Inflammatory bowel disease. Chances are, you or someone you know has it. Three million Americans are believed to have IBD, which includes ulcerative colitis or Crohn’s disease. It’s an ugly condition that has no cure by mainstream medical methods. However, integrative and functional medicine can bring these diseases under control and even completely into remission. Many people have had their ulcerative colitis or Crohn’s go into remission without relying on lifetime immunosuppressant drugs or surgery. Integrative and functional medicine investigates the root causes of inflammatory bowel disease and shuts down inflammation in the gastrointestinal tract so the gut is happy, healthy, and disease-free.

Read a real-life success story of how diet, gut microbiome supplements, and digestive enzymes reversed Crohn’s disease.


My grandmother had Crohn’s disease. I was a little girl when my mom explained her diagnosis to me. My grandmother looked so strange with the steroid-induced weight gain in her face. But that wasn’t enough, she continued to have symptoms. She had to get an ileostomy, where surgeons make an opening to the outside of the body directly from the small intestine. They bypassed her colon and she had to use a bag for poop to collect outside the body. She almost died during the procedure due to septic shock. But otherwise, she lived with the ileostomy bag without further inflammatory bowel problems. Now that I know about food sensitivities, and that many in my family are sensitive to dairy, we often recall my grandmother’s penchant for ice cream. It may have been a key trigger in her Crohn’s disease that was never discovered or treated.


Crohn’s disease and ulcerative colitis are inflammatory bowel diseases that have no true characteristic medical signs and symptoms except for chronic intestinal inflammation. There is often pain, diarrhea, weight loss, malnutrition, and rectal bleeding. The two diseases aren’t all that different really. It’s just inflammation here or there. IBD symptoms come and go, meaning there are times of extreme flare ups, and there are times of relative quiet or remission. IBD has been considered autoimmune, meaning the immune system is mistakenly attacking a person’s own tissues. However, recent evidence suggests IBD isn’t an autoimmune attack. It’s an overactive immune attack against normally harmless microbes, viruses, or foods, which accidentally damages gut tissues. When the disease progresses, it can venture outside of the gut, setting off inflammation and damage to the joints, for example. As if being sick with intestinal inflammation wasn’t enough, there can be joint inflammation, too (and more)! Ugh.


The Usual UC and Crohn’s Treatments Aren’t Good Enough

The standard treatment for IBD is a lifetime of medications to control intestinal inflammation.1 These include anti-inflammatory drugs like mesalamine (Asacol), immune-suppressing drugs like azathioprine (Imuran), and/or biological therapies like Adalimumab (Humira), or infliximab (Remicade) to shut down the immune system.2

The sad thing is that it doesn’t work very well. Inflammation keeps getting worse. Medications keep getting stronger (as well as their side effects).3 And once you’re at the end of the line with medications, the next step is surgery, to remove the inflamed part of the gastrointestinal tract. Unfortunately, that hardly works either! 50% of Crohn’s patients who get bowel surgery have a relapse within two years.1


Another Perspective on IBD Treatment


Integrative and functional medicine practitioners look at this condition from a WHOLE other perspective. What is causing the inflammation? Why is the immune system so angry and aggressive? Using this approach, they look for underlying causes of the disease process. Some of the absolute most important areas to investigate in IBD are: diet, food sensitivities and allergies, the gut microbiome, other infections, nutrition, and leaky gut. Then they try to alleviate or balance those areas so the body can return to a healthy balance.


Children with ulcerative colitis or Crohn’s disease are ideal candidates for an integrative and functional medicine approach. No one wants a child to be on immunosuppressant medications. And the disease threatens their nutrition and growth. It worries me that a child with inflammation of the intestines could be given powerful medications and even worse, lose a portion of their GI tract, while underlying causes go unnoticed by all of their medical providers.



Food Is King


Diet is everything when it comes to an inflamed bowel. It is estimated that we eat almost one ton (or 2,000 pounds) of food each year. What you eat and drink constantly sends messages to your gut, your heart, your blood, brain, and joints. Those messages can be healthy, life-sustaining, anti-inflammatory messages. Or they can be damaging, harmful, disease-causing, pro-inflammatory messages. Not all people with IBD have the same trouble with certain foods so each person needs a diet customized for him or her. In general, we want to start with a whole-foods, plant-based diet, with grass-fed or free-range proteins. We want to get rid of all sugar and refined carbohydrates (packaged foods like crackers, pasta, sweets, chips, etc).


Dr. Jill Carnahan is a pro when it comes to putting IBD into remission. In her blog, “Cure Inflammatory Bowel Disease (IBD) Without Medication” she recommends the Specific Carbohydrate or elemental diets to reset the gut. On the SCD, patients eliminate most carbohydrates including grains, starches, dairy, and sugars with only specific carbohydrates that require minimal digestion allowed. Fresh fruit, most vegetables, grass fed meat, and wild-caught fish are allowed while starches, grains, and processed or canned foods are not. The SCD diet has been shown to improve clinical and laboratory measures of Crohn’s disease and induce beneficial changes in the microbiome.4,5


You can make a lot of changes to your diet by yourself or with an integrative and functional nutritionist or health coach. However, many are hidden. You may need to dive deeper to figure out specific foods that are giving you trouble. That leads us to food sensitivities…


Are The Foods You Eat Everyday Making You Sick?

