Let me do a big shout out to the fruit many people think of as a vegetable, the avocado. It has up to 8 grams of carbs per the whole avocado. Try to work this in as much as possible as it is one of the healthiest foods you can eat.


Spices and herbs, apple cider vinegar, hot sauce (with no additives or sweeteners), unsweetened mustards, homemade mayonnaise (egg yolks, lemon juice, apple cider vinegar, extra virgin olive oil), and homemade salad dressings are all “on your list.”  Check out the Keto Social media groups for recipes. Also, check out the Keto Etsy bakers and the companies that now cater to making keto foods, snacks and desserts. Sweeteners considered safest for health include stevia and monk fruit. However, I’ll also include xylitol (toxic for dogs, so–pick up your gum!) and erythritol-not sucralose, which destroys the microbiome.


Of course, you can drink water and unflavored sparkling water. Lemon wedges really add a lot of flavor, but remember to count the carbs from them. I hope you know that diet soda is “toxic waste.”   Coffee doesn’t need to be black and unsweetened or filled with “bulletproof” butter and MCT oil. I love my morning coffee and cannot stand oil in my coffee, no matter how good it might be to get me into ketosis when I occasionally “do ketosis” for health reasons.

However, if you want to try putting grass-fed butter and MCT oil in your coffee, go right ahead. Just heat your blender and blend this concoction. Power to you if you like it. I just don’t like it and can only “go so far” regarding healthy practices. For me, my morning cup of coffee is just plain sacrosanct. You can have coffee with stevia and coconut creme or a blend of coconut creme and almond milk. Or you can have heavy cream. You just need to account for the carbs. Drink all the organic (not teabag) tea you want, but the same rules apply. You’ll be happy to note that you can have very dry wine, champagne, or clear alcohol such as vodka, tequila, or gin in moderate amounts on my keto diet plan. As always, you need to account for the carbs.

How to calculate how much protein you need per day

You’ll need to keep re-calculating as your fat mass goes down and lean mass goes up. You can calculate this by figuring out your lean body mass. If you don’t have access to calipers or other body fat measuring scales, do an estimate. If you cannot take a “real” body fat measurement, use this calculator and then just experiment with amounts of protein, carbohydrate, and fat that can keep you in ketosis. It isn’t hard at all. Stick to the right foods and eat enough fat.

The Formula

Do you have your % of body fat? Your % of lean body mass is 100 – your % of body fat. Figure out what you weigh in kilograms by dividing your weight in pounds by 2.2. Take that number and multiply it by the % of lean body mass you have. That gives you the number of lean body kilos you weigh in with and tells us how much protein you need. You need a gram of protein per kilo of lean body mass.

An example is a 120 lb woman with 30% body fat, meaning, by definition, 70% lean body mass. 70% of 120 is 84. 84 divided by 2.2 is 38. Therefore, she only needs 38 grams of protein per day. This might be shocking as you are probably familiar with much higher quantities of protein in low-carbohydrate diets, right? Well, if you eat too much protein, it will convert to glucose. As a result, it will kick you out of ketosis.

So, watch the protein. It adds up really quickly. Ten almonds have six grams of protein! One egg has 6.3 grams. A piece of meat or fish the size of a deck of cards (4 ounces) has 20-25 grams. Be careful not to load up your protein into one meal, either. Your liver will kick you out of ketosis with more than 20-25 grams of protein at one sitting. All of this is obviously individualized. Everyone is unique. Figure out what you need and how much protein is in what you like to eat. Make a list if it helps.

How many carbs?

This is where you get to do some personal experimenting. Most people do the best eating somewhere between 20-50  grams of net carbs daily. “Net carbs” means you can subtract fiber and sugar alcohols (like xylitol) out of your daily carb count, but now that I’ve told you that- you could forget it; just eat what’s allowed and measure your ketones. I know this flies in the face of advice to “weigh everything,” measure everything and count all grams of everything at all times. I have read that sort of advice, and it makes me want to stab my eyes out just reading and imagining doing all of that. Doing this my way (which I’ll re-iterate at the end) just makes it all easier and more doable. Note that it is typical to lose a lot of water weight the first two weeks and experience thirst. Make sure to drink plenty of water during this time.

How much fat?

Let’s just say it will be more fat than you have ever eaten if you are a chronic dieter. It will feel quite odd eating so much fat, and you’ll wonder, “how can this be?” Well, let me assure you that the process of ketosis does indeed increase your metabolic rate, and you can just get yourself into ketosis and stay there with fat at every meal.  Again, you want to eat what amounts to up to 2-3 TBPS of fat at every meal—calculate this in with the fat in your meat, eggs, and so on.

What should your week and day look like?

Your week: Eat high fat, very low carb (<50g net carbs/day) 6 days a week, then have a carb re-feed on day 7 (150-250 grams of net carbs). Remember, this day is your low-protein day to help your body detox. This is 5-10 grams of protein only, and it “goes quickly!” If you have carb cravings on your re-feed days (it happens), have l-tyrosine and the SAMe handy to amp up your dopamine. If you can’t do the 6 and 1 as suggested for athletic (or just plain intolerance) reasons, do re-feeds as many as 2-3 days per week on your training days. Only restrict protein one day, though. These instructions assume you have done your first two weeks of ketosis where you eat controlled protein, high fat, and very low and low carb veggies only.

Your ketotic day at a glance 

Breakfast: If you get yourself right into a high level of ketosis each morning, you’ll have more “brain energy” and absolutely no hunger all day. Have your morning coffee as described above. Use MCT oil or ketone supplements as needed. After the first two weeks, if you want to add some eggs, that’s fine.

Lunch: Since this all “works better” and is healthier (due to good biochemical pathways being activated), if you confine all eating to a 6-8 hour window, and you will not be hungry until 3-5 P.M. anyway, delay lunch until 2 to 3ish. Then have a ton of low-carb veggies with a 1/2 card deck size of meat or fish protein.

Dinner: How does dinner at 7 or 8 sound? After the first two weeks, we can really have fun with this meal. Have some olives or a deviled egg made with your special mayo. Enjoy a cocktail; no mixers, but just as listed above. Have a lovely salad with homemade dressing. If you are at a restaurant, ask for EVOO (extra virgin olive oil) and lemon. Give back the breadbasket. Better yet: ask them not to bring it. Instead, have tons of vegetables, drenched in ghee and seasoned well.

Make your veggies creamy by taking 1/3 of whatever you made, putting it into a blender, and then blending it back into the veggies. Yes, you’re back home again. Now, go ahead and have some dessert. First, you can make “jello” by using flavored herbal tea, gelatin, and stevia. Next, you can make an amazing keto pumpkin pie and shave a teensy bit of dark chocolate and top it with whipped coconut creme.

Indeed, have dessert every night! In my world, that makes this eating plan 100% doable. You won’t miss chips if you can have chocolate mousse and/or specially made ice cream every night, will you? You can shave 85% chocolate on top of your coconut whipped cream every single night if you budget correctly!

I didn’t list “it” as I don’t want to encourage too much dairy, but you certainly can budget for some real whipped cream, stevia-sweetened, too. Search the internet, look for “keto bombs,” find a good cookbook and go to town. You can actually enjoy losing weight on the keto diet plan if you get creative enough.

Many of my patients tell me that they experience a surge of energy, brain focus and are just “happy as clams” doing this keto diet plan. It may or may not “be for you,” and you’ll know if it is “right” within the first 6 weeks. If it is “right for you,” my wish for you is that you achieve and then maintain your ideal weight for the rest of your life.

How to Boost your Immune System

We suffered not just from sickness and loss; we have been shut in, shut down, and zoom-fatigued.  Something that has emerged as almost a national obsession has been the urge for lots of self-care, including care that prevents infection. Such care now includes strategies to boost our immune system. We want not simply  to mask up, but to also, well- “immune up!”  Shall we?

Basic Lifestyle Strategies for Immune Health

Diet: I advise all patients to eat some form of an anti-inflammatory diet. To keep it super simple-eliminate highly processed foods, watch your sugar and starchy carbs consumption, and be careful with gut-damaging lectins. Foods that are highly processed or high in lectins such as gluten-containing grains, beans, nightshade vegetables, and low-fat dairy products  lead to gut lining damage which means “leaky gut.” Eating this way then causes inflammation which is one of the root causes of all diseases. I’ll go into inflammation more in-depth in one of the following sections. See the first page of my website for a free, downloadable diet.

Immune-boosting foods include garlic, horseradish, and wasabi. Garlic is anti-viral, and while used as a supplement, I won’t explicitly cover its use in this article.  It’s also essential to eat to support the health of your microbiome. Microbiome health equals far greater immune health; I’ll cover that in a separate section further on in the discussion. Dietary constituents with exceptionally high anti-inflammatory and antioxidant capacity include vitamin C, vitamin E, and phytochemicals such as carotenoids and polyphenols. Let that sentence serve as an introduction to the next topic, oxidative stress, followed by inflammation.

Oxidative stress

What is it? Oxidative stress is an imbalance between the production of free radicals (will explain) and the ability of your body to counteract or detoxify their harmful effects via neutralization by antioxidants. Oxidative stress is the condition in your body when it does not have enough antioxidants to neutralize free radicals. Just as an apple not coated with lemon (an antioxidant) turns brown when exposed to air, our cells can “rust” when we have oxidative stress- caused by unopposed free radicals.

Free radicals are unstable molecules that react with certain substances in your body to damage cells or create abnormal ones. Free radicals chemically react with cell components such as DNA, proteins, or lipids and steal their electrons to become stabilized. This process destabilizes the cell component molecules, seeking out and stealing an electron from yet another molecule, triggering a large chain of free radical reactions.

A proper diet can reverse this unhealthy but common condition. Eat five to twelve servings of organic fruits and vegetables daily or supplementing with a high-antioxidant multi-vitamin. I always measure patient’s levels of oxidative stress with a Raman spectroscopy unit. Other Functional doctors may use blood or urine testing. The bottom line: if you’re aware of this phenomenon, you can prevent it! Here’s what to watch out for and adjust your intake of antioxidants accordingly.

What Causes Free Radicals? Free radicals are simply a byproduct of energy consumption in our mitochondria, the factories that produce energy in each of our cells. When we exercise, we increase our respiratory and heart rate, creating more free radicals that need to be quenched by good levels of antioxidants. However, the free radicals that deplete our antioxidant supply are environmental and result from our lifestyles. Here are the big offenders.

Exposure to tobacco smoke: Imagine this-tobacco smoke contains more than 4,000 toxic chemicals that all can cause oxidative stress. One cigarette produces millions and millions of free radicals. How’s that for incentive to stop? We who use Raman Spec scanners have discussed the data, which shows that smokers score in the lowest range, equivalent to those with active cancer cases!

Consuming a “bad” diet: As referenced in the “diet section,” it’s essential to eat as if your health depends on it (because it does!). Eating too many calories, sugars, refined or starchy carbohydrates, processed and fast foods, and lectins do indeed cause oxidative stress and inflammation. Unhealthy foods force our mitochondria to work harder and release more “exhaust,” creating higher levels of free radicals burning toxic foods for energy. Speaking of diet, let’s look at two other popular lifestyle choices.

Excessive alcohol: Alcohol consumption increases your levels of inflammatory cytokines-inflammatory molecules linked to oxidative stress.

Eating charcoal-broiled foods: These foods-not just meats-contain polycyclic aromatic hydrocarbons, which contribute to oxidative stress. And yes, char-broiled meats are indeed carcinogenic. Now, let’s move onto some other lifestyle factors in oxidative stress levels.

Excessive psychological stress: The stress hormone cortisol increases inflammation, which further increases free radical production. It also causes a leaky gut, an asymptomatic cause of chronic inflammation, and the root cause of autoimmune disease.

Exercising too much: Exercise (which will be discussed in another section) is crucial for optimal health. However, too much of it can increase oxidative stress in our bodies. As a rule of thumb, more than 60 minutes per day is considered excessive. Therefore, all elite athletes need to supplement adequately.

Lack of sleep: Sleep deprivation increases oxidative stress through a complex series of chemical reactions. Yes, I’ll discuss sleep in more depth, too.

Exposure to air pollutants: Air pollution, industrial pollution, and even airborne allergens increase oxidative stress.

Chronic infections: Hidden (asymptomatic) infections will contribute to oxidative stress. One example is a biofilm secreting sinus organism called MARCoNS, found in people with mold and mycotoxin illness. Dental infections are another excellent example. If you have root canals, you will not feel apical abscesses-so get a panoramic X-ray annually.

Ionizing radiation and EMFs: Exposure to x-rays, excessive sun, radon, cellphones, hairdryers, airplanes, electric blankets, and heating pads can all contribute to oxidative stress.

Exposure to fungal toxins: Environmental molds (like those in basements and bathrooms) and internal fungi (such as those colonizing your gut in excess) can produce mycotoxins that increase oxidative stress.

Inadequate GI-tract detoxification: When the liver is overwhelmed with toxins from food (e.g., too much sugar) or the environment (e.g.:exposure to pesticides or toxic mold), it becomes inflamed and then produces more free radicals. And now that you know what causes this problem go ahead and fill your diet with antioxidant-rich food, smoothies, and supplements to combat it. Next, let’s look at OS’s evil twin: inflammation.


What exactly Is Inflammation?: Let me first explain “acute inflammation.”  Think about what happens when you get a splinter in your finger. If you don’t remove the shard, the whole area turns red and gets a little puffy. That’s acute inflammation, and it’s a good thing, as it’s your body responding appropriately to a situation. It’s mostly your immune system rushing to the area to fight off any viruses or bacteria that might have gotten in. With a physical injury, if you leave the spot alone and don’t irritate it any further, the swelling will go down, and everything will go back to normal. The signs of acute inflammation: heat, redness, swelling, and pain will all dissipate.

However, if you keep stabbing yourself with fragments in the same spot, the re-injury would maintain the high levels of inflammation burning. That’s what is going on with chronic internal inflammation, but you can’t  “feel the stabbing.” The inflammatory response is short and relatively precise. When it’s chronic, inflammation can be “silent,” can make you feel lethargic, or contribute to many other health problems. Here are the major causes of chronic inflammation. 

Your weight: Inflammation risk is guaranteed if you are obese or even just overweight. Overweight and obese men and women have higher levels of inflammatory blood markers than men and women of the same age who are not obese or overweight. Inflammation drops when men and women lose weight, according to many clinical studies.

Unhealthy diets: I know you hear this repeatedly from me, but consider that it’s that important to eat a healthy diet. Common foods processed just like sugar and therefore considered”inflammatory” are sugary foods, high-processed carbohydrates, high-industrial fat, and seed oils, high-gluten, and all overly processed and fast foods, save the lone naked salad. I know this is the typical U.S. diet. Toxic foods are why our population is so inflamed!  Further, this poor eating pattern also causes oxidative stress, which in turn worsens inflammation.

Insufficient omega-3 intake: Omega-3 fats are the precursors for anti-inflammatory eicosanoids, an integral part of the inflammatory response. Poor omega-3 status means inadequate production of anti-inflammatory eicosanoids and a lopsided anti-inflammatory reaction to normal stimuli. It’s easy to get good blood levels: eat omega-3-rich fish such as salmon or sardines and take good omega-3 fish oil supplements.

Excessive omega-6 intake: Omega-6 fats form the precursors for inflammatory eicosanoids, which are also an integral part of the inflammatory response. High omega-6 status (especially when combined with poor omega-3 status) means excessive production of inflammatory eicosanoids and a lopsided inflammatory response to normal stimuli. Cut down on your omega-6 intake by reducing your intake of meat.

Chronic stress: Life can be stressful, indeed. Everything all adds up, doesn’t it? Notably, if it becomes too much for you to handle, your body will have a physiological, inflammatory response to emotional stress. This physiological reaction includes a rise in cortisol, as mentioned earlier.

Lack of downtime: When you’re always on your phone or checking your social media accounts, you are not relaxing. When you hear a “ding” and rush to answer a text or email, you are always “on.” You may think you’re relaxing because your body is stationary, but you’re not relaxing-are you?

Lack of sleep: Poor sleep causes elevated blood inflammatory markers. Poor sleep is a chronic problem in the U.S. Either we go to bed too late, wake up too early, or use too many electronics late at night and disrupt the sleep quality we get. I’ll go more in-depth into the topic of sleep further on in this article.

Toxins cause Inflammation: Heavy metals, biotoxins such as mold and Lyme toxins, and more can cause chronic inflammation.

Lack of outdoor time: We all spend too much time cooped up in offices or, worse, in office cubicles, or even at home, doing zoom calls. We just plain don’t spend enough time in nature.

Your exercise and movement patterns: Insufficient exercise and even inadequate “movement” (more below) adds to inflammation.

Lack of movement: Most of us lead far too sedentary lives. A lack of activity causes systemic, low-grade inflammation. We don’t usually need to walk to get to our destinations. We take escalators and elevators. We sit for hours on end and then don’t make time for regular exercise. Suppose this is you-make time to move more. Get up on your feet for two to three minutes each hour you’re sitting. Better yet, do some burpees, jumping jacks, or push-ups.

Poor recovery and Overtraining: On the other hand, some people move, but they exercise too much, with too little rest and recovery. Overtraining is a form of chronic inflammation. Not just elite athletes, but even casual 10K runners and others who train frequently can overtrain. This degree of over-exertion can cause inflammation, as well as elevated cortisol levels, and disrupted sleep. Now that I’ve gone through some ways not to exercise, why don’t I discuss how to exercise?


