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.

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.


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