Many, many people are sensitive to foods and don’t realize it because they are eating gobs of those foods every day. The most common culprits are wheat, dairy, soy, eggs, and corn. Almost everyone feels better when they take wheat and dairy out of their diets. An elimination diet is the gold standard method for figuring out food sensitivities. Remove the food from your diet for 4-8 weeks. Then eat a serving or two on a single day and watch for symptoms. Some people have trouble with nightshades. Those include potatoes, tomatoes, peppers, eggplant, and more.

Testing is available to help figure out food sensitivities but the immune system is complex and testing is imperfect. That’s why I recommend that people first collect blood for a food sensitivity test and then start on an elimination diet. That is the most thorough way to assess food sensitivities.

People with IBD could have food allergies that have been undetected. Unlike food sensitivity, true food allergy often presents with telltale symptoms like hives or anaphylaxis. The problem is that it can also be overlooked because it might just cause diarrhea. Food allergies can contribute to asthma and eczema. If this sounds like you, consider an IgG and an IgE test to look at both food sensitivities and food allergies.

Most integrative and functional medicine practitioners take all of their IBD patients off of gluten and dairy. These simple dietary changes can transform health. Gluten sensitivity or celiac disease can cause colon or small intestine inflammation.  Test for celiac disease using both blood tissue transglutaminase antibodies and a test for the celiac genes.

FOR PRACTITIONERS: Are you teaching patients about food sensitivities in your clinic? Use this patient prep video to educate and motivate patients to test and remove foods from the diet for better health.

Building a Strong Gut Microbiome and Fighting Infection


To reduce IBD symptoms, the gut microbiome (the bacteria, fungi, and other microorganisms that live in the gut) are absolutely critical. Study after study shows us that the microbiome is fragile in people with IBD. Their gut bacteria are imbalanced.6 Sometimes it’s even an inappropriate immune attack on good bacteria that causes inflammation.7 I have seen cases where antibiotics triggered an IBD flare-up. And studies show that probiotics– which modulate the microbiome- help in IBD. This means that the microbiome is running the show. For me, IBD is a synonym for a disturbed, unhappy, and fragile microbiome. Everyone with IBD needs to put significant attention into the health of their gut microbiome.


Stool testing is an essential tool for getting rid of any infections or imbalances that contribute to IBD. As a medical education consultant working at laboratories, I have seen many IBD patients with pathogenic bacterial infections,7 parasites, Helicobacter pylori, opportunistic bacterial overgrowth such as Klebsiella, or Candida overgrowth. An advanced stool test will also measure your friendly gut bacteria, the ones that protect you from infections and make your immune system happy. If you have IBD, you do not want to miss this information! Mainstream medical doctors will not even run an advanced stool test on you. They might look for one pathogen, like Clostridium difficile, and call it done. They certainly don’t run tests to see how your good bacteria are doing. I recommend the GI-MAP from Diagnostic Solutions but there are others from Doctor’s Data or Genova Diagnostics.

There is a time and a place for herbal antimicrobials, and occasionally antibiotics, in patients with IBD. But these should be given with extreme caution. Antibiotics can put an IBD patient into a downward spiral by clear-cutting their good gut bacteria. In IBD, the microbiome is very fragile and a small change can have exponential consequences. That’s why I suggest using advanced stool testing to measure the gut microbiome before treatment. Use testing to monitor the outcomes of dietary and nutritional treatment, then tweak the protocol accordingly. The key to IBD is harnessing the power of the gut microbiome to turn off inflammation. That means diarrhea, abdominal pain, and bleeding go away and you can participate in normal life without being tethered to the bathroom.

FOR PRACTITIONERS: Are you teaching patients about gut health in your clinic? Use this patient prep video to educate and motivate patients to run the stool test and follow your recommendations for better gut health. Your patients will learn about a patient with ulcerative colitis who avoided surgery and got her life back after her doctor ran a stool test and addressed the findings. Or you can download our FREE customizable one-page patient education handout on gut health!

Heal and Repair the Gut with Excellent Nutrition


One of the worst effects of ulcerative colitis and Crohn’s is malnutrition. With intestinal inflammation causing swelling, pain, ulcers, and redness, the small intestine can’t do what it was meant to do- absorb nutrients! And inflammation of the large intestine (colon) means that you can’t absorb fluids and electrolytes. On top of all of this, pile on a reduced appetite and pain with eating, and you have a perfect set-up for malnutrition. If your body can’t get protein, healthy fats, complex carbs, vitamins, and minerals, then the gut cannot repair itself. It can’t heal. The body loses energy and fatigue sets in. The immune system can’t perform properly. And it sends the person into a more serious state of chronic illness that is more challenging to recover from.