Multiple studies in both humans and animals have demonstrated the profound impact exercise has on the immune system. There is an overwhelming consensus that regular bouts of short-lasting (30 to 45 minutes) moderate-intensity (e.g., brisk walking, vacuuming, dancing, doubles tennis, and “shooting hoops”) exercise is beneficial for proper immune function. This correlation has been demonstrated particularly well in older adults and people with chronic diseases.

Exercise is probably healthy for intestinal flora composition, so remember this when you read the section about the microbiome. Some investigations have shown that activity is associated with increased microbiome biodiversity with attendant beneficial metabolic functions. Gut microbiota (innately linked to all immune functioning) can, in turn, influence the pathophysiology of several distant organs, including the skeletal muscle. A gut-muscle axis may regulate muscle protein deposition and muscle function. This gut-muscle axis may involve maintaining skeletal muscle with aging and contribute to insulin sensitivity and blood sugar levels, which brings me to the next topic called glycation.


Cellular glycation is the stiffening and aging of all cells. It occurs at fasting blood sugar levels somewhere in the range of 75-85 ng/dL. Research continues to lower the bar at which we set the definitions of glucose-intolerant, diabetes, and simply “cellular glycation.” I don’t think I need to mention that blood sugar levels increase with increased body mass.

Higher blood sugar levels are associated with immune system depression, increased risk of dementia, heart disease, cellular aging, and even cancer. Cancer is an immune-mediated and mitochondrial dysfunction disease that is largely preventable. Some studies demonstrate that certain cancers respond to treatment more effectively when blood sugar is lower, achievable via ketosis or medication. Studies also link better blood glucose control to better sleep. Here’s what you need to know about sleep.


Sleep has powerful effects on immune functioning. Studies show that sleep loss can affect different parts of the immune system, leading to the development of a wide variety of disorders. Here are a few interesting studies to consider before giving you my recommendations for adequate, restful sleep.

Sleep loss is a risk factor for lessened immune response and infection. Restricting sleep to 4 hours per night for six days, followed by 12 hours of sleep per night for seven days, resulted in a greater than 50% decrease in antibody production to influenza vaccination than subjects who had regular sleep hours.

Restricting the time allowed for sleep to 4 hours for one night reduced natural killer (NK) cell activity to an average of 72%, compared with NK cell activity in participants who had a full night’s sleep. NK cells are essential for infection clearance; they also have a significant role in killing tumor cells. Reduced functioning of NK cells is associated with an approximate 1.6 times higher risk of dying from cancer.

In addition, restricting sleep to 4 hours for (again) just one night led to the generation of measurable inflammatory cytokines, which play an essential role in developing metabolic and cardiovascular disease. So, how much “good” sleep do you need?

How Much Sleep Do You Need? There is only a little individual variability in regards to how much sleep we all need. Most adults need  7 to 8 hours of good-quality sleep per night. What’s “good quality sleep?” Good quality means that the “sleeping episode”  doesn’t include frequent arousals and is long enough for the individual to feel refreshed upon awakening. All wrist gadgets aside: most of us move correctly through the stages of sleep depth, including REM, and if we don’t, we don’t feel refreshed-plain and simple.

Researchers have identified genetic mutations in some people who naturally sleep six or fewer hours a day and appear healthy and functional. These people show less deterioration in performance when they are sleep-deprived under laboratory conditions. However, note that the percentage of the population with these gene mutations is minute. Most people who say they do not need much sleep are just pushing themselves to sleep less. As a consequence, they then struggle to stay awake and tend to function suboptimally during the daytime. They are putting themselves at risk for obesity and chronic illness.

Want to figure out your ideal sleeping time? The average sleep times across 5 to 7 relaxed days estimate your required sleep duration. Just record the length of time you sleep during a 7-10 day vacation, when you are awakening spontaneously, without an alarm, and go to bed when you are tired. During this time, remember to keep caffeine intake to no more than 2 cups of regular coffee a day (about 200 mg of caffeine). And speaking of a relaxing vacation, try to do an activity to reduce your stress levels daily at least a couple of times per day to mimic how you feel on holiday. Stress management is not simply to make you feel better; it’s a matter of your health.

Stress Management 

Stress depresses the immune system. It does this via several different mechanisms. First, sustained high cortisol levels caused by stress cause gut hyper-permeability (i.e., “leaky gut”), which causes inflammation and subsequent disease. Cortisol also interferes with T-cell (a type of white cell) production and function, making your body more susceptible to pathogens. Stress is why you get more head colds when you are under pressure. Finally, cortisol kills brain cells (neurons), further interrupting the gut-brain axis crucial for proper immune function.

Manage your stress before it manages you. Incorporate movement and exercise into your day. Activity can be as simple as making sure you get up from your chair and walking around for a few minutes every couple of hours. Exercise should be something you will do, not something you’d like to envision yourself doing. Deep breathing and meditation are great habits to cultivate. If you don’t have the patience, you can activate the vagal (parasympathetic system) nerve by singing and even gargling. Some people also benefit from liposomal GABA supplements and peptides with anti-anxiety benefits. I touched on gut health, and now I’d like to go a little deeper into that topic with a discussion about the microbiome.

Microbiome Health 
The human microbiome is between 10 and 100 trillion genetically unique (mostly) bacterial cells. The healthier your gut microbiome is, the better it is for your immune system, which is also (primarily) located in your gut. Unhealthy gut bacteria thrive on the things that create inflammation in our body, including refined carbs, sugar,  unhealthy fats, and processed foods. Conversely, the healthy foods and activities discussed previously all contribute to microbiome health. To augment all of these healthy habits, we can add prebiotic fiber and probiotics into the mix. First of all, we need to eat good prebiotic foods as “fertilizers” for probiotics.

Prebiotic fiber: This is non-digestible carbohydrates found in fibrous foods that assist in the growth of healthy bacteria in the gut. White and even tastier-red onion, as well as asparagus, chicory, garlic, unripe banana, and artichoke-especially Jerusalem artichoke, are great “gut bug food.” They assist gut health primarily by helping healthy gut bacteria produce substances such as butyrate. Butyrate helps protect the gut lining and has anti-inflammatory properties in the gut. Now let’s seed this fertilizer.  

Probiotics: High-quality kefir or yogurt (home-made) and fermented foods such as sauerkraut can supply a fair amount of good bacteria, but I generally supplement everyone to ensure they get enough probiotics to augment immune function. We see some good evidence that sporulating probiotics are more immune-supporting and microbiome-diversity-supporting than the strains of probiotics we used to recommend only recently.

Immune enhancement with hot and cold therapy

Heat shock proteins form in the body when you immerse your body in ice-cold water or a tub or sauna at 104 degrees F.  They are great for your immune system and will enhance many positive immune modulation functions.

Cold therapy lowers cortisol levels when you do it on a repeated basis. I just reviewed why you want nice, controlled cortisol levels, and this is now another way to get them. As a reminder, bringing down your cortisol will not only help your gut lining stay intact, it will enhance the 70% of your immune system which resides in your gut. In addition, studies show that cold therapy improves anti-tumor white blood cell activity. Finally, NK (natural killer T cell) activity also gets a boost with cold therapy.

Various heat shock proteins induced by saunas (conventional and FIR) trigger positive effects in the immune system regarding infections, autoimmune disease, and even cancer therapy. Suffice it to say, for this article, that hot and cold treatments are fantastic for your immune health. Now, let’s discuss supplementation.

Supplements to boost the immune system 

Multivitamin supplements

Over 10,000 vitamin companies are selling their multivitamins. You want to choose GMP, NSF certified, and high antioxidants, especially forms of vitamin A called carotenoids. Good MVI supplements also contain iodine and selenium, which are important for proper immune system function. The addition of polyphenols is an excellent “add” when you can find them, and they are suitable for the care and feeding of your microbiome. You need more vitamin C  than you get via multivitamins: I’ll address that separately.

Vitamin D

You need vitamin D for a properly functioning immune system. We’ve more than learned that during this past year’s COVID crisis.

Vitamin D inhibits negative (harmful) immune pathways and promotes positive ones. It also positively impacts the composition of the microbiome and enforces the gut barrier. Clinical studies show low vitamin D levels are a risk factor for coronavirus infection. Previous studies correlate low levels of vitamin D with more “flu”; in general.

Vitamin D dosing: You want a level of 75-80 ng/dL which requires most Americans to take doses of 5000-10,000 IU per day.

Vitamin C and Zinc 

Vitamin C concentrations in the blood plasma and white blood cells quickly decline during infections. Likewise, zinc deficiency impairs cellular mediators of innate immunity such as natural killer cell activity, phagocytosis of infectious organisms, and the generation of an oxidative burst.

Supplementation of vitamin C improves various components of our immune system: natural killer cell activity, migration of white blood cells (chemotaxis), the appropriate and proper proliferation of specific white cells called lymphocytes, and overall antimicrobial activity. Vitamin C contributes to the antioxidant status of cells, thereby protecting them against reactive oxygen species generated during the inflammatory response. Supplementation with zinc has shown similar benefits, which, in some studies, are augmented by the flavanoid-quercetin.

Therefore, both nutrients play important roles in immune function and help attenuate the risk of infection when taken as dietary supplements. They have reduced the risk, severity, and duration of many infectious diseases. When taking long-term zinc supplementation, make sure you are ingesting enough dietary or supplemental copper.

Zinc dosing: Ideal dosing is about 25-60 mg per day.

Vitamin C dosing: Liposomal preparations can be taken in doses up to 3 grams (usually 1 TBSP) per dose without GI distress for most people. Many clinical studies use 1.5 grams 4 times per day (6 grams total), but I generally recommend 1 TBSP 2x/day during “flu season,” including during this past COVID-year.  Take regular buffered vitamin C  as a 500 mg dose- just space that out accordingly.


Melatonin is a potent anti-inflammatory and anti-oxidant-not simply a sleep aid. The fact that it helps establish our circadian rhythm is an immune boost– right there. Many people find this surprising, but it’s accurate! When we are infected, It functions mainly to blunt our over-active inflammatory response, limiting tissue damage. It does much more, but for this article, I’ll state that it’s good for your immune system and will indeed help you sleep more soundly. There’s a good reason that the “expanded” use of melatonin won its scientists the 2017 Nobel Prize in “physiology or medicine.”

Melatonin dosing: Studies have the maximal efficacy at 10-20 mg per night.

Reishi mushroom extract

Many types of mushrooms contain polysaccharides called beta-glucans in their cell walls. Beta-glucans boost the immune system via several mechanisms. They enhance the action of macrophages (a type of white blood cell that kills foreign invaders), activate the “complement” component of the immune system, and boost natural killer (NK) cell function. There is an especially immune-boosting species of mushrooms called Ganoderma lucidum or reishi mushrooms. They are not especially tasty but are used to formulate potent immune-enhancing supplements.

Reishi dosing: Find a good brand that uses cracked reishi spores to make the powder put in capsules and take 1000 mg per day.


The hormone DHEA is well known to impact adrenal function positively and, therefore, cortisol levels. It has verifiable anti-inflammatory properties and is most likely immune-supporting via several complex hormonal pathways.

DHEA dosing: Important note: Men with a history of prostate cancer and women with PCOS or a history of breast cancer must take the keto form of this hormone, if at all, since the keto form is not study-proven as an immune enhancer. Otherwise, men should take a daily dose of 50 mg; women-25 mg.

Nitric Oxide

Nitric oxide (NO) is bactericidal, which can act directly as an anti-microbial compound that can destroy bacteria.  Certain families of immune cells called dendritic cells can produce NO, contributing to the resolution of both viral and bacterial infections. The non-proven inference is that higher NO levels contribute to a more rapid and efficient clearing of bacterial and viruses. It’s good for your vasculature and heart, indeed very well might be immune boosting, so because of all of this, it makes my list.

NO dosing: Look for a product with an equal amount of l-arginine and l-citrulline such that you take 1.5 grams of each 2x/day.

The Research Continues

Many organ systems function better by restoring male hormones and female hormones to youthful levels, and we know that human growth hormone is immune-boosting. We understand that the alpha-thymosin 1 peptide is so good at boosting the immune system (increased NK cell activity, increased antibody response to viruses, increased T cell function, and more) that the FDA pulled it off the market. Yes, that happens all the time with compounded products used successfully by Functional doctors. But studies are ongoing with other peptides.

There are other varieties of mushrooms (lion’s mane, for one) currently under investigation for immune enhancement. And finally, the most exciting research involves the use of stem cells and exosomes.

Hashimoto’s Thyroiditis Treatment

Before we start discussing Hashimoto’s thyroiditis, let’s just touch on the traditional treatment you are probably getting. You are not on a special diet to heal or protect your gut. You have elevated antibodies and are told “don’t worry about them.” You are simply placed on a synthetic version of T4, not a combination of the inactive T4 and the active T3, tailored to your physiology. You are told that your thyroid will “just burn out” if you aren’t yet on thyroid replacement, and that, at that point, you will be treated with synthetic T4. There are many disease processes; notably autoimmune diseases, where the traditional medicine I used to practice really seems dead wrong. One of these instances is Hashimoto’s thyroiditis treatment. You’ll see why after you read this article.


Hashimoto Thyroid Disease, AKA Hashimoto’s thyroiditis, is the most common autoimmune disorder in the U.S., affecting between seven and eight percent of the population. While not all people with Hashimoto’s have hypothyroid symptoms, thyroid antibodies are a marker for future thyroid disease. When we talk about hyperthyroidism vs. hypothyroidism, the majority of “Hashi’s” patients are diagnosed after TPO antibodies have destroyed enough of their thyroid gland, so they have low (hypo) thyroid function. Hypothyroidism is characterized by weight gain, loss of the outer 1/3 of the eyebrows, brain fog, dry skin, fatigue, constipation and more. The sad state of medical treatment is such that doctors fail to treat the autoimmune disease and then, simply replace the lost thyroid hormone with synthetic hormones. Standard treatment fails to address many concerns including the underlying cause or the necessary Hashimoto diet. In this article, I’ll discuss Hashimoto Thyroid Disease and treatment including:

  • Get the correct laboratory tests
  • Fix the real or functional hypothyroidism
  • Make sure you’ve got the minerals “right”
  • Treating the autoimmune condition-getting rid of the antibodies
  • Fix the Leaky Gut
  • Diagnose and treat the SIBO
  • Eat an A.I.P. diet
  • Have an adequate Vitamin D level
  • Consider the use of low dose naltrexone
  • Fix the microbiome
  • Treat the ancillary issues

Necessary Laboratory Tests

I (personally) find it shocking that the new patients I see who tell me they have “thyroid issues” have never had proper bloodwork done. It’s not hard to order the correct tests, and now I’m going to teach you what to ask your doctor to order. To begin, start with the “usual and customary labwork” including a complete blood count, liver and kidney function tests, a complete chemistry profile, urine analysis and so on. Then for the thyroid specifics, here’s what you want to have done.

Ask your your doctor to order a TSH, a Free T3, Free T4, CRP, r (reverse) T3, TPO antibodies, and anti-thyroglobulin antibodies. Rarely are TSH-stimulation blocking antibody (TSBAb) positive but get those done, too. TPO antibodies are much more apt to be the positive antibodies you find in Hashimoto’s thyroiditis, but why not be thorough? Reverse T3 is a test that has been criticized as being “useless” by Endocrinologists who all tend to ignore an elevated rT3. What is rT3? It’s a metabolite of the inactive form of thyroid hormone- T4. The problem with an elevated rT3 level, is that it means it is clogging up the actual T3 receptor sites. When the receptor sites are clogged, the converted and functional Free T3 cannot bind to the receptors and you are therefore “functionally hypothyroid.” Let’s discuss what that means.

Treating rT3 Syndrome

If your lab work shows a high reverse T3 level- you are converting most of your T4 into reverse T3. Reverse T3 is simply an isomer of T3. If you recall-Free T3 is the active form of thyroid hormone and it is converted from T4 as needed by two enzymes called deiodinases. The problem with rT3 is that it binds to T3 receptors but it has no metabolic activity-meaning-high rT3 levels can give you signs of being hypothyroid even though your Free T4 and Free T3 are the “normal range”.

Medical issues that will results in increased rT3 levels are any sort of severe illness, starvation, excessive nutritional deficiencies and high cortisol levels-generally caused by stress. This is why you have likely heard that adrenal and thyroid function are linked. Those with adrenal fatigue or adrenal stress tend to be functionally hypothyroid. It is also more common in hypothyroid patients who have SIBO-more to come on this topic. rT3 obviously will then slow down metabolism and is therefore theorized to aid in survival.  A quick fun fact: hibernating bears have high rT3 levels.

We treat high rT3 with T3 for 2 or 3 months. The negative feedback to the pituitary slows down the production of T4- that then slows the production of rT3.


Most physicians don’t analyze why they often see a normal Free T4 and a sub-par Free T3 on a typical patient’s lab work. Here’s the answer: for proper enzymatic (deiodinase) function, these enzymes require quite a few minerals for optimal function. While most people think of iodine and some are aware of selenium as being important for thyroid function, I’ll bet you didn’t know that you also need zinc, molybdenum, boron, copper, chromium, manganese, and the proper balance of calcium and magnesium, did you? Well, neither do your doctors! They also don’t know about the iodine to selenium balance that needs to occur, which we’ll discuss in the next section.

Endocrinologists continue to use the typical thyroid replacement—a synthetic hormone: Levothyroxine (Synthroid). However, if you don’t have a “high enough” Free T3 which is defined as being more than 2.9 pg/ml, you are going to be clinically hypothyroid. And this a totally separate issue from having a high rT3. Now let’s get into the selenium/iodine issue.

Too Little Selenium

Selenium (not iodine!) deficiency is one of the main reasons for clinical hypothyroidism. It’s crucial for the production of thyroxine (T4).  It is also needed for the deiodinase to convert T4 to the active T3. But, there’s more: a total of 11 selenium-dependent enzymes have been identified as necessary for thyroid function.  If you take iodine without selenium, you can cause selenium deficiency. Conversely; if you take selenium without iodine, you can cause iodine deficiency. Since all regular salt is iodized, you are much more likely to have selenium deficiency if you use iodized salt. Use Himalayan pink salt instead, and it will be less likely to contain plastics, too.

The current recommended dietary intake of selenium in adults is between 55 and 75 mcg daily. Foods rich in selenium are brazil nuts, mushrooms, oysters, most types of meat, and sunflower seeds.

Too Much Iodine 

Many people are under the impression that too little iodine is the issue when it comes to any type of thyroid disease. This probably dates back to the days when “goiter” was linked to the lack of iodine; hence the subsequent iodization of our salt supply. However, our national over-consumption of iodized salt now usually causes the opposite problem. Many clinical (epidemiologic) studies demonstrate the presence of more autoimmune hypothyroidism in iodine-replete demographic areas than in iodine-deficient areas.

A number of studies even indicate that mild or moderate iodine excess (meaning a urinary iodine excretion of 220µg per 24 hours) is associated with hypothyroidism. To make matters worse, other studies show that  low-dose iodine supplementation may even be associated with increased thyroid autoimmunity. Regardless of the “mechanism”, now will you ditch the iodized salt shaker in exchange for some pink Himalayan salt?

 Treating the Autoimmune Condition

Conventional medicine simply does not have safe, effective treatments for any autoimmune disease. In fact, steroids and even more toxic drugs such as “biologics” are often used to suppress the immune system. If you have Hashimoto’s, it’s even worse, as the autoimmune condition is left to simmer like a boiling pot on a stove. Let me explain.

If you have elevated-let’s say- TPO antibodies, it means your thyroid gland is under attack. Often, the CRP (a biomarker for inflammation) is elevated. If you don’t address (and then lower) these antibodies being made, the thyroid gland will continue to be under attack, and systemic inflammation will continue. Symptoms such as fatigue, sleep disruptions, hair loss, dry skin and more will just continue until the thyroid gland is burned out, at which point you will be deemed “hypothyroid” and placed on thyroid hormone for life. But there’s even more to this story of autoantibodies and inflammation.

All autoimmune disease starts with leaky gut: we’ll cover this topic next. Anyway, since Hashimoto’s thyroiditis also starts with leaky gut, causing systemic inflammation, if you don’t repair the gut, you can’t reduce the antibodies. You’ll also need to change your diet to reduce the antibodies. Here’s why. It is clear that there is thyroid gland tissue and gluten biomimicry—and there are likely also IGG food allergies to things like milk, grains, eggs, and more. Therefore, to get rid of “possible food offenders” and start getting antibody levels and inflammation down, you need to eat an “autoimmune protocol diet”  (phase 1-a bit strict) while your gut is healing: the first two months of treatment. A benefit most people love is that they effortlessly drop some unwanted pounds.

Leaky gut and Hashimoto’s thyroiditis 

Leaky gut (AKA gut hyper-permeability syndrome) is an extremely common condition. It can be caused by antibiotics, anti-inflammatory medications, antibiotics, stress (leading to high cortisol which wrecks your gut and brain), mold and mycotoxins or just “typical American food.”  If you have leaky gut, you may or may not have gastrointestinal symptoms. If you are already hypothyroid from your Hashimoto’s thyroiditis you will probably be constipated and possibly have some bloating after meals.

Getting you into remission from any autoimmune disease starts with fixing your leaky gut. Changing your diet to my autoimmune diet is the first step towards healing your gut and reducing your auto-antibody production. Functional doctors use gut-healing peptides and supplements such as collagen powder and l-glutamine. Vitamin D levels need to be normalized, and sporulating probiotics with their “fertilizer”-prebiotics, should be added when the symptoms start to subside. We’ll discuss all of this in upcoming sections.

As you heal your gut over two months, your (probable) food sensitivities and, therefore, your bloating will diminish. If it doesn’t, it often means you have SIBO, which is quite common in those diagnosed with Hashimoto’s thyroiditis.


First, let’s posit that a fair number of those diagnosed with Hashimoto’s thyroiditis have actual or functional hypothyroidism. Since gut motility decreases when someone is hypothyroid, constipation is a common symptom of Hashimoto’s. This constipation, decreased gut motility, as well as the leaky gut, often leads to small intestinal bacterial overgrowth (SIBO.) Small intestinal bacterial overgrowth is an increased number and/or abnormal type of bacteria growing in the small intestine section called the jejunum, a part of the bowel that is supposed to be sterile. It’s estimated in numerous studies that a minimum of half of those with Hashimoto’s have untreated SIBO.

The symptoms of SIBO symptoms are often confused with those of other GI disorders. The most common symptoms are bloating and flatulence and bloating after meals. Other symptoms include abdominal discomfort, constipation; but often- diarrhea, too. This causes many patients to be labelled as having irritable bowel syndrome and never having their symptoms clear up. Multiple food intolerances are also common. If symptoms are mild, they are often “blamed” on the hypothyroid state. Those with SIBO are more likely to have T4 to rT3 conversion issues, causing even more gut issues.

To diagnose this condition, the lactulose hydrogen breath test (LHBT) is often used. However, because breath tests are not very sensitive or specific (up to 60% false negatives), many experienced Functional doctors will treat a patient if they exhibit classic symptoms associated with typical underlying conditions.

Treatment in the non-Functional GI world is typically a long course of Rifaximin-an antibiotic which is not absorbed by the gut. Herbal therapies are at least as effective as rifaximin for curing small intestinal bacterial overgrowth in comparison clinical trials. Some effective herbals include oregano oil,  barberry, berberine, olive leaf extract, and wormwood.

The Hashimoto Diet

What Do You Eliminate for Two Months?
  • Refined sugars. Yes, there are substitutes.
  • Fast foods. Selected ones will be back month 3.
  • Processed foods. Some minimally processed foods can return month 3.
  • Dairy products-yes, a form of them will be back month 3-4!
  • Grains. Yes, in your re-intro diet, one, perhaps two- low-lectin grains will be back.
  • Eggs. For most-these are back in month three.
  • Legumes, such as beans, lentils, and peanuts. For some, pressure cooked low-lectin beans (such as lentils) might come back.
  • Seed oils, such as vegetable and canola oil.
  • Coffee and chocolate (often reintroduced in month two), and you can have tea month one.
  • Nuts and seeds. Many will come back month 3-4.
  • Herbs from seeds, like coriander, cumin, and nutmeg.
  • Nightshade vegetables, such as eggplant, potatoes, tomatoes, peppers, and okra. Note: Japanese sweet potatoes taste like our Idaho potatoes.
  • Spices made from nightshades, like chili powder, paprika, cayenne, chipotle, red pepper.
  • Alternative sweeteners such as xylitol and mannitol with stevia and monk fruit being OK.
  • Alcohol. Month 3-back.
  • Dried fruits. Month 3-back.
  • Food additives such as gums and emulsifiers.
What can you Eat?
  • Poultry, meat, and fish; It should be grass-fed, organic, wild-caught, humanely raised.
  • All vegetables other than nightshades and white potatoes; Sweet potatoes are fine. Cruciferous veggies are also fine as long as they are cooked and not eaten in excess.
  • For cooking: Healthy, high-flash-point oils (avocado, coconut, palm) and animal fats such as ghee.
  • Condiments: Vinegar; restrict to apple cider vinegar for two months. Dried, “safe” herbs.
  • Small quantities of berries and fresh lemon/lime wedges.
  • For salads: Extra-virgin olive oil. The safest is from California; not imported. Try this with squeezed lemons.
  • Tea: Herbal is best, but some mildly caffeinated brands (loose, organic; not teabag) are fine
  • Other beverages: Bone broth, loose herbal tea (hot or iced), water and unsweetened sparkling waters.

You can actually get creative with this limited list. As mentioned, you’ll drop the pounds you wanted to lose while you’re at it. You’ll feel great on this diet which is naturally the most anti-inflammatory diet you can eat. To help you: there are many  social media groups, pages and websites that contain creative recipes. If you’re my patient, I’ll be communicating with you about your food preferences, and sending you links for food services, alternative bakeries and so on. I’ll help you transition to month 3, 4 and onward, adding as many foods as your Hashi’s can tolerate.

Vitamin D and Immune Modulation

 There is firm evidence of a correlation between Vitamin D deficiency and several autoimmune diseases. Notably examples include systemic lupus erythematosus, multiple sclerosis, mixed connective tissue disease, rheumatoid arthritis, type 1 diabetes mellitus,  celiac disease, and more.

In general, Vitamin D tends to activate the innate immune response and to regulate the adaptive immune response. This improved adaptive immune response, in the presence of higher levels of vitamin D appears to hold true in autoimmune thyroid disease as well.

Data in Hashimoto’s Thyroiditis/Chronic Autoimmune Thyroiditis

Most data on Vitamin D and autoimmune thyroid diseases have come from cross-sectional studies and tend to support the existence of an association. There is additional evidence supporting a relationship between vitamin D and Hashimoto’s thyroiditis in particular.  Approximately ten recent studies identify lower 25(OH)D levels in individuals with Hashimoto’s thyroiditis versus control subjects, with a tendency for a higher prevalence of (vitamin D) deficiency in patients with hypothyroidism than those with normal thyroid function tests.

The relationship with antibody titers is characterized by more inconsistent data.

Vitamin D may also affect disease manifestations. There have been several reports of a significant correlation between mild cognitive impairment  and 25(OH)D deficiency in adult patients with Hashimoto’s thyroiditis. This complication will be covered in the last section of this article.

Low Dose Naltrexone 

Approximately one third of patients with Ulcerative colitis or Crohn’s disease are resistant to all currently available “drug” pharmaceuticals, or they relapse over time. Therefore, when the doctor who first realized that LDN (low dose naltrexone) was helping his patients with multiple sclerosis, he turned the researchers of IBD onto the concept of looking closely at LDN. And, indeed the studies have been remarkable for inflammatory bowel disease and a host of other autoimmune disorders. It works by increasing endorphin levels, secreted by the posterior pituitary gland, and by yet another mechanism which also bolsters the part of the immune system responsible for autoimmunity.

There have been a paucity of controlled, clinical trials using LDN in patients with Hashimoto’s thyroiditis simply because there has been “no will” to do so. If you take a patient with IBD that flares, they have serious gastrointestinal issues such as explosive, non-stop diarrhea, rectal bleeding, awful abdominal cramps and more. If you have a patient with either multiple sclerosis or ALS, the neurological effects can be drastic and are readily observed.

When someone with Hashimoto’s thyroiditis “flares” it may be nothing more than some fatigue, sleeplessness and mild “tummy” upset.  Of course, these symptoms are quite bothersome to the patient with Hashi’s, but I strongly believe this is why the research is sorely lacking. Meanwhile, everyone who treats autoimmune disease functionally uses LDN, and patients report that they feel considerably better taking it. I am not one to treat patients based on “anecdotes” but until we get some better research done on Hashimoto’s thyroiditis patients, that’s really what we’re all doing. As an addendum: we all see that it decreases antibody levels and there is one great study showing that pregnant women with Hashi’s who tend to miscarry in the first trimester, not only have significantly less miscarriages when they are taking LDN, but the babies all have better outcomes. That’s a great start, right? Now, let’s talk about something we know is good for everyone’s immune system: having a well balanced microbiome.

Repair the Microbiome

In recent years, numerous studies have elucidated the crucial role of gut microbiota on multiple metabolic as well as autoimmune diseases, such as diabetes mellitus, obesity, systemic lupus, Alzheimer’s disease, and inflammatory bowel disease. The active form of thyroid hormone can influence the gastrointestinal structure and function, especially motility of the gut. And on the flip side, a healthy gut microbiota also has quite a  beneficial effect on thyroid function.

Numerous studies show that the gut microbiota composition in Hashimoto’s thyroiditis patients are considerably less diverse  than in any control group. Interestingly, among the factors that influence the stability and variety of gut microbiota, T3 is thought to be one of the most important.

A healthy gut microbiome is not only beneficial for the function of the immune system, but also for proper thyroid function. It’s not well known, but the prevalence of co-existence of thyroid and intestinal diseases are far larger than mere coincidence. For example, Hashimoto’s thyroiditis is the most common autoimmune thyroid disease and often co-occurs with both Celiac Disease and Non-celiac wheat sensitivity.  This can be explained by the damaged intestinal barrier (leaky gut) and the subsequent increase in intestinal permeability, which then allows antigens to pass more easily and activate the immune system or cross-react with extra-intestinal tissues such as the thyroid gland.

Finally, the composition of the gut microbiota influences the availability of essential micronutrients for the thyroid gland we’ve discussed earlier. Iodine and copper are crucial for thyroid hormone synthesis, selenium and zinc are necessary for converting T4 to T3, and vitamin D assists in regulating the immune response. Those micronutrients (and more) are often found to be deficient in Hashi’s patients, resulting in malfunctioning thyroid glands. Supplementation with sporulating probiotics have repeatedly shown beneficial effects on thyroid hormones and thyroid function in general.

Additional Factors Affected by Hashimoto’s Thyroiditis

There are many considerations, when treating someone with Hashimoto’s thyroiditis. Your Endocrinologist will tell you to take your Synthroid, not worry about your antibody levels, not inquire about gut function, and tell you to rest if you’re fatigued. That’s all you’re going to get. You probably won’t even get other important female hormones measured (if you’re a woman).

In functional medicine, we recognize that patients prefer not to have ongoing leaky gut, inflammation, brain inflammation, brain fog, hair loss, skin dryness, sleeping issues and so on. So we treat each and every issue separately and completely. We also take it very very seriously regarding the amount of first term miscarriages that Hashi patients have due to high antibody levels. It’s just not acceptable to us to give someone a T4 synthetic product, and do nothing about the rest of the syndrome. I would hope you would agree.

We can treat the brain issues with designated peptides: Oral or intra-nasal, with two of my favorites being dihexa and semax. We address sleep issues because sleep is when everything repairs, and with inadequate sleep, people feel just awful all day. We address mitochondrial dysfunction; often a product of autoimmune issues, and “fix the energy issues”. We repair the dry skin and the hair loss; even the eyebrow loss. Yes, there are peptides for this, too.

Lastly, since this is yet another disease where we see TNF-alpha elevation, and drugs which lower TNF-alpha are commonly used, It’s certainly worth trying natural supplements which lower TNF-alpha: resveratrol, curcumin and PQQ. They all have a host of other benefits, too! Meanwhile, a whole host of research continues.


Get Rid of Bloating by Addressing the Root Cause 

To get rid of bloating symptoms, you must identify the root cause. Depending on what is wrong, you’ll need to do “the basics” and then, typically, some other personalized steps. The gastroenterology literature compartmentalizes bloating into what they call “functional” (translation: they find no cause for it) and “non-functional” (translation: they can pinpoint a cause). Since Functional medicine prides itself on always finding and then addressing the root cause of symptoms, I’m not going to use this classification. What I’ll do, instead is go through some basic explanations, and then review the common causes and treatments for issues that cause bloating. You’ll learn not just how to reduce bloating but hopefully, how to get rid of bloating; either on your own, or with the help of a good functional medicine doctor.

  • What is bloating?
  • Can I “just” bloat?
  • General happy gut hygiene
  • Happy gut supplements
  • Bloating due to Leaky Gut/Solution
  • Bloating due to a Disordered Microbiome/Solution
  • Bloating due to Insufficient stomach acid/Solution
  • Bloating due to gut motility issues/Solution
  • Bloating due to hypothyroidism/Solution
  • Bloating due to SIBO/Solution
  • Bloating due to SIFO/Solution
  • Bloating due to carbohydrate intolerance/Solution
  • Bloating due to food sensitivities/Solution
  • Bloating due to Inflammatory Bowel Disease/Solution
  • Bloating due to Celiac Disease/Solution
  • Bloating due to Rapid weight loss or gain/Solution
  • Bloating due to Irritable Bowel Disease
  • Bloating due to Constipation/Solution
  • Bloating due to Hormone Imbalance/Solution
  • Bloating due to Chronic Stress/Solution
  • Concluding comments
What is Bloating?

Bloating is caused by the physical sensation of having gas trapped in your belly. Put “more medically”-abdominal bloating is the subjective sensation of trapped gas, gassiness,  or a feeling of pressure or being distended with or without obvious visible distension. It is decidedly not caused by fluid retention. You might have a bloated belly but have some fluid retention in other parts of your body (such as your feet and ankles) if you have a condition that’s causing both problems.

Patients also describe a sense of fullness or pressure, which can occur anywhere in the belly. We like to break it down into “above the belly button” (epigastric), belly button region, lower belly or diffuse so that we can analyze whether it’s an “upper belly” issue such as undiagnosed reflux, a small intestinal issue such as SIBO, or a lower bowel issue such as inflammatory bowel disease. All of these conditions will be covered in the “16 health issues” below.

Abdominal distension is the objective physical manifestation of an increase in abdominal girth. Male and female patients commonly describe how they look- “like I’m pregnant” when they have moderate to severe bloating with distension. Abdominal bloating and distension can occur independently, although they often occur together. Studies have reported that 50% of patients with “bothersome” bloating report abdominal distension. Remember when I said I wouldn’t talk about “functional bloating?” I’m going to break my rule this once: in so-called functional issues such as irritable bowel disorders patients are less likely to pair up bloating with visible distention than in decidedly non-functional disorders such as SIBO. Now that you know this, you can forgot I mentioned it.