Put Out the Raging Fire In the Gut

People with Crohn’s disease or ulcerative colitis have inflammation of the intestines- it is like having a raging fire burning in the gut. There are things you can take to lower inflammation to get immediate relief. Medications like Asacol or prednisone can try to put out the fire. There are herbs to lower inflammation, such as aloe vera, curcumin, resveratrol, or quercetin. UltraInflamX is a nutritional anti-inflammatory protein powder that can calm down inflammation in the gut. But the number one most important thing is to look for the causes of the raging fire of inflammation. This brings us back to diet- since it’s a surefire source (and a HUGE source) of many questionable foods and chemicals that can set fire to the gut. Anti-inflammatory diets can be helpful but each person with IBD often has specific sensitivities and triggers so he or she will need a customized diet to ward off flare-ups.

This is one of my main beefs with mainstream medical approaches to IBD. They are just covering up inflammation. With medications, they are putting a band-aid on the symptoms of IBD. When those stop working, they surgically remove the parts of the intestines that are inflamed. And even surgery doesn’t fix the problem in 50% of Crohn’s patients. With such poor results, why don’t they look for the causes of inflammation in the first place? Then people could avoid potentially harmful medications and keep their guts intact.



Reset the Immune System by Healing Leaky Gut

Intestinal permeability, or leaky gut, is pretty much a given in people who have ulcerative colitis or Crohn’s disease because inflammation is damaging the GI tract. The lining of the gut is a critical immune defense7 because it keeps things from the outside world (food, drinks, bacteria, fungi, parasites) in the gut, where they belong. In leaky gut, the intestinal lining develops tiny holes in it and things from the outside world “leak” into the bloodstream, where they don’t belong. When undigested food proteins or microbes or chemicals leak into the bloodstream, they can set off a whole other immune cascade, but causing systemic inflammation this time. It’s not pretty. Most clinicians assume that there is leaky gut in IBD and it is a major keystone when restoring gut health, especially if there are other signs of systemic inflammation, such as inflamed joints, heart disease, diabetes, or pain.

FOR PRACTITIONERS: Are you teaching patients about leaky gut? Use this patient prep video to educate and motivate patients to test and address leaky gut for better overall wellness. They will see a powerful animation that shows how leaky gut causes systemic inflammation. If leaky gut doesn’t get identified and corrected, other treatments may have little to no benefits.

Don’t Give Up on Your Gut

Harmful medications and surgery can be avoided. Find an integrative and functional medicine practitioner to help you address the root causes of Crohn’s disease or ulcerative colitis. They can also tailor a pharmaceutical protocol to get the inflammation under control in the short-term, without putting you on lifelong immune-suppressing medications.

Find an integrative and functional medicine clinician near you and put ulcerative colitis or Crohn’s disease in its place.



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  2. Jean L, Audrey M, Beauchemin C, Consortium O. Economic Evaluations of Treatments for Inflammatory Bowel Diseases: A Literature Review. Can J Gastroenterol Hepatol. 2018;2018:7439730.
  3. Adegbola SO, Sahnan K, Warusavitarne J, Hart A, Tozer P. Anti-TNF Therapy in Crohn’s Disease. International journal of molecular sciences. 2018;19(8).
  4. Dubrovsky A, Kitts CL. Effect of the Specific Carbohydrate Diet on the Microbiome of a Primary Sclerosing Cholangitis and Ulcerative Colitis Patient. Cureus. 2018;10(2):e2177.
  5. Suskind DL, Cohen SA, Brittnacher MJ, et al. Clinical and Fecal Microbial Changes With Diet Therapy in Active Inflammatory Bowel Disease. Journal of clinical gastroenterology. 2018;52(2):155-163.
  6. Lopez-Siles M, Enrich-Capo N, Aldeguer X, et al. Alterations in the Abundance and Co-occurrence of Akkermansia muciniphila and Faecalibacterium prausnitzii in the Colonic Mucosa of Inflammatory Bowel Disease Subjects. Frontiers in cellular and infection microbiology. 2018;8:281.
  7. Sartor RB. Mechanisms of disease: pathogenesis of Crohn’s disease and ulcerative colitis. Nature clinical practice. 2006;3(7):390-407.


Cass Nelson-Dooley, M.S.

Cass Nelson-Dooley, M.S.

Cass Nelson-Dooley, MS, is a researcher, author, educator, and laboratory consultant. She studied medicinal plants in the rain forests of Panama as a Fulbright Scholar and then launched a career in science and natural medicine. Early on, she studied ethnobotany, ethnopharmacology, and drug discovery at the University of Georgia and AptoTec, Inc. She joined innovators at Metametrix Clinical Laboratory as a medical education consultant helping clinicians use integrative and functional laboratory results in clinical practice. She owns Health First Consulting, LLC, a medical communications company with the mission to improve human health using the written word. Ms. Nelson-Dooley is an oral microbiome expert and author of Heal Your Oral Microbiome. She was a contributing author in Laboratory Evaluations for Integrative and Functional Medicine and Case Studies in Integrative and Functional Medicine. She has published case studies, book chapters, and journal articles about the oral microbiome, natural medicine, nutrition, laboratory testing, obesity, and osteoporosis.