Nearly all of us has experienced, at one time or another, a sensation of being bloated, gassy, or distended. For many people, these are merely annoying but transient sensations that occur after eating, resolve spontaneously, and do not lead to medical consultations. For others, however, abdominal bloating and distension are chronic, bothersome, and negatively affect their daily lives, whether they have a definitely treatable cause or a diagnosis of irritable bowel syndrome.

The occurrence of bloating with distension is significant, ranging from 15% to 30% in the general population, and is as high as 65%–90% in patients with irritable bowel syndrome (IBS). Women generally report higher rates of bloating than men, while patients with IBS with constipation predominance (rather than diarrhea predominance) have higher rates of bloating with distension. Seventy-five percent of patients with bloating (who do not have IBS) characterize their symptoms as moderate to severe, while 50% report that symptoms are so severe that they cause a reduction in daily activities.

To simplify the concept of bloating think of your gut as a digestion and bacteria factory. For some reason, you have inadequate protein, sugar and/or carbohydrate digestion which then causes foods to ferment. This can be caused by any of the medical issues I discuss below.  You  also have an imbalance in your gut bacteria or microbiome. This just “goes with the territory.”

Non-functional etiologies for abdominal bloating and distension that will not be discussed in this article include pancreatic insufficiency, diabetes, gastroparesis, Scleroderma, Chronic idiopathic pseudo-obstruction, Acute gastroenteritis, Gastric malignancy, Bowel malignancy, Ovarian malignancy, and ascites; an accumulation of fluid in the abdomen.

It is unusual but possible for any gastrointestinal bloating to actually represent fluid collecting inside your belly. This is not bloating. It is a potential medical emergency, and what you think is bloating, we call “fluid distension.” It could mean an infection such as hepatitis or even cancer. It could mean bowel obstruction from scars caused by prior surgery or adhesions from ongoing inflammatory bowel disorder. If you have sudden gastrointestinal distention, please see a doctor ASAP! Now let’s talk about the bloating that you came to read about. First, bloating by itself: can it happen with no other symptoms?

Does bloating occur by itself?

Yes it can.  If so, it is typically due to SIBO, SIFO or food sensitivities which I’ll address shortly. Other than these three things, it’s very unusual for bloating to occur without gas (upper or lower), diarrhea, or constipation. Lower intestinal gas is the primary “second” symptom associated with bloating. Constipation is second and is often helped with proper “happy gut” measures.

How to have a happy gut=how to reduce bloating

Chewing is obviously the first step towards the digestive process. The enzyme (amylase) is released immediately from your parotid glands, and makes digestion much easier on your stomach. Sicca syndrome (dry mouth), aging or having even a minor reflux disease (heartburn: with or without symptoms) can interfere with this initial process and cause bloating. So, your first digestive “job” is to chew your food thoroughly. We’ll get into whether or not you’ll need digestive enzymes.

In addition to chewing your food thoroughly, eat enough soluble and insoluble fiber (25-30 grams per day) to keep your colon “moving along regularly.”

Both soluble and insoluble fiber help bulk up your stools and can be used as a food source for good bacteria in your large intestine. Soluble fiber draws water into your gut, which softens your stools and supports regular bowel movements. Examples of healthy high soluble fiber foods include broccoli, sweet potatoes, avocados and figs, to name a few of my favorite foods. Two great examples of insoluble fiber include nuts and cauliflower.

Hydrate well which just means drink enough water so that your urine is clear. Too much of any fiber without enough fluid-added at once will cause constipation. Add fiber slowly and make sure you add more water or fluids to your diet at the same time. The combination of hydration and fiber keeps the GI tract moving along the way it’s supposed to do.

Exercise regularly. Exercise also helps with the GI tract’s peristalsis which is it’s rhythmic propulsion forward.

Eat a healthy diet. Fast food and processed food causes an array of gut issues- from leaky gut to dysbiosis.

Happy gut supplements

Any time the GI tract is “stressed” (causing any symptoms), I advise patients to chew food more carefully, cook meat and veggies more thoroughly, and take digestive enzymes to decrease the GI tract’s workload. A good digestive enzyme will contain HCL or betaine, and enzymes made by the pancreas and gall bladder. If you’re a gardener you know that you get better results with good fertilizer and good seeds. Your gut fertilizer is prebiotic fiber. Prebiotics and natural prebiotic fiber are a great addition to anyone’s diet. Some examples of good prebiotic fiber food: onions, asparagus, Jerusalem artichokes and un-ripe bananas. Unless you are making your own A2-milk kefir or yogurt, it’s a good idea to take a sporulating probiotic daily. Other products are required for specific symptoms or issues and will be discussed in conjunction with their specific issue.

Bloating due to Leaky Gut

This extremely common condition is often caused by anti-inflammatory medications, antibiotics, stress (discussed later on in this article) or just “bad American food.” None of these things differentiate between “good” and “bad” bacteria when they are killing off organisms in your gut. Healing a leaky gut isn’t that hard. If you have one, you are likely not just uncomfortable, but you’re a set-up for autoimmune disease.

Getting you into remission from any autoimmune disease starts with fixing your leaky gut. Changing your diet to my A.I.P. diet plan is the first step in healing your gut and reducing your auto-antibody production. As you heal your gut over two months, your (probable) food sensitivities and, therefore, your bloating will diminish. If it doesn’t, it often means you have SIBO, which is not uncommon in those with leaky gut. We’ll discuss that in an upcoming section.

Solution: Use (under medical care) proper gut-healing peptides and (if needed), supplements for leaky gut such as l-glutamine and collagen powder. Vitamin D levels need to be normalized, and sporulating probiotics with their “fertilizer”-prebiotics, should be added when the symptoms start to subside. More about re-balancing your microbiome (the prebiotics and probiotics)  coming up next.

Bloating due to a disordered microbiome

An imbalance in our microbiome is called dysbiosis. Dysbiosis an be caused by seemingly innocuous things from using too much mouthwash to stress to the use of hand sanitizers and consumption of OTC medications. When we carry around more pathogenic bacteria than we should, and also lack the proper diversity and number of protective bacteria we need, the microbiome is unbalanced, unhealthy, and will not serve our bodies well.

In the colon, there are trillions of healthy (and unhealthy) bacteria which compete for space. When the number of “bad bacteria” outweigh the “good bacteria”, the imbalance can lead to abdominal bloating and gas.

We obviously require a higher ratio of gut-friendly microbes to outnumber the harmful ones in order to stay symptom-free and optimally healthy. Unfortunately, due to multiples of bad habits, most people’s microbiomes are filled with billions of potentially dangerous bacteria, viruses, and other pathogens.

Solution: It’s all about the fertilizer and the seeds: the prebiotic fiber and the probiotics. First, a quick note about yogurt. The only healthy yogurt is made from A2 dairy, using live cultures. Even then, we all recommend that you avoid dairy-based yogurt until your gut heals. Therefore, at least initially, your probiotics should be from capsules so you’re in charge of the dosing.

If your gut microbiome is unbalanced with “bad bugs” in the majority, you need to use prebiotic fiber to feed a lot of good bacteria (and-if there is no mycotoxin illness- a little “good yeast”) to overtake the bad bacteria. You want to consume about  50 to 100 billion probiotic CFU’s per day. Some of the literature suggests that a mixture (in your main probiotic) of Bifidobacterium species and Lactobacillus species is necessary. Also, add in some friendly yeast called Saccharomyces boulardii. However, the latest research supports the use of sporulating probiotics for most conditions, especially for the treatment of Crohn’s disease and ulcerative colitis. No matter what we’re treating, there are strong suggestions that the sporulating probiotics will result in a more diverse (and therefore more healthy) microbiome. Here’s what to look for.

Find a probiotic that contains a few strains of the bacillus species, which are all delivered to the gut as spores which then encapsulate beneficial bacterial strains. Look for b. subtilis, b.coagulans and b.clausii, as they have been studied and documented as beneficial. If the amount of CFU’s found in one of these probiotics (rarely) gives you diarrhea, simply open and empty 1/2 of a capsule out before taking it.

Bloating Due To insufficient stomach acid

Although it seems totally counter-intuitive, reflux-or heartburn- is the result of insufficient stomach acid. It is indeed sometimes caused by the H. pylori bacterium, but a short course of antibiotics and proton-pump inhibitor medication (or the natural alternatives if you’re my patient) are indicated solely in these documented cases. The bloating for this one condition tends to be around or above the belly-button.

Here’s the problem with PPI medications like Nexxium or Prilosec. They were intended for short-term use but instead, are either prescribed or bought over-the-counter and used for years. When you do this, it alters your microbiome, suppresses your immune system and may even increase your risk of heart disease. As for your gut heath, it’s awful for that, too.

Note this is not how the PPI drug was intended to be used–ever! In the instances where people take over-the-counter PPI medications for their heartburn symptoms, the low stomach acid impedes the digestive process, making those individuals a total set-up for leaky gut!

Solution: To correctly treat run-of-the-mill heartburn, you need digestive enzymes containing pancreatic enzymes and bile acids. If that isn’t enough to quiet down your symptoms, add betaine (HCl) capsules; taken 15 minutes before meals. If your heartburn persists, you should be breath-tested for H. pylori.  If you still have bloating (especially below your belly-button), you have lower gut issues. You might have developed leaky gut and/or food sensitivities, for instance. It’s time to seek Functional integrative care.

Bloating due to gut motility issues

In cases of leaky gut, with or without SIBO, as the gut lining becomes destroyed, some segments of the small and large intestine will propulse “out of sync” causing intestinal cramping and, often, constipation; sometimes, diarrhea as well. This can be easily addressed, but before we jump to the solution, let re-visit the concept of fiber a bit.

I’ve mentioned the need for fiber above but honestly, aren’t most people aware that they need to eat adequate amounts of dietary fiber for optimal gut health? To review: fiber is a non-digestible carbohydrate which you can find mainly in plant foods such as fruits, vegetables, legumes and whole grains. In addition, fiber helps maintain a healthy microbiome and supports healthy bowel movements (via motility and bulk) to decrease the risk of diverticulosis and colon cancer. The recommended amount of fiber is a minimum of 25 grams per day for women and 38 grams per day for men. This doesn’t even include the prebiotic fiber or “fertilizer” we’ve discussed previously. And yes, if you cannot manage to eat your prebiotic fiber it’s just fine to take powder-fiber supplement mixes which contain things such as inulin, citrus pectin, prune powder, and psyllium husk.

So, if you are experiencing cramping, constipation and some diarrhea while your leaky gut (let’s say) is healing, here’s what you need to do.

Solution: In this case, we usually recommend products to either bulk up the stool (e.g.: modified citrus pectin), and/or a fiber blend as noted above. We can also improve GI transit at the smooth muscle level with 5-HTP supplementation if constipation is the primary issue. While we wait for the 5-HTP to “kick in” we use non-stimulant and osmotic products to draw water into the colon and relieve constipation: trifala and magnesium hydroxide.

Bloating due to hypothyroidism 

Since gut motility decreases when someone is hypothyroid, due to sluggish, slower or weaker smooth muscle gut contractions, constipation is a common symptom of Grave’s and Hashimoto’s disease. The resulting constipation, due to decreased gut motility is due to a decrease in FreeT3 which acts directly on the gut’s smooth muscle layer. This decrease in Free T3 can be due to T4 to T3 conversion issues but is often due to an unchecked increase in rT3 which is clogging up T3 receptors, rendering a patient “effectively” hypothyroid. This occurs quite often when someone has developed constipation which leads to leaky gut and then leads to SIBO-something we’ll discuss in the next section. It’s estimated that a minimum of 50% of those with Hashimoto’s thyroiditis have untreated SIBO. SIBO symptoms are often confused with those of other GI disorders and will be reviewed thoroughly in the next topic. Meanwhile….

Solution: Make sure you have all of the right thyroid hormones and auto-antibodies checked, including a reverse T3. Correct the hypothyroid state, and augment gut motility (methods above) as needed. Check for, and treat SIBO as discussed below.

Bloating due to SIBO 

SIBO (small intestinal bacterial overgrowth) is an increased number and/or abnormal type of bacteria growing in the small intestine section called the jejunum, a part of the bowel that is supposed to be sterile. For years, a culture of the small bowel was the way we diagnosed SIBO based on the presence of ≥1 × 105 bacteria (colony-forming units (CFU)) per cubic centimeter of jejunal aspiration. However, this definition is now under a great deal of scrutiny, and current thinking is that “normal” rarely exceeds 1 × 103cfu/ml. Furthermore, the idea that someone needs to see a Gastroenterologist and have a procedure called an endoscopy is rapidly falling out of favor in Functional medicine.

SIBO It is associated with anything that disrupts intestinal mucous, the microbiome and happens to be a quite common, undiagnosed cause of chronic constipation. It is a frequent result of chemotherapy, is (naturally) associated with leaky gut and with mycotoxin illness. As just mentioned above, it’s quite common in people who are hypothyroid.

The most common symptoms of SIBO are bloating and flatulence; particularly right after eating. Other symptoms include abdominal discomfort, constipation with interspersed bouts of diarrhea. It can be labelled as irritable bowel disease due to the alternating diarrhea and constipation.  Multiple food intolerances are relatively common.

Solution: Diagnosis. First- get the right diagnosis!  As mentioned above, the endoscopic procedure of bacterial sampling and quantification has fallen out of favor due to the variability of data regarding diagnostic parameters, patient discomfort, and inherent procedure risk. Breath tests are now routinely used as an alternative to direct aspiration because they are noninvasive and considerably less expensive. The most commonly used breath test is the hydrogen breath test.

The lactulose hydrogen breath test (LHBT) is the most widely used hydrogen breath test.  After the oral administration of 10 grams of lactulose, we take breath samples at 15-minute intervals for 3 hours. There is a catch: there are a huge number of false negatives- up to 60%!  Because breath tests are not very sensitive or specific, many Functional doctors will treat a patient if they exhibit symptoms and have underlying reasons for them.

Treatment includes antibiotics that are not absorbed by the gut (specifically Rifaximin) or with natural (herbal) substances. Herbal therapies are at least as effective as rifaximin for resolution of SIBO in head-to-head clinical trials. Herbals also appear to be as effective as triple antibiotic therapy for SIBO therapy for rifaximin non-responders. Some effective herbals (which should be given under medical supervision) include berberine, oregano oil,  barberry, garlic, olive leaf extract, goldenseal, wormwood, Oregon grape, garlic, caprylic acid and pau d’arco.

As a last comment, in addition to the sporulating probiotics, often your bloating and gas will respond almost immediately to 10 billion units of L. plantarium daily.

Bloating due to yeast overgrowth-SIFO

Yeast overgrowth often occurs at the same time as SIBO. It occurs in the same scenarios as described for SIBO, and especially for those in moldy homes.

Solution: If you’re living in a toxic home, that needs to be cleaned up, or the SIFO just won’t get better. It is also very important that you exclude all sugars from your diet as this is what feeds the yeast. The medication nystatin is used by some doctors to kill intestinal yeast infections. Natural yeast-killers include oregano oil, olive leaf and caprylic acid.

Bloating due to Carbohydrate Intolerance

Lactose, fructose, and other carbohydrates intolerance means that you cannot digest certain carbohydrates due to a lack of one or more intestinal enzymes. Symptoms include diarrhea, bloating with abdominal distention, and flatulence. The most common carbohydrate intolerance is lactose intolerance. This occurs when the enzyme that is required to digest lactose (the sugar found in milk and various dairy products) is not readily produced in the body, leading to symptoms as minimal as mild cramping or as much as just described.

Solution: For lactose intolerance, the diagnosis is “clinical”-meaning-take away dairy products and the symptoms cease. For other hard-to-pin-down carbohydrate intolerances, a more accurate version of the hydrogen breath test is used. Treatment is simply-removal of the causative disaccharide from the diet. Or in the case of lactose intolerance, consumption of less-lactose-containing A2 dairy products in combination with the enzyme lactase, taken with the A2 dairy meals can be quite effective.

Bloating Due To Food Sensitivities

Food sensitivities are not the same thing as food allergies. If you have an IgE-mediated food allergy, you have an immediate and quite unpleasant reaction such as a rash or hives and/or throat tightening. We’re not discussing these issues, due to, for example: peanuts.

The foods which cause most food sensitivities are (in this approximate order) gluten, dairy, eggs, corn, soy, shellfish, peanuts, citrus, lectins (namely beans) and nightshade vegetables (tomatoes, eggplant, white potatoes and peppers.) Food sensitivities most often develop in conjunction with other issues such as leaky gut, SIBO, chronic constipation, mold exposure and so on. If you are indeed sensitive, eating any of these foods can contribute to inflammation and even autoimmune responses such as skin rashes, migraine headaches, weakened immunity and even worsen or trigger the onset of autoimmune diseases.

Let’s discuss a few important specifics. Sometimes GI symptoms are caused by mild  gluten sensitivity. This probably has to do with the fact that almost all U.S. wheat is GMO and is added to many products as a thickener. Estimates show that a minimum of 30% of the U.S. population has some variant of gluten sensitivity. Try removing it from your diet-if it’s the problem, your symptoms will resolve.

A last word about beans. We joke about flatulence being caused by beans. This is simply a matter of your digestive enzymes being overwhelmed or a true sensitivity to the lectins in the beans. An example of a high-lectin bean is the kidney bean, with lentils being fairly low in lectins.

Note there are sophisticated tests (Doctor’s Data labs, etc.) that can detect specific food sensitivities if you have eliminated the “frequent offenders,” fixed your gut, and other issues to be discussed below. However, most people find that removing the above foods and then slowly reintroducing them will pinpoint the foods you need to avoid. This doesn’t account for FODMAPS foods (to be discussed).

Solution: The vast majority of people find that their food sensitivities start reversing in concert with the reversal of their GI symptoms. You can try doing an Elimination and re-intro diet if you still have food intolerances. If you’d like more specific data, the lab “Doctor’s Data” does the most accurate food sensitivity blood testing. I have not found that Cyrex labs (who seem to be popular with the public- perhaps due to social media advertising) to be all that predictive.

Bloating due to Inflammatory Bowel Disease

If you have an inflammatory bowel disorder, you started out with a leaky gut, didn’t have treatment and it then produced more symptoms and finally evolved into Crohn’s disease or Ulcerative colitis. Leaky gut can indeed be asymptomatic, and you might shrug off some post-meal bloating as due to something you ate. Inflammatory bowel disease symptoms such as explosive diarrhea or rectal bleeding can come, seemingly, out of nowhere. To get the plethora of symptoms under control, and your disease in remission is not only possible, but something that we Functional doctors who “treat a lot of guts”- do all the time. When I discuss solutions, for this topic, getting into remission is not something you can do “on your own.”

Solution: You’ll need to start out with a strict AIP diet and make sure there are no environmental factors (e.g. mold) contributing to your problem. Next, you need your leaky gut healed, and if you’ve had bloating and constipation, SIBO and SIFO will need to be evaluated and addressed. We now use peptides and LDN to treat IBD, so find a good Functional doctor who can do this for you. You’ll need good prebiotic fiber with sporulating probiotics. It might even be a good idea to suppress TNF-alpha and IL-6 with supplements. Some patient also benefit from a low-FODMAP diet: please refer to the IBS section below for more details on this.

Bloating due to Celiac disease

If you feel that gluten is causing severe symptoms such as cramping, bloating and explosive diarrhea, you might have Celiac disease, which is not the same as gluten intolerance. Individuals with Celiac disease are considered to have an autoimmune disease, with detectable antibodies on lab testing.

Solution: Blood testing for Celiac disease and then elimination of all gluten from the diet. The website Celiac-dot-com is quite helpful.

Bloating due to Weight loss or gain

Rapid weight loss or (much more commonly) weight gain are associated with abdominal bloating. How common is this?  In one study, recent “COVID weight gain” occurred coincidentally with new onset bloating in 25% of the study participants. Why? A possible mechanism may involve an abnormal feedback mechanism from the abdominal adipose tissue which helps modulate the brain–gut axis.

Solution: You probably know that I’m going to recommend that you slowly achieve your ideal weight and try to “stay there.” If you have cravings or binges, a little tweaking of your brain chemicals is done with intra-nasal peptides or integratives which are precursors to “happy brain chemicals.”

Bloating due to Irritable Bowel Syndrome

IBS (Irritable bowel syndrome) affects 7–15% of the U.S. population. Many people with a diagnosis of Irritable bowel syndrome have a treatable disorder. For instance, diarrheal-type IBS is often a problem called bile-acid malabsorption (BAM). Leaky gut, as you’ve read, causes bloating, constipation and diarrhea; often similar to IBS. You might have a chronic parasite infection if you are a world traveler or live near and recreate in a fresh-water lake.

Constipation-dominant IBS is quite often undiagnosed SIBO. In fact, some studies show that up to 80% of those diagnosed with IBS have SIBO!

Solution: If you do indeed have IBS, the #1 currently effective treatment is a low-FODMAP diet. Eliminating high-FODMAPS from your diet will help with symptoms; specifically bloating. The FODMAPS acronym stands for Fermentable Oligo, Di- and Monosaccharides and Polyols sensitivity. Foods containing glucose, fructose, polyols, and lactose can all cause symptoms for everyone with IBS and some people with IBD.

The mechanism of action of low-FODMAP diets is probably a reduction in small intestinal absorption of osmotically active polyols, resulting in diminished intestinal water content and beneficial effects on colonic fermentation and subsequent gas production. Other treatments include stool bulking agents such as modified citrus pectin, good prebiotics and probiotics, and if needed; anti-spasmodic medications. A few clinical trials show some benefit from biofeedback and even meditation.

Bloating due to Constipation and Outflow Obstruction

Functional (meaning perceived with nothing in particular being diagnosed) abdominal bloating and distension may be related to constipation and to functional outflow obstruction. Now, this being said, I’ll bet you that most cases of “functional” constipation are just cases of diagnoses not being made. At any rate, retained stool in the rectum can cause impaired gas evacuation and slowing of intestinal transit.


Yes, there have been positive clinical trials with drugs for constipation-type IBS, but since I don’t like the drugs one bit, I’m not going to name them. What I always go back to is “what is the root cause” of the slow transit. Let’s talk more about serotonin than we did in the gut motility section. Serotonin is the happy brain chemical that you probably think is made in the brain. However, in both men and women, about 90% is made in the GI tract!

When your GI tract is not making enough serotonin, not only are you anxious and a little depressed, you have less GI motility and therefore constipation. You can have low GI motility due to a lack of serotonin, be constipated and not feel depressed or anxious as a FYI. Slowly adding some 5-HTP to your evening supplements will increase your gut motility, as mentioned previously. And you can also add trifala and magnesium hydroxide if needed, too. Please don’t get into the habit of taking stimulant laxatives, as this can cause permanent neurological damage to the propulsion in your gut.

Bloating Due to Hormone Imbalance 

Bloating is a common sign of low progesterone. During the luteal phase of your menstrual cycle (after ovulation), both water and sodium retention increase with low levels of progesterone and high levels of estrogen. This occurs because the estrogen lowers the “osmotic threshold” for which water being reabsorbed in the body. When estrogen levels are high, this threshold is lowered and therefore less water is excreted through urine. This then causes the body to retain water and creates the sensation of bloating. Since this type of bloating, unlike “GI bloating” is indeed due to fluid retention, it’s different but often perceived as the same thing.

Low progesterone symptoms include the sensation of lower abdominal bloating. The bloating symptoms are usually accompanied by other low-progesterone (cyclical)  symptoms such as irritability, sleep disruption and a little brain fog. If you have low progesterone due to perimenopause or early menopausal symptoms, your symptoms are less cyclic and you might, then blame your GI tract. Be on the lookout for this mistake.

Since progesterone helps gut motility via serotonin increases, low levels will generally cause some constipation. Men can also suffer from low progesterone symptoms, in addition to low testosterone issues, by the way.

Can chronic low progesterone lead to SIBO? Or leaky gut? Interesting questions which haven’t been studied but I would say a definitive “yes.”

Solution: Treatment is simple. Bioidentical hormone replacement with progesterone will clear up the bloating and constipation. Sometimes a little 5HTP is needed as well. A temporary measure is to use pregnenolone (non-prescription) which partially breaks down to progesterone. Progesterone creams sold over-the-counter are absolutely ineffective.

Bloating Due to Chronic Stress

If you  “feel stressed” a good part of your workday, chances are good that you have a high fasting cortisol level. High cortisol levels can easily cause the breakdown of your GI lining. It slows down both GI motility and the entire process of digestion. As a result, some people experience “heartburn” while others have no symptoms whatsoever. Blood flow subsequently decreases to all of the digestive organs. This then adds insult to injury and results in a higher concentration of toxic metabolites which then whittle away at your gut lining. You can see that if the cortisol alone doesn’t give you leaky gut, the entire shutdown sure will. And if this isn’t enough, there’s actually more to this story. Simply being stressed out can lead to leaky gut, then to constipation, then to SIBO and food sensitivities.

Solution: Stress-management techniques are a must but it’s hard to find the time to do them if you’re already over-worked and over-stressed, right? If you can’t find the time for yoga, meditation or deep breathing exercises, try intermittent parasympathetic activation via your vocal cords. Do this by gargling salt water or even singing. You can get your cortisol down with adrenal adaptogens, as well. Do this not just for your gut, but for your brain, and arteries and more!

Final thoughts

If you have a little bloating once in a while, you can probably clean up your diet and your microbiome and maybe even identify an offending food or two, and voila, you’ll be fine. If you have been “abusing your gut” with processed foods, toxins, pharmaceuticals or stress, you’ll need functional medical help to get it all repaired and get rid of not just your bloating, but your other GI symptoms. GI symptoms are painful and bothersome. Don’t put up with them, now that you have some answers.

Mitochondria are the key to energy and health -Important update: I can now get NAD+ troches for you! 

Before I dive right into a discussion about mitochondria, I’d like to ask you why you are reading this article? If you are looking for improved health and longevity, this article will give you lots of actionable information. However, if you have been feeling ill, with fatigue being a prominent component of whatever is wrong, you need Functional Medical care. You can’t “fix fatiguing illness” yourself. That’s all I’m going to say about that; now I’ll get into the topic you came for: how to boost and why to boost your mitochondrial function. Mitochondria are involved in many vital processes in human cells, including energy production, fatty-acid oxidation, and the Tricarboxylic Acid (TCA) cycle, calcium signaling, apoptosis (cellular death), and heat production. However to simplify things let’s talk about energy and longevity which is what their function translates to for practical purposes. And to help this occur, we can review the health practices, along with the best supplements to improve mitochondrial function.

  • Why do we want well-functioning mitochondria?
  • What happens when mitochondria malfunction?
  • What about mitochondrial function and aging in general?
  • Mitochondria boosting health practices
  • Mitochondrial specific exercise
  • CoQ10
  • Alpha lipoic acid
  •  PQQ
  • L-carnitine
  • D-ribose
  • Phospholipids
  • NAD
  • Miscellaneous supplements
  • Final words

But before we begin, I’d like to give every one of my readers “patient access” to my Designs-For-Health account so that if you want to purchase supplements, you’ll receive a 15-25% discount from their Amazon price. Here is their website: and then my practitioner code is: kimcrawford, allowing you to create a un and pw for your own account. You’re welcome! If you want to try just one supplement, this one is probably your best bet. In addition, mitochondria reproduce and put out more of their “good stuff” when you lower sympathetic nervous system activity. Here’s the best and easiest way to do VNS to accomplish that goal quickly.  Feel free to use and share my patient code: DrKim25 for a $25 discount on the best thing you’ll buy this year.

Mitochondria: Why do we care?

First, let’s discuss the “energy part.” Mitochondria produce Adenosine Triphosphate (ATP). In the cell, the energy in the form of ATP is produced in two ways: in the cytosol as a product of glycolysis and in the mitochondria as a product of oxidative phosphorylation. The substrates, in the form of fatty acids and pyruvate, are oxidized via fatty acid β-oxidation and the TCA cycle, respectively. The Nicotinamide Adenine Dinucleotide (NADH) and flavin adenine dinucleotide (FADH2) produced by these reactions are used by the electron transport chain to generate ATP. Just remember from this complex discussion of energy production that you need ATP and you need NAD+/NADH to make that ATP, so you feel as if you have enough energy.

Proper mitochondrial functioning is crucial for every nucleated cell in a body. A number of diseases are characterized by dysfunction of muscular or neural systems or metabolic reactions. All these diseases and pathophysiological conditions are developed against a specific genetic background, together with environmental factors.

Mitochondria produce energy as ATP (adenosine triphosphate), which your body then uses to fuel your daily activities. Some cells have more mitochondria than others. Your brain, muscles, and heart cells are full of mitochondria. Putting diseases and aging to the side: you want your mitochondria working at full strength to keep your energy levels up, your brain sharp, and your muscles and heart at their peak performance. The creation of new mitochondria (mitochondrial biogenesis) is needed for optimal aging, which we now call our healthspan. Not to be repetitive, but always remember this is mandatory to keep your energy levels at a peak. It’s also a part of what’s needed to protect you from oxidative stress. As you would predict, mitochondrial dysfunction tanks your energy and contributes to numerous physical ailments.

Mitochondrial Dysfunction and Disease

Mitochondrial dysfunction, characterized by a loss of efficiency in the synthesis of ATP, is a characteristic of aging and, essentially, of all chronic diseases. Loss of function in mitochondria can result in excess fatigue and even other symptoms in just about every chronic disease you can imagine.  These conditions include neurodegenerative diseases, such as Alzheimer’s disease and Parkinson’s disease, and Amyotrophic Lateral Sclerosis.

Metabolic syndrome, heart disease, and diabetes are all associated with mitochondrial dysfunction. Metabolic syndrome is a group of conditions that combine hypertension, hyperglycemia, abdominal obesity, and abnormal cholesterol or triglyceride levels. Metabolic syndrome greatly increases the risk of cardiovascular disease, stroke, and Type two diabetes. There are numerous reports mentioning mitochondrial dysfunction and lower oxidative capacity in patients with Type two diabetes compared with healthy individuals.

The cardiovascular system strongly depends on mitochondrial function. Cardiomyocytes (heart cells) have very high mitochondrial content in order to produce the necessary ATP, and mitochondrial dysfunction inevitably leads to the development of cardiovascular diseases.

There is now increasing evidence of mitochondrial dysfunction in Alzheimer’s Disease, Parkinson’s Disease, Huntington’s disease, and Amyotrophic lateral sclerosis. Even some psychiatric conditions, such as autism spectrum disorders, schizophrenia, and bipolar mood disorders, are included.

In addition, mitochondrial dysfunction plays a significant role in the inflammatory response in acute human pathologies. Systemic Inflammatory Response Syndrome (SIRS) is a pathological state with a systemic immune reaction to severe damage, including ischemia, acute pancreatitis, trauma, and sepsis.

Autoimmune diseases such as rheumatoid arthritis, Crohn’s disease, and systemic lupus erythematosus are all characterized by mitochondrial failure. Of course, truly fatiguing illnesses, such as CIRS (mycotoxin and mold illness and Chronic Lyme), Chronic fatigue syndrome, fibromyalgia, and Gulf War Syndrome have mitochondrial near-failure as a prominent component. Lastly, as you might predict, cancer and chronic infections round out the list of disorders. If you have any one of these disorders, you will need to improve your mitochondrial health and function in order to recover.

Mitochondria and Aging

A number of age-related processes (e.g., “normal aging of the brain”) are associated with mitochondrial dysfunction, so most of the popular aging theories take this into account. The mitochondrial theory of aging posits that the accumulation of damage to mitochondria DNA promotes the process of cellular aging of both humans and animals. The theory claims that there is a  vicious cycle involving the accumulation of damage in mitochondrial DNA, which then leads to more oxidative damage due to defects in the mitochondrial respiratory chain. Let’s say that this theory is true. What, then can we do to save our precious mitochondria and therefore slow the aging in our cells and help prevent diseases?

Mitochondrial health practices

Eating an anti-inflammatory diet is one of the easiest ways to improve mitochondrial function. Polyphenol-rich foods such as blueberries, red and purple foods (e.g. raspberries and purple cabbage), and many fresh green foods are high in healthy mitochondrial-boosting polyphenols. Using intermittent fasting methods such as timed eating and intermittently “going keto” are also mitochondrial boosters.

Heat shock proteins produced by extreme cold or extreme heat are great for your mitochondria. Cold exposure is an easy way to give your mitochondria a boost. Studies have demonstrated benefits with “ice jackets”, facial submersion, and ice baths. Even cryotherapy tanks! And “ice swimming.”  Based on what I personally find tolerable and affordable, you can get enough of a boost by doing the following. At the end of your daily hot shower, just turn the temperature to cold for 30 seconds. It is mostly quite invigorating!

Far-infrared saunas are another way to generate heat shock proteins.  An FIR is a great investment in your health, as it is also a great way to do a bit of a detox.

Meditation and yoga also boost your mitochondrial output.

Ten minutes of direct sunlight is great for a burst of mitochondrial activity. Conversely, most data suggest that fluorescent lighting puts a damper on ATP production and mitochondrial biogenesis. The data is rather murky when it comes to EMFs, blue-blocking glasses, and so on, but it’s something to watch, as there seems to be some correlation between better health and less high-level EMF exposure, as well as less blue light exposure.

Exercising For Mitochondrial Health

Many types of exercise are mitochondria-healthy. Walking is great. Running is great. Weight training is great. Yet, the very best type of exercise for your mitochondria is high-intensity interval training. This doesn’t need to be complicated, but do get medical clearance if this is a new activity for you. Do you know how to do a burpee? Do burpees until you’re short of breath. Then catch your breath and do it again. Repeat this a total of 6 times if you can, less if you can’t.

You can do HIIT outside, too of course. If you have access to a track, great! If not, use a treadmill if you’re inside or run in your neighborhood if you’re outside. Sprint one lap. Or half of a lap. Whatever gets you short of breath. Then, walk until you catch your breath and you can even lie down on your back for faster autonomic neurological adaptation for up to 90 seconds if you need that long to catch your breath. I do this in our lap pool and it’s far more fun than simply “swimming laps” to me.

Now, let’s discuss the best supplements to improve mitochondrial function.

The best supplements to improve mitochondrial function

I see people perk right up within (literally) 24 hours of proper mitochondrial supplementation. If someone has a chronic and/or fatiguing illness or are just suffering from age-related mitochondrial failure, supplementation absolutely works. It sure beats energy drinks which end up causing adrenal issues and potentiating energy problems.

Here are the mitochondrial supplements that have been studied and proven effective.

Co-Q 10

CoQ10 is an essential electron carrier in the mitochondrial respiratory chain. In other (more complex) words, CoQ10 passes electrons between NADH-ubiquinone oxidoreductase,  succinate-ubiquinone oxidoreductase, or succinate-cytochrome C oxidoreductase. You can now just forget you read that and rub your eyes. Basically, CoQ10 can be found in both oxidized (ubiquinone) and reduced (ubiquinol) forms, and the conversion between these oxidized and reduced states allows it to act as a cofactor of enzymatic reactions via the transfer of electrons.

CoQ10 is a critical part of the mitochondrial oxidative phosphorylation system. Over ten well-done studies show that supplementation with this vitamin-like antioxidant compound in individuals with reduced CoQ10 levels results in increased energy production and reduced fatigue. The most dramatic results are in those individuals with degenerative diseases. Here are some examples.

In studies using Alzheimer’s disease models, CoQ10 administration significantly delays brain atrophy and characteristic β-amyloid plaquing. In a 4 month clinical study on around 100 Alzheimer’s patients who took an oral mixture of vitamins E, C, CoQ10, and α-lipoic acid, the group receiving supplementation showed significant reductions in oxidative stress markers and subsequent DNA damage.

Individuals with Parkinson’s disease tend to show increased levels of oxidized (and by definition: damaged) CoQ10.  They also have significant increases in markers of oxidative stress and damage in their brains, which is partially reversible with CoQ10 administration.

One last important clinical note: recall that the heart is filled with mitochondria which are partially powered by CoQ10. If you are taking a statin drug, please be aware that they deplete your body of CoQ10, so supplementation is a must.

Alpha-lipoic acid

ALA is a potent fat and water-soluble antioxidant vitamin. It is also a metal chelator (helping to remove iron, copper, mercury, and other heavy metals). It is also a fairly decent anti-inflammatory supplement. Clinically, α-lipoic acid has been used mostly to help treat complications associated with diabetes such as neuropathies and vascular (blood vessel)  complications. It also improves cognitive (brain) and mitochondrial function, adding to the evidence linking oxidative damage to mitochondria and cognition. The use of α-lipoic acid for chronic fatigue syndrome (CFIDS) has not yet been studied in controlled clinical trials. However, it is widely used in “fatigue regimens” (200-600 mg) as a way to both support mitochondrial function and reduce oxidative stress.

Despite its various potentials, the therapeutic efficacy of ALA is reduced due to its “pharmacokinetic profile”. Data shows that ALA has a short half-life and bioavailability (only about 30%) due to degradation in the liver and chemical instability in the stomach. The R isomer of ALA (R-lipoic acid) shows better pharmacokinetic parameters, including increased bioavailability as compared to the S isomer, ALA. Translated: just use R lipoic acid or a double dose of alpha lipoic acid for approximately the same results.


Pyrroloquinoline quinone (PQQ) is contained in fruits and vegetables such as kiwi fruit and green peppers. It has received a lot of research attention in the past several years. PQQ can reduce reactive oxygen species (ROS) levels and improve the apoptosis (death) of tumor cells. PQQ protects tissues by regulating the redox (electron transfer) reaction. Moreover, PQQ protects overall tissue function by improving the mitochondrial function of the liver, neurons, and other important tissues. It can also reduce atrophy in mouse skeletal muscles.

PQQ decreases oxidative stress (production of ROS) and inflammation which, by definition, will protect mitochondria. It also increases mitochondrial biogenesis, which is the formation of new, young-acting mitochondria. It is neuroprotective, too. Here’s how. Recall that you have read about GABA versus glutamate or inhibitory (relaxing) versus excitatory (too stimulating) neurotransmitter activity. We want more GABA than glutamate, plain and simple. Too much glutamate damages brain cells. PQQ protects neurons by preventing the long-term over-activation of the glutamate (NMDA) receptors, which results in toxic excitotoxicity of neurons. This over-stimulation of brain cells is associated with many neurodegenerative diseases and seizure disorders.

Recall again that you have the largest concentration of mitochondria in your brain, heart, and skeletal muscles. The brain “wins” pound for pound by a little edge, which is why you feel tired after using your brain all day. With this in mind, remember that when we protect the brain, we’re protecting brain mitochondria. PQQ protects the brain (to a certain extent) against neurotoxicity induced by mercury and other potent toxins such as mold mycotoxins. Lastly, it too helps to prevent the accumulation of amyloid tau and beta proteins associated with Parkinson’s and Alzheimer’s diseases.


Acetyl-l-carnitine is a naturally occurring fatty acid transporting amino acids. L-carnitine supplementation has long been studied and then used in many mitochondrial dysfunction disorders. These disorders are also characterized by low concentrations of serum l-carnitine levels such as heart disease, diabetes, kidney disease, and overwhelming infections.

An important cellular longevity function of l-carnitine has been to increase the rate of mitochondrial oxidative phosphorylation (ATP production) that declines with age. A  study where old rats were fed acetyl-l-carnitine resulted in the reversal of age-related decreases in l-carnitine levels, an increase in fatty acid metabolism, and an increase in mitochondrial activity. Acetyl-l-carnitine also reverses the age-related decline in muscle mitochondria.

Clinical studies show that L-carnitine supplementation may also be useful in alleviating fatigue symptoms in hypothyroid patients, especially in those younger than 50 years and those who have hypothyroidism after thyroidectomy for thyroid cancer. Note: L-carnitine is the nomenclature used for many clinical studies, but due to l-carnitine’s ability to increase TMAO, experts suggest that all human supplementation be done with acetyl-l-carnitine.


We know that D-ribose has documented positive mitochondrial effects for those who are genetically d-ribose deficient. It’s a popular bodybuilding supplement which “hardcore” bodybuilders credit as being helpful with their muscular fatigue. Studies have looked at neurodegenerative diseases such as Multiple Sclerosis and ALS with promising results. Due to these studies, I decided to use it in a protocol on a dog named Charlie. Charlie is a very beloved and smart standard poodle, belonging to a favorite patient of mine. The patient (another M.D.) contacted me, quite distraught that his dog had received the diagnosis of degenerative myelopathy or “doggie ALS” as I  found upon doing some research. Charlie, it seemed, couldn’t get himself up off the floor. The same mitochondrial problem has been identified in both dogs and humans. So, I got to work on Charlie’s protocol.

I calculated doses of supplements based on Charlie’s 48-pound weight. I recommended a mitochondria-boosting ketogenic diet. Then I added ALA, ALC, CoQ10, PQQ, and NAD (discussed below), as well as some d-ribose powder. I had my patient add some antioxidant powder to Charlie’s food, too. “Why not” I thought. My patient said that 24 hours after Charlie started his regimen, he was noticeably stronger, up and walking, and even playing! The patient’s Veterinarian was astounded and has gone on to use my protocol on other dogs. Now, let’s give an honorable mention to another concoction.


Mixtures of probiotic, phospholipid, and antioxidant preparations have shown some clinical promise in fatiguing illness. This mixture is made using antioxidant powders, probiotics, and phosphatidylserine. The bulk of the studies have been with patients who have fibromyalgia and/or chronic fatigue syndrome (CFIDS).


NAD is now the big news, thanks largely to the research by Dr. David Sinclair and his best-selling book, “Lifespan.” Recall the mentions throughout this article about the conversion of NAD+ to NADH, and vice versa, as essential reactions in creating ATP. Recall that ATP is cranked out by mitochondria, and gives cells (and you) energy. Therefore NAD and its substrates are crucial for cellular energy, mitochondrial biogenesis and it turns out; cellular longevity. All that remains to be seen, is proof positive that one “form” of NAD is superior to another. Here are some of the data.

Oral NADH supplementation can reduce symptoms in patients with chronic fatigue. One study on patients with chronic fatigue syndrome treated participants with micro-encapsulated, oral NADH or a placebo for a month’s time. 8 of 26 study participants (about 1/3) responded positively with increased well-being and energy levels to the NADH compared with 2 of 26 (8%) in the placebo group.

This supplement also shows promise for neurodegenerative disorders such as Parkinson’s and Alzheimer’s diseases. The increase in measured NADPH levels correlates with a marker for aging: an increase in telomere length.

NAD will stimulate the SIRT1 pathway which is notably dysfunctional in those with metabolic syndrome, diabetes, and more. When you stimulate the SIRT1 pathway, you lower leptin levels, making it again possible to lose weight, improve blood sugar, cholesterol, and triglyceride levels, and in fact, all aspects of metabolic syndrome.

Taken orally, NMN (nicotinamide mononucleotide) is rapidly absorbed and converted to NAD+. In numerous studies, supplementation with NMN increases NAD+ biosynthesis, suppresses age-related fatty tissue inflammation, enhances insulin secretion and its action, improves overall mitochondrial function, and in the brain, it improves mitochondrial as well as neuronal function. In animal studies, it extends lifespan. In fact, NMN given to mice does quite a bit. Before I discuss NMN, let me give a shoutout to nicotinamide riboside- also converted to NAD+. As well as NMN? We don’t know, and the research continues. Meanwhile, we have a lot of data from mice studies.

Orally administered NMN is rapidly converted to NAD+ in mice. NMN has been shown to enhance energy metabolism and physical activity, suppress age-associated weight gain, improve insulin sensitivity and even improve ocular function. It improves mitochondrial metabolism and prevents age-related negative changes in gene expression. In mice bred to be obese or diabetic, NMN improved both the action and secretion of insulin.

NMN also protects the mouse heart from ischemia and/or reperfusion injury. It restores skeletal muscle mass in aging mice. Of special interest to those of us who treat many patients with brain issues, it has been shown to slow cognitive decline in a mouse model of Alzheimer’s disease, by improving the survival of neurons, improving energy metabolism, and reducing oxidative stress. It may also help maintain the integrity of the blood-brain barrier.

NMN also probably suppresses the increase in systemic inflammation associated with aging based on the studies which show that it lowers adipose tissue inflammation associated with age. In fact, surprisingly enough, older mice appear to be more responsive to NMN, in comparison with younger mice.

Some studies appear to suggest an increase in blood vessel formation called angiogenesis with artificially increased NAD levels for prolonged periods of time. This is why, despite the fact that I use a lot of NMN and intra-nasal NAD in my clinical practice, I have patients take intermittent breaks from it, and will do so until more data is available on this phenomenon.

Additional supplements with much promise

Studies are increasingly showing that mitochondrial illnesses are fueled by oxidative stress; implicating the use of antioxidants such as natural vitamin E and NAC (the precursor to glutathione) as well as glutathione as additional treatment considerations. We know that the sirtuin pathways are boosted by resveratrol and ECGC-green tea extract; implying mitochondrial benefit. Branched-chain amino acids, vitamin D, and creatine are all pro-mitochondrial health supplements as well, despite being poorly studied for this particular issue. Finally, there is emerging data for mitochondrial health with berberine, magnesium threonate, selenium, and even immune-boosting melatonin. B vitamins are likely involved as well. It appears that the more useful a supplement has been proven to be (vitamin D as a prime example), the less it is studied for other, more complete benefits.

Final words

In any good health regimen, you want to eat an anti-inflammatory diet and take a few supplements. It makes sense to take vitamin D and high antioxidant power supplements for many reasons, including mitochondrial health. At this juncture, if you are healthy and have specific goals in mind, you might choose, let’s say, some acetyl-n-carnitine if you are lifting weights, or some PQQ if you have a family history of neurodegenerative disease. And currently, if you have metabolic syndrome, SIRT pathway issues, or fatiguing illness, it seems prudent and helpful to take NMN and/or NAD intra-nasal spray. Yes, IV NAD is beneficial, but I am “not a fan” of this current craze of “drip bars” and feel that consumers are being, quite frankly, ripped off by this trend when alternative routes of administration can be utilized. Finally, if you’d like my opinion on what would be good for you, just ask me.


Introduction to Inflammatory Bowel Disease

The etiology of Inflammatory bowel disease (ulcerative colitis and Crohn’s disease) is complex, with genetic predisposition, an altered microbiome, environmental factors and a weakened epithelial (“gut”) barrier function triggering a chronic immune response in the mucosal layer. These two disorders of chronic intestinal inflammation affect approximately three million people worldwide. U.C. therapy and Crohn’s disease treatment starts with a good understanding of the disease process itself.

Currently, allopathic (versus functional medicine) Crohn’s disease treatment, for example- starts off with with brain and gut damaging corticosteroids and 5-aminosalicylic acid products, adds “immunomodulators” (Azathioprine, 6-mercaptopurine, methotrexate), and eventually, “biological agents” which are “TNF-alpha inhibitors” (infliximab, adalimumab, certolizumab, and golimumab). The story is just about the same for Ulcerative colitis. Just. too. toxic. for. words.

Not one of these drugs are curative, and their long-term use often causes severe side effects including cancer. Around 30% of patients with inflammatory bowel disease (IBD) are refractory to current IBD drugs or relapse over time. As a result, patient surveys show that almost 40% of Crohn’s and U.C. patients use alternative therapies to complement their conventional medical care. The first thing I now do with new patients is to get them using a VNS device to bring down inflammation quickly. Here is the only device that works, is not too pricey, and kicks in immediately. When you purchase yours, feel free to use and share my discount code for $25 off: DrKim25.

Furthermore, because we Functional docs (in conjunction with happy, cooperative patients) obtain such stellar symptomatic control with our IBD patients, many of them will switch entirely to Functional care, stay symptom-free, and experience far less invasive colonoscopies, since a fecal calprotectin level is a great way to monitor all disease activity. U.C. and Crohn’s disease treatment is fairly easy in the “functional world”, and it is helpful to know what it is that you can do to prevent disease occurrence or, at least, lessen your symptoms.

First, I’ll explain the five major factors that you can control regarding what causes inflammatory bowel disease to occur and to flare: the “root cause.”. Then, I’ll review the following list of items that will help you get into and more importantly-remain in remission:

  1. Change your diet to an autoimmune eating plan
  2. Be careful when it comes to consuming pharmaceuticals.
  3. Heal your gut lining
  4. Manage your stress (cortisol).
  5. Clear up toxins (if needed).
  6. Take herbals to clear up toxic bacteria and/or yeast.
  7. Get your hormones balanced.
  8. Re-balance gut motility (often needed).
  9. Eat prebiotic probiotics foods and choose probiotic supplements.
  10. Use peptides
  11. Use low-dose naltrexone
  12. Consider lowering TNF-alpha with supplements-it can’t hurt!


The Root Cause of Crohn’s Disease and Ulcerative Colitis

Traditional medicine teaches us that risk factors officially implicated with ulcerative colitis and Crohn’s disease include low fiber-high carbohydrate diets, smoking, altered microbiomes and gut permeability as well as medications such as non-steroidal anti-inflammatory drugs. Each of these things will cause leaky gut, so what you’ll read next will not contradict these conventions. Leaky gut is the root cause of all autoimmune disease, including ulcerative colitis and Crohn’s disease. Here are the reasons you are more likely than not to have some degree of gut hyper-permeability syndrome AKA “leaky gut.”

Environmental contaminants and toxins

Direct gastrointestinal toxins we consume or absorb such as the methylmercury in canned tuna fish, the excessive use of plastics for food storage and even the fluoride in unfiltered water- can all damage our gut lining and disturb our microbiome. We even accumulate toxins via skincare products, and from non-filtered showerhead water. We breathe polluted air if we are in or near a city or a factory. We don’t think of “bad air” as a gut issue, but it is. If we’re in a dusty house, even if we don’t have dust mite allergies, dust mites have been demonstrated to cause leaky gut.

Lastly, another problem we don’t generally associate with gut health is mold. The reason I mention this outright is because 25% of us cannot (genetically) clear mold toxins so they not only damage our gut, they are responsible for a host of symptoms and long-term medical problems. If you have or had mold in your home (50% of structures in the U.S. fall into this category), you likely have mycotoxins in your HVAC that you’re breathing in and out of your lungs which may or may not ultimately damage your gut and may or may not cause ulcerative colitis or Crohn’s disease.

Depending on how well your detoxification systems both recognize and clear certain toxins, your toxin loads can build up to damaging levels. Something to keep in mind is the gut-brain barrier. Once the gut barrier is breached, so is the gut-brain barrier which then typically adds brain fog and things like concentration and mood issues to your “gut issue.” Now, let cover the most common way for Americans to wreak havoc on their guts: food.


The food you eat can absolutely cause leaky gut. People who consume the “standard American diet” (SAD) with it’s high-processed and fast foods as well as it’s high-sugar content are putting their guts (and therefore their total health) at risk. As you are likely aware, gut-damaging GMO foods are now dominating the soy, wheat, and corn markets.  GMO-gluten used all too ubiquitously in our food supply is increasingly being blamed for non-celiac gluten sensitivity and leaky gut. It’s estimated that 25-75% of Americans have some type of food sensitivity. The most frequent offenders are (in this order) wheat, dairy, eggs, and corn.

Consuming gluten, artificial sweeteners, GMO foods, dyes and additives so non-food-like that they are now dubbed appropriately “franken-foods” as well as the massive amount of sugar (including HFCS and other hidden sugars) in our typical diet results in leaky gut. Add in non-sprouted grains and lectins (found-for example-in beans and nightshade vegetables), fruit juice and excessive caffeine and alcohol, and it’s a wonder we all don’t have leaky guts.

Actually those of you eating a standard inflammatory American diet likely do have a degree of leaky gut. Enough to trigger you to the other side of U.C. or Crohn’s disease? Do you really want to find out the hard way? And if you are someone who has I.B.D. and just “eat what you want” while taking a potentially harmful biologic drug-would you be willing to alter your eating style for improved health and a promise for a better chance for remission? What about your over-the-counter drugs habits? You can certainly alter those, can’t you? Sure you can! You, first, however need to know what is potentially problematic.


Americans pop OTC painkillers as if they’re candy. T.V. commercials feature actors who are pleased with themselves that they take just one non-steroidal anti-inflammatory gut irritant in the morning; and not again, until the end of the day!  Your gut lining can be interrupted by everything from Aleve and Ibuprofen to Vioxx or even Tylenol. The majority of people who take OTC pain relievers daily have some degree of leaky gut.

Another category of awful-for-the gut drugs is antibiotics. I hate to bash my own profession, but am always amazed at the amount of antibiotics my new patients tell me they were given for dubious bacterial infections. Antibiotics not only cause leaky gut, they also upset the good to bad ratio of bacteria in the GI microbiome. We now also have proton pump inhibitors sold over the counter; thus sky-rocketing their use. These drugs were never designed for more than short-term use. Many people use these PPI’s (Nexium, Prevacid or Protonix, ) for chronic heartburn and slowly etch away the lining of their GI tract.

Synthetic hormone medications such as birth control pills or cortisone-containing steroids (e.g.: prednisone or a Medrol dose-pack) can propagate the growth of excess candida (yeast), which also often damages the gut lining.

Hormonal imbalances can also cause chronic constipation such as low progesterone levels and low thyroid hormone levels. Indeed, this can readily lead to small intestinal bowel overgrowth (SIBO) as can many types of cancer chemotherapy agents. SIBO disrupts the gastrointestinal balance dysbiosis), often causing gas, bloating and eventually, leaky gut.

Chronic Stress

If you constantly “feel stressed”, chances are very good that you have a high cortisol level. High cortisol-apart from everything else we’re discussing-can cause the breakdown of your GI lining. It does this by slowing down both GI motility (peristalsis) and the process of digestion. When this happens, some people experience reflux, or “heartburn” while others have absolutely no symptoms. Blood flow then decreases to all of the digestive organs. This results in a higher concentration of toxic metabolites which then whittle away at your gut lining.

Gut Dysbiosis

Dysbiosis of the gut means that your GI microbiome (gut-bacterial-environment) is out of balance. A properly balanced GI microbiome is absolutely crucial for optimal GI function, immune function, and  brain function. Yeast (candida) can invade the lining of the intestinal wall to cause SIFO; small intestinal fungal overgrowth. Toxic E. Coli species are common culprits in SIBO (small intestinal bacterial overgrowth) issues. Other organisms such as giardia (a parasite) and Helicobacter pylori (responsible for ulcers and cases of severe heartburn) can also chip away at the intestinal lining. Deserving of a mention in this section are three things that can lead to lower gut motility and therefore SIBO and SIFO: hypothyroidism, low progesterone levels and low serotonin levels. Lastly, toxins are increasingly found as a cause of leaky gut.


This topic is worth re-visiting. Although the amount of plastics (as an example) we consume is escalating, what is getting a lot of attention as definite gut-busters are mold toxins called mycotoxins.  Since 50% of the buildings in the U.S. are estimated to have water damage-a set up to mold growth; with the increasing climate events, we are seeing more and more water damaged buildings and more mold (especially toxic mold) growth.

We know that approximately 25% of the population is genetically unable to recognize and clear mold toxins, leaving them vulnerable to all sorts of medical problems including fatigue, brain fog and leaky gut. Now that we’ve discussed what causes leaky gut which can then lead to ulcerative colitis or Crohn’s disease, let’s talk about how we treat these two conditions with the best Functional Medicine has to offer.

Treat Underlying Gut Issues as an Integral Part of your Ulcerative Colitis and Crohn’s Disease Treatment

Change your Diet

It’s necessary to eliminate foods from your diet that can directly cause leaky gut. Initially, this is typically a huge lifestyle modification that is structured as such so that treatment doesn’t miss any offending foods. Over time leaky gut can precipitate as host of  IGG-mediated food sensitivities which can cause a plethora of symptoms. It is much simpler to  start with a basic diet and then reintroduce certain foods (e.g.: eggs) when you have your symptoms under control.

If you are eating a standard American diet, you’ll notice that the modifications you need to make will cause you to shed some pounds, have more energy, and in general, you’ll feel better. The first thing to do is to clean out your pantry and make yourself a list of “allowed foods.”

The best diet to follow is an AIP (auto-immune protocol) diet which restricts the “usual gut offenders” such as gluten, dairy, eggs, corn, sugar, processed foods, fast foods, citrus, nightshade vegetables, legumes, grains, as well as alcohol and caffeine. Yes, just like the Paleo diet!  It also restricts high FODMAP foods if they cause GI distress, which for most patients, is necessary. You cannot blame your gastrointestinal symptoms on specific foods if you eat this way for the two months it takes to heal a leaky gut. Yes-this diet is restrictive, but it will help to get you well and in two months, you can reintroduce some food items.

The Crohn’s and U.C. Diet Plan

What Do You Eliminate?

  • Processed foods
  • Legumes, such as beans, lentils, and peanuts.
  • Grains.
  • Dairy products.
  • Seed oils, such as vegetable and canola oil.
  • Nightshade vegetables, such as eggplant, potatoes, tomatoes, peppers, and okra.
  • Fast foods.
  • Refined sugars.
  • Eggs.
  • Soy.
  • Nuts and seeds.
  • Herbs from seeds, like coriander, cumin, and nutmeg.
  • Coffee.
  • Chocolate.
  • Dried fruits.
  • Food additives, like gums and emulsifiers.
  • Caffeinated teas: herbals are fine.
  • Spices made from nightshades, like chili powder, paprika, cayenne, chipotle, red pepper.
  • Alternative sweeteners such as xylitol and mannitol with stevia being OK in small amounts.
  • Alcohol.
After eliminating all potentially allergenic foods, the remaining basics are:
  • Meat, fish, shellfish, mollusks and poultry.
  • Low-sugar; small quantity fruits (berries only at first) and all vegetables, except for the nightshades.
  • Fruit oils (avocado, coconut, olive, MCT, palm) and animal fats such as ghee.
  • Bone broth (or gelatin/collagen).
  • Tea-Herbal is best, but some mildly caffeinated brands (loose, organic; not teabag) might be fine.
  • Vinegar: Restrict to apple cider initially.

Follow this eating plan (along with whatever else your Functional M.D. prescribes) until the “explosive diarrhea” wanes. For most people, this occurs within 3-4 weeks. At that time, you can add in a small cup of brewed coffee with a splash of additive free coconut or almond milk. Coconut milk is not included at first because it is a high FODMAP food  in more than tiny amounts. Reintroducing food is quite personalized, so I can’t advise you what to add back from this list-if ever-or when.


We’ve reviewed what not to take- so what do you use instead? Instead of NSAIDS for pain, use tylenol. Better still, if your GI tract is healed, use fish oil and curcumin- proven in clinical studies to out-perform even the priciest NSAIDS. For heartburn, try one white Rolaid or TUMS. Better yet: find good digestive enzymes. Herbals can often be substituted for antibiotics and anti-fungals, but you will need guidance for those. Hopefully, this article will make you aware of what you’re taking, and the effect it has on your gut.

Heal your Gut 

Getting you to remission and being asymptomatic from U.C. or Crohn’s disease starts with fixing your leaky gut. Changing your diet is the first step in healing your gut. Use (under medical care) proper gut-healing peptides ( discussed below) and (if needed), supplements for leaky gut such as l-glutamine and collagen powder. Vitamin D levels need to be normalized, and sporulating probiotics should be added when the symptoms start to subside so that they don’t “leak back” into the bloodstream. At this time, you’ll also add prebiotic fibrous carbohydrates (such as a half of an unripe banana) to your diet. More about re-balancing your microbiome (the prebiotics and probiotics)  coming up soon. But first, let’s talk about what’s plaguing most of us: stress.

Control Stress to Lower Cortisol

Stress is honestly just terrible for your health. We innately know this- but do you know the physiology of why this is? We know cortisol is a direct neurotoxin; likely being a risk factor for Alzheimer’s disease. We know it adds fat to the belly. When we’re talking about U.C., Crohn’s disease or any autoimmune disease for that matter, we’re looking at the direct effect high cortisol has on the gut. As previously mentioned, sustained high cortisol can be the sole reason for having a leaky gut. As a “not-so-fun-fact”-this is the probable reason so many “hardcore” bodybuilders (who all have high cortisol levels) have leaky gut.

Adrenal (herbal) adaptogens, glandulars, liposomal GABA and certain types of aromatherapy are proven to lower cortisol levels. Stress-busting techniques such as “vagal breathing,” meditation, and yoga are great relaxation practices. Finally, just activating your hypoglossal and therefore your vagal nerve to tone down your sympathetic nervous system will help. Simply sing, or even gargle!

Clear out Toxins

Common toxins that routinely cause leaky gut are the mycotoxins, the dust mites that usually are not numerous enough to be an issue unless there is actively growing mold, (AKA dust mite food) and lastly-heavy metals such as mercury. How do you know if mold is making you sick? If you have gut issues, fatigue and a foggy brain, with a history of mold exposure, there’s your answer. Dust mites? Not nearly as guilty– but in the line-up. Heavy metals? This depends on your environmental history and more. As does “toxicity” in general. Let me explain.

Toxins play more of a critical role if you have “faulty genetics” including glitches in your detoxification pathways. Having a few mercury amalgam fillings isn’t usually “enough” to cause leaky gut. We generally say “having eight or more fillings” is a problem that needs to be addressed after we get the general health of the patient under better control. However, be careful with your diet as a steady diet of canned tuna-fish or tuna sushi is actually enough to cause methylmercury build-up with effects on the gut and other organs.

Clear up Infections

If you have a history of vaginal yeast infections, you can cross-over infect your gut, especially if you have some sort of gut motility issue as mentioned earlier-things such as thyroid issues, low progesterone or low serotonin. Many cases of small-intestinal-bacterial-overgrowth (SIBO) occurs when colonic bacteria “backwash” into the usually sterile jejunum. The most common yeast (SIFO) and SIBO symptoms are gas, bloating and constipation. Also, be aware of Helicobacter infections, and parasites. When in doubt, breath test, and treat. Sometimes symptoms are just so obvious that we simply treat- especially since Functional doctors tend not to treat SIBO with antibiotics, nor do we treat SIFO with anti-fungals.

Balance your Hormones

Both female hormones and male hormones need to be balanced for optimal gut motility, necessary to prevent “backwash” and infections. The gut “works better,” and the microbiome stays more in balance when your hormones are in balance. A full discussion of this is beyond the scope of this article. Be aware, however that during menopause, the decrease in estrogen causes a rise in cortisol, something we just discussed. Also be aware that adequate progesterone is necessary, as is adequate thyroid hormone for optimal gut motility. Gut motility depends on a healed gut which includes a healed smooth muscle propulsive layer.

Re-balance Gut Motility  

As the gut lining becomes destroyed, some segments of the small and large intestine (depending on where the involvement of the disease is) get destroyed and therefore “out of sync.” As the gut heals, we sometimes need to use products to bulk up the stool and therefore improve the transport of “contents” such as modified citrus pectin or a multi-fiber blend. Sometimes we need to also improve GI transit at the smooth muscle level (by utilizing the serotonin precursor 5-HTP for example.) As mentioned, hormones need to be normalized as well. It’s strange to realize that diseases which produce “explosive” diarrhea can actually cause bloating and constipation while healing occurs, but indeed, this can happen. Now, let’s discuss what needs to happen to your microbiome.

Re-Balance your Microbiome

By definition, when you have leaky gut, you have more “bad bacteria” than “good bacteria” populating your GI tract.  Use prebiotic fiber to feed the good bacteria and (if you are not in a “mold situation”) a little bit of “good yeast” to re-create a healthy gut microbiome. State of the art care is to add a friendly yeast called Saccharomyces boulardii (by prescription: Florastor). Regarding prebiotic fiber, start with asparagus, Jerusalem artichokes, red onions and naturally fermented (not pickled) foods such as sauerkraut. If you like un-ripe bananas, they make great prebiotic fiber.

When your gut lining is coming together-usually the 2 to 3 week mark, add probiotics. Do not purchase or even make your own yogurt; you can’t have dairy yet, remember? Historically, we have recommended 50 to 100 billion probiotic CFU’s per day. A mixture (in your main probiotic) of Lactobacillus species and Bifidobacterium species is probably fine, but there is increasingly more evidence supporting the use of sporulating probiotics for an even better microbiome.  A generic product, VSL3, has yielded some positive remission studies, as have the probiotic strains Lactobacillus casei and Lactobacillus rhamnosus.

The most current research supports the use of sporulating (soil-based) probiotics to create a more diverse and therefore more healthy microbiome. These sporulating probiotics are so potent, you need to be careful not to “overdose”, or you can experience cramping and diarrhea. Start as low as 5 billion and increasing to as many as 25 billion CFU’s daily (best done under a doctor’s supervision). These probiotics are species of Bacillus with b. subtilis and b. coagulans being the most studied. Finally, if you see your diarrhea disappear but still have gas and bloating studies are promising for using 10 billion CFU’s of Lactobacillus plantarum. If that doesn’t work, consider the SIBO/SIFO angle if you haven’t done so already. Next, let’s discuss what has revolutionized the treatment of Crohn’s disease and ulcerative colitis: peptides and LDN. First, let’s discuss peptides.


Peptides are short strings of amino acids, typically composed of 2–50 amino acids. The peptides used in functional medicine are derived from human secretions and therefore bioidentical; meaning no side effects such as what we see with pharmaceuticals. There are many peptides being used for many functions in functional and integrative medicine, but three in particular which are used in various forms, combinations and doses for ulcerative colitis and Crohn’s disease treatment.


The pentadecapeptide Gly-Glu-Pro-Pro-Pro-Gly-Lys-Pro-Ala-Asp-Asp-Ala-Gly-Leu-Val, M.W. 1419, named BPC 157 has been demonstrated to counteract peritonitis and heal intestinal lesions-especially colitis lesions.

Gastric pentadecapeptide BPC 157 (GEPPPGKPADDAGLV, M.W. 1419 as above) is stable in human gastric juice, now found to be effective both in the upper and lower GI tract, and remarkably free of side effects. BPC 157 has been demonstrated to be an efficient therapy of inflammatory bowel disease. It has been shown  to interact with the nitric oxide protective system, providing endothelium protection and counteracting severe complications of advanced and poorly controlled inflammatory bowel disease.


The human peptide GHK-Cu (glycyl-l-histidyl-l-lysine) has multiple biological actions, all of which appear to be positive. It stimulates blood vessel and nerve outgrowth, increases collagen, elastin, and glycosaminoglycan synthesis and supports the function of dermal fibroblasts. GHK’s ability to improve tissue repair has been demonstrated for skin, lung connective tissue, bone, liver, and stomach lining. It has been extrapolated to have reparative effects on the lining of the entire gut.


α-Melanocyte-stimulating hormone (α-MSH) is a cleavage product of a melanocortin that has protective and anti-inflammatory effects. Its anti-inflammatory activity has been shown to be mediated by three N-terminal amino acids: lysine-proline-valine (KPV). The KPV peptide alone has been found to exert an even stronger anti-inflammatory effect than the whole α-MSH peptide.

KPV has been demonstrated to attenuate the inflammatory responses of colonic epithelial and immune cells and reduce the incidence of colitis  upon oral administration. KPV exerts its anti-inflammatory function inside cells, where it inactivates inflammatory pathways by a decrease in pro-inflammatory cytokine expression. Very importantly, unlike the drugs currently used for U.C. therapy and Crohn’s disease treatment, KPV is a naturally derived tripeptide without any notable side effects. And now to what many of us consider the “game changer” for all autoimmune disorders: low dose naltrexone.

Low Dose Naltrexone 

Close to a third of patients with inflammatory bowel disease are resistant to all currently available pharmaceuticals, or they relapse over time. Investigators have turned their eyes to studying the effects of “LDN” on the gut epithelial barrier in treatment resistant patients with ulcerative colitis and Crohn’s disease.

One study utilized low dose naltrexone for 47 patients who were followed prospectively for 12 weeks. Where available, endoscopic data including tissue biopsies were collected. The effect of LDN on wound healing and tissue biopsies from endoscopic procedures were evaluated. The results? Spectacular in my book. Low dose naltrexone resulted in “significant clinical improvement” in 75%, and complete remission in 25% of patients.

Another clinical study involves close to 600 inflammatory bowel patients. Among the 250 or so patients who became persistent LDN takers, there were reductions in the number of users of all previously consumed drugs (down by 12%), intestinal anti-inflammatory agents (down by 17%), other immunosuppressants (down by a whopping 29%), intestinal corticosteroids (also markedly decreased by 32%), and aminosalicylates (decreased by 17%). Of importance: this study did not manipulate diet or use any other gut-healing agents. Not even any probiotics!

The most recent clinical study assessing LDN in IBD involved 28 patients affected by Crohn’s disease and 19 by ulcerative colitis. Patients with an intractable (meaning basically untreatable by conventional methods) active phase of IBD received a daily dose of LDN  in addition to standard treatment. Follow-up lasted for approximately 3 months and 35 patients (75%!) responded to therapy with  a decrease in disease activity which lasted for at least a month. Six patients achieved full clinical remission, including five of them having a complete endoscopic remission.

Just imagine if the above patients had been put on my autoimmune diet, given peptides, vitamin D, sporulating probiotics with good prebiotics- along with their LDN? And just imagine that we could add in some supplements? What, then would the response rate be? Let’s finish up with some possibly helpful supplements.

Supplements and more for TNF-alpha Reduction

“Conventional medicine” offers Crohn’s and U.C. patients “biologics,” which come with an array of potentially fatal side effects. I’m not saying they don’t work, and I also don’t suggest that you stop anything “cold-turkey.”  We know that these drugs all lower a laboratory biomarker called TNF-alpha. Disease activity appears to correlate with the level of this marker. We don’t yet know if reducing this marker will reduce disease activity in humans. However we know that TNF-alpha is likely a toxic lab value that we’d probably prefer to get as low as possible, no matter what. If that’s the case, then the following “in vitro” information is relevant.

We know that nutritional ketosis will inhibit TNF-alpha. Resveratrol, curcumin, melatonin, PQQ and vitamin D will also all inhibit TNF-alpha. We understand that some activities (ice baths, FIR saunas, and even cold showers, and baths) will suppress TNF-alpha, and have other beneficial physiologic effects. So, as a last thought on these things, why not?

Finally, this article contains a great deal of information that can inform you- the patient and can also inform your doctor. It is not information that is intended to diagnose or treat patients who have inflammatory bowel disease. As with all procedures and “meds” used in the practice of medicine, the dose, timing, mixture, and monitoring of symptoms and laboratory tests is crucial to obtain optimal results. Not to mention the cooperation between the patient and an experienced, board-certified Functional doctor.

Symptoms of low progesterone   (If you have read this and conclude this is the problem, here is something to hold you until you get to a Functional doctor-use my code:KimCrawford to get a group discounted rate)

You may have “heard” that premenstrual syndrome; PMS, or even the worse premenstrual dysphoric disorder (PMDD) is due to low progesterone. You might have read that one of the common signs of progesterone deficiency is premenstrual bloating. However, this article will review the common symptoms and then the signs of progesterone deficiency that are not often discussed. In fact, many symptoms (complaints) and signs (physical findings) related to low progesterone levels are simply not widely known, even amongst even the most knowledgeable Ob-Gyns or Endocrinologists. Many of the patients I personally see have been to an array of doctors who haven’t picked up on the fact that they are dealing with simple cases of low progesterone symptoms, which, in turn, cause a host of problems. All reversible. And yes, a Functional Internist who is an expert in female hormones is your best bet. Let’s start with the obvious.

Gynecological Issues

Women often attribute all of their premenstrual symptoms to what they call PMS. There are a host of symptoms, with low progesterone as the root cause, but they are not all categorized together. I’ll explain.  You might be having fertility issues. You might develop ovarian cysts. Most women and even most doctors believe that fibroids and endometriosis are estrogen-dependent. Not so. It’s the ratio of estrogen to progesterone that is important, so low progesterone can cause these issues too. Similarly, fibrocystic breast disorder can be caused by low progesterone.

Your libido is (mostly) controlled by your free testosterone level but progesterone also plays a role. Estrogen deficiency isn’t the only hormone that can cause hot flushes. Progesterone deficiency or cortisol excess (early adrenal fatigue) can also cause hot flushes. Lastly, mold and mycotoxin exposure can also cause hot flushes. I won’t go into these other little “nuggets of information” on this article, as they are off-topic. Let’s get started with the major gynecologic issues.

Menstrual Irregularities

During the luteal (second) phase of your menstrual cycle, your uterine lining (endometrium) is building up to receive a fertilized egg. This phase becomes shortened when you are progesterone deficient. Your periods might then be irregular due to progesterone deficiency. You might have some spotting right before your period and then some clots during your period.

The principal cause of irregular periods is the lack of normal ovulation. Lack of normal ovulation, where the egg is not released from the ovary- causes low progesterone because your body is not preparing for pregnancy by building up the endometrium. Other reasons for irregular periods can be PCOS, stress (high cortisol), or simply coming off of oral contraceptives. However, remember that an early “pre-menopause” can mean that you have lower-than-normal progesterone levels, with or without significant symptoms.

Heavy Periods

Approximately 50% of females who report heavy menstrual bleeding, do not meet the requirements of 80 mls (about 1/3 cup)  or more of blood “release” per menstrual cycle. Heavy menstrual blood loss usually includes clotting and having to change pads or tampons every two hours or more. Heavy bleeding is thought to result from imbalances in estrogen and progesterone, and is generally successfully treated with supplemental progesterone. If you are experiencing heavy periods, you will need a full work-up to exclude other causes of heavy menstrual flow such as polyps, endometriosis or adenomyosis (endometrium growing in the uterine wall), as well as other (less common) issues including bleeding or clotting disorders.


Another one of the signs of progesterone deficiency is premenstrual syndrome- PMS. Premenstrual syndrome is defined as life-disrupting physiological and/or psychological signs or symptoms which occur in the luteal phase of the cycle. Symptoms include headaches, cramps, fatigue, bloating, nausea and mood swings. When menses begins, symptoms will generally disappear. The reason PMS is thought to occur is due to the difference in hormone levels between estrogen and progesterone. Many women respond to progesterone supplementation, while others need a more varied approach-similar to women suffering from the more severe variant- PMDD.


Most women are aware of the typical symptoms of PMS. In fact, how many of us have experienced fluid retention (bloating), breast tenderness, or even a little bit of a mood swing? However, women with PMDD (less than an estimated 10% of the female menstruating population) have symptoms that can last all month. Not only that-the symptoms are a gross exaggeration of PMS symptoms. Mood swings are prevalent and severe. Depression brings on “fits” of crying or feelings of hopelessness. Often the most reasonable women experience intense anger and conflict with other people. Tension, anxiety, and irritability. No interest in your usual activities. Trouble concentrating. Fatigue. Appetite changes with binge eating. Not your ordinary PMS. This disorder is associated with measurable drops in serotonin levels, as well as exaggerated estrogen to progesterone dips and drops.  Treatment includes serotonin precursors, progesterone and more.

Breast Tenderness

Another sign of low progesterone is breast tenderness. This is a PMS symptom that will typically occur and then worsen during the mid to late luteal phase. Imbalances in estrogen and progesterone can worsen breast tenderness and pain.

Cyclic mastalgia is not considered as a part of PMS, even though it is indeed related to the menstrual cycle. It is bilateral, diffuse, poorly localized, and generally described as soreness that often radiates to the underarms and even down the arms. It occurs mostly during the luteal phase of the menstrual cycle due to increased water content in breast stroma caused by increasing hormone levels. Cyclic breast pain occurs more commonly in younger women, often will resolve spontaneously, and is classified differently than as being a part of premenstrual syndrome.


Bloating is a common sign of low progesterone. Studies have shown that, during the luteal phase, water and sodium retention increase with low levels of progesterone and high levels of estrogen. This occurs because the estrogen lowers what is called the “osmotic threshold,” for which water is reabsorbed in the body. The hormone ADH (arginine vasopressin) is responsible for the reabsorption of water into the bloodstream. When estrogen levels are high, this threshold is lowered, and therefore less water will be excreted through urine. This then causes the body to retain water and creates the sensation of bloating. It could be as little as noticing your rings are tight or as much as being unable to zip up your jeans. This looks and feels differently than the belly fat you start accumulating during pre-menopause.

Painful Periods

Dysmenorrhea (painful periods) is typically experienced as painful cramps before or during menstruation. Secondary dysmenorrhea is due to gynecological issues such as endometriosis or adenomyosis. What we’re discussing here is simply primary dysmenorrhea as a result of “normal” female anatomy. The cramps in the uterus are caused by high levels of prostaglandins.  Prostaglandins are a group of fatty molecules made at sites of tissue damage or infection. They control processes such as blood flow, the formation of blood clots, degree of inflammation, and even the induction of labor. Prostaglandins work in opposition to progesterone, so when progesterone decreases right before menstruation, prostaglandin levels will increase. This then causes uterine contractions, cramps and pain. Treatment is not necessary for “mild cramps”, but more severe cramps usually require prostaglandin inhibition. “Natural” ways to do this are with fish oils and curcumin supplements.

Ovarian Cysts

Ovarian cysts are sacs filled with fluid that are attached to or adjacent to the ovaries. Ten percent of women have ovarian cysts, which can be an “incidental finding” on pelvic exam or ultrasound, or a cause for pelvic pain and other symptoms. Cysts are usually classified according to whether they are a variant of the normal menstrual cycle, referred to as a functional or follicular cyst. Frequent follicular cysts can be one of the signs of low progesterone.

Ovarian cysts are considered “large” when they are over 5 cm and giant when they are over 15 cm.  Most cysts are benign and cause no pain, but others do cause pain as they sometimes don’t resolve with the menstrual cycle and then grow larger over time. Symptoms of an ovarian cyst are heavy cramping with abdominal pain, irregular periods, and pain during bowel movements.  In some studies, progesterone supplementation in the early stages of cyst growth reduced its size, ability to grow and sometimes induced ovulation.


Adequate progesterone is necessary for healthy fertility. Progesterone helps to maintain the integrity of the uterine lining so that a fertilized egg can implant. Without optimal progesterone, you are at a higher risk of miscarriage. Many studies have documented the benefits of administering progesterone to patients who are experiencing infertility to increase conception as well as to-term pregnancy rates. This leads us to the next logical topic; miscarriage.

First Trimester Miscarriage

It is critically important to have optimal progesterone levels for a healthy pregnancy. The first trimester of pregnancy is typically when most miscarriages occur. If progesterone levels are low, studies have found that those who are administered progesterone in the first trimester have a better chance of reducing their chances of miscarriage.

Metabolic Issues

Chronically low progesterone levels are often associated with low-grade depression, a topic we’ll cover soon. Low progesterone will lower serotonin levels. If you get sugar cravings, they are often due to low serotonin levels. If you crave sugar and feel happier after you eat an ice cream cone or cookie, this is likely a physiological fact. If you self-medicate your low serotonin levels with too much sugary food, you’ll gain weight, raise your blood sugar, and levels of inflammation in your body.

And it’s not just the serotonin. Low progesterone (in and of itself) is the beginning of the rise in the hunger hormones leptin and ghrelin. Ghrelin is an actual “hunger hormone”, stimulating your appetite but leptin is a bigger problem for most women. As leptin rises, your fat cells will “hold onto fat”, starting often with belly fat. This makes fat loss much more difficult if you are progesterone deficient.

Since progesterone helps to normalize thyroid hormones, it can lower those, causing your metabolic rate to drop. This will often be reflected in a lowering of your morning basal temperature as well as your energy levels. However, fatigue is more likely to occur due to another problem which I’ll discuss next.

Sleep issues

You need two brain chemicals (neurotransmitters) to help you fall asleep and then stay asleep for the night. The fall-asleep brain chemical you need is called GABA, and the stay-asleep chemical is our good friend, serotonin. When progesterone levels fall, so do levels of both GABA and serotonin. This then makes both falling and staying asleep more difficult. When these two neurotransmitters drop, women often get a poor night’s sleep which leads to daytime fatigue and, eventually, all sorts of other problems. Women’s sleep cycles have been studied in depth.

Many studies have found changes in sleep architecture across the phases of the menstrual cycle, with most sleep disturbances occurring in the luteal phase. In the luteal phase, women experience increased sleep onset and awakenings and lower sleep efficiency and quality compared to the follicular phase. Women in the luteal phase have less REM sleep and more non-rapid-eye-movement (NREM) sleep, with an increase in slow wave sleep (SWS) in particular. EEG (electroencephalogram) power density varies throughout the menstrual cycle, with the highest density of sleep spindles occurring in the luteal phase.

The luteal phase is also associated with elevated core body temperature, which could potentially interact with sleep processes to impact sleep quality. During the luteal phase, some women experience nocturnal PMS symptoms of discomfort, such as stomachache, backache, headaches, and nausea. And as a corollary, those with PMS are more vulnerable to sleep disruptions during the luteal phase. Women with PMS report having more unpleasant dreams, nocturnal awakenings, morning tiredness, and increased mental activity at night in comparison with women without PMS.

Several studies have shown that progesterone supplementation has a better ability to restore normal sleep when there was a disturbance in the night compared to the control groups. Progesterone administration seems to enhance sleep duration and sleep quality, mainly by improving slow-wave sleep (SWS). As an aside, let me mention that disturbed sleep and daytime fatigue are very common issues for all  of my women patients. I usually end up giving at least half of my patients integratives to raise their GABA and serotonin levels; not just supplemental progesterone. As a final note in this section; ongoing research is pointing to the increasing role of progesterone in regard to growth hormone and melatonin secretion as well. And yes, both of these carry implications for sleep as well.

Mood issues

We touched on the topic of mood swings during the discussion of PMDD. You might recall that as your progesterone levels drop, so too, do your serotonin levels. Serotonin is one of your happy neurotransmitters, so for some, this drop is enough to cause depressive symptoms. Don’t think that anti-depressants are the answer. Why wouldn’t you want to treat your mood issues more physiologically with progesterone and some serotonin precursors?

We also discussed the diminution of GABA levels in regard to sleep initiation. But GABA levels also control how much anxiety and even panic you’ll have to deal with as you move through peri-menopause and then menopause. However, the degree of symptoms you’ll experience as a result of decreased serotonin and GABA levels is a reflection of your “baseline” levels.

Anxiety is the experience of feelings of worry, fear, or at worst-panic attacks that can completely overpower aspects of your day. Progesterone has anti-anxiety effects due to its boosting relationship with GABA, your natural relaxation mood chemical. If your progesterone is low or you are not producing enough each cycle this can show up as anxiety because you are not producing as much GABA. This is often corrected with supplemental progesterone and pure GABA. A word of warning: if your doctor prescribes an anti-anxiety medication such as Xanax, run, don’t walk, to find a Functional Specialist that won’t give you prescriptions for highly addictive drugs.


Pain and discomfort cause feelings of stress and elevated cortisol levels. As described above, there are many ways that having low progesterone levels cause you discomfort- from cysts, to cramps, to PMS, to sleep disruption. Stress will lower dopamine levels, and this then causes irritability and can even contribute to a depressed mood. Low dopamine lowers GABA even further, thus compounding any anxiety issues you might have. We’re talking about close to half of a month of distressing symptoms, all due to a simple lack of progesterone!  Studies have found that there were significant improvements in mood and irritability due to progesterone administration compared to a placebo. And please do note: there are ways to naturally increase dopamine levels as well. Also note: oral GABA is destroyed by stomach acid and rendered ineffective.

Cyclical headaches

Cyclical headaches are defined as recurrent headaches which occur during the same time with each menstrual cycle. They are classified as a complication of PMS, and are one of the less common signs of low progesterone.  When progesterone is low, you are in (by definition) an estrogen-dominant state. Early to mid-luteal cyclical headaches are thought to be caused by the estrogen-dominant effect on cerebral blood vessels. These cyclical headaches are successfully treated with progestins (synthetic progesterone) in clinical studies. It would make sense that the more safe, bioidentical progesterone would be effective for these types of headaches. To make matters just that much more complicated, a small percentage of women get “estrogen-drop” headaches at the very end of their luteal phase, just as menses starts.


Speaking of headaches, we must differentiate cyclical headaches from migraine headaches which are also associated with low progesterone levels. Low levels of brain serotonin have been linked to migraines, accounting for the statistical increase in migraines reported by women with documented low progesterone levels. Indeed, bioidentical progesterone is an effective (partial) treatment for a select group of migraine sufferers. Recent studies have shown that, compared to a regular diet, a nutritional ketosis diet might also help to ears to be great for keeping migraines at bay. And speaking of headaches……


This is one I’ll bet you didn’t know about. While normal levels of progesterone and indeed the progesterone spike a week before your period can cause constipation which is immediately relieved when you get your period, if progesterone levels are low for your entire luteal phase, it’s a different story. It’s also a different story if you are pre-menopausal, with constantly low progesterone levels or post-menopausal, with inadequate progesterone replacement dosing.

Numerous studies suggest that the interplay between progesterone and the serotoninergic system could underlie altered bowel habits in women. Serotonin (5-hydroxytryptamine or 5-HT) is known to play a key role in the motor function of the GI tract by stimulating smooth muscle contractility. It has been shown that progesterone administration increases 5-HT levels by decreasing the level of  5-HT reuptake, monoamine oxidase mRNA expression, and increasing the availability of 5-HT precursor, tryptophan. This effect of progesterone on the serotoninergic system is not surprising because 5-HT promotes peristalsis. The moral of this story is that curing chronic constipation in women is often a matter of simply restoring progesterone and serotoninergic balance.

Memory issues

It astounds me that so many women who I speak with about hormones think that it is “normal” to start becoming forgetful and foggy-brained at age 40! However, being foggy-brained and having memory lapses can indeed by directly caused by progesterone deficiency. We don’t think of progesterone as a sleep supplement or a brain supplement, but in fact, BI progesterone is just that. As with so many hormonal issues, this is also complex.

Studies demonstrate that increased levels of GABA increase our cognitive performance. Other studies demonstrate that serotonin is important for memory consolidation and storage in the hippocampus.  In fact, there is a higher incidence of dementia in people with chronically low serotonin levels. And finally, progesterone is neuroprotective in animals and women. There is a firm biological rationale for the view that progesterone plays an important role in brain function and there are discernible effects on cognition in animals. Moreover, progesterone exposures are linked to patterns of brain activation during cognitive processing in women.

However, if I am to be scientifically accurate; despite my bias, it remains to be shown that endogenous progesterone or exogenous progestogens exert clinically meaningful effects on short-term or long-term cognitive function in healthy women.


Studies are ongoing to investigate the role that progesterone may have in preventing or lessening seizure activity. As noted above, it is thought to be neuroprotective in animals and in women. As such, it is being investigated as a modality to aid in the treatment of traumatic brain injury.


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