Inflammatory bowel disease doesn’t have to be a life sentence. It doesn’t mean you have to spend your life on immune-suppressing medications or eventually have a part of your colon or GI tract removed. Ulcerative colitis or Crohn’s disease can be put into remission- without medications. How?

You can have a happy, healthy gut if you make the diet, lifestyle, and supplementation changes that are needed to reverse Crohn’s disease or ulcerative colitis. You and your practitioner will need to drill down to the root causes of your inflammatory bowel disease. Integrative and functional medicine has made strides in improving treatments for gut inflammation.

If you or a loved one is suffering from Crohn’s disease or ulcerative colitis, you need to know about the many tools, tests, and treatments available to help calm down inflammation in the GI tract. Here is a real-life success story of “Roxanne,” who had terrible diarrhea and a recent Crohn’s disease diagnosis, which was reversed using a functional medicine approach.

Refer to my first blog on this topic for more details, “Ulcerative Colitis and Crohn’s: Address the Root Causes of Inflammation and Bring About Remission Without Drugs or Surgery.

We are grateful to our sponsors for making this blog possible: Metabolic Maintenance and Diagnostic Solutions Laboratory.

A Crohn’s Disease Vanishing Act

Roxanne was a 45-year-old woman struggling with recurrent Clostridioides difficile infection, diarrhea, multiple antibiotic rounds, abdominal pain, urgency, gas, bloating, and blood in her stool. Her gastroenterologist detected inflammation in her colon and gave her a diagnosis of Crohn’s disease and a prescription for Remicade infusions. Roxanne was not enthusiastic about taking immune-suppressing medications during the COVID pandemic, which was only three months underway. She wanted better answers about her chronic gut symptoms as well as an effective solution for her Crohn’s inflamed bowel. She sought out an integrative and functional medicine team who ran the GI-MAP stool test on her. The test found depleted good bacteria and very high levels of Klebsiella species in the stool as well as other opportunistic bacteria.

Roxanne was given a low-allergen diet for her Crohn’s, herbal antibacterials, digestive enzymes, and high-dose probiotics. Within one month of treatment, Roxanne had formed stools “for the first time in forever.” After four months of her functional medicine treatment, she was “feeling awesome.” She had no abdominal pain, regular stools, she no longer needed her medications for abdominal cramps, and she was at a healthier weight. Follow-up colonoscopy showed no sign of Crohn’s disease with healthy mucosa in the colon and terminal ileum. This case shows that an integrative and functional medicine approach to Crohn’s disease can identify root causes, relieve gut symptoms, turn off colon inflammation, and help to reverse damage to the GI as measured by colonoscopy.

Inflammatory Bowel Disease

Crohn’s disease and ulcerative colitis are inflammatory bowel diseases that have no true characteristic signs and symptoms save for chronic intestinal inflammation, which is evident by colonoscopy, biopsy, and radiographic analyses. 1.6 million Americans are believed to have IBD.

Crohn’s disease symptoms include:

  • Diarrhea
  • Abdominal pain
  • Fatigue
  • Weight loss
  • Anemia
  • Malnutrition
  • Rectal bleeding
  • Fever
  • Recurrent fistulas
  • Extraintestinal manifestations, such as joint inflammation and pain1

The usual UC and Crohn’s treatments aren’t good enough.

Crohn’s is usually a chronic, progressive, and destructive disease.2 Medications and surgery are the mainstay treatments for Crohn’s and ulcerative colitis. Anti-inflammatories, immune-suppressants, and then biological therapies are used to control bowel inflammation.2,3

If inflammation cannot be kept down, surgery removes the diseased portion of the gastrointestinal tract. Patients have a 40-55% risk of major abdominal surgery over ten years and a risk of 35% for a second bowel resection.2 Even surgical intervention does not remedy the disease however, as 50% of Crohn’s patients relapse within five years.2

Given the poor prognosis and side effects related to standard treatment of Crohn’s disease and ulcerative colitis, it is understandable that patients like Roxanne want better treatment options – and better outcomes. Clinicians and patients should seek out other options including diet, supplements, and integrative and functional testing to put IBD in remission without medications.


Roxanne’s Unhappy Gut

Roxanne was a 45-year-old white female who had diarrhea 10-15 times daily in May of 2020. She weighed 155 pounds. She said it felt like a raging fire in her gut. Everything she ate went right through her, she said. She joked that her stools looked like a Jackson Pollack painting (liquid and stringy). She was too exhausted to cook and said the illness had “stomped her to the floor.” GI symptoms and back pain kept her from walking her dog.

Roxanne also complained of abdominal pain, occasional urgency after eating, gas, bloating, and blood in stools. For abdominal cramps, she was taking dicyclomine and hyoscyamine. Two months earlier she had had a sinus infection which was treated with antibiotics and her GI had been acting up ever since then. Roxanne was taking Phillips Colon Health Probiotic 2 times a day (1.5 billion CFUs) and Florastor twice daily (250 mg).

Roxanne was prescribed antibiotics once or twice a year, either for an upper respiratory infection, a sinus infection, a skin lesion due to an ingrown hair, or a surgical procedure on her back that required antibiotics.

Roxanne ate a standard American diet. She knew that she did not eat healthy and she needed to make better diet choices. She noticed that she reacted to foods in her diet, sometimes immediately, sometimes the next day. She did cook at home sometimes. She drank water only. She admitted to binging on junk food on her bad days, which outnumbered her good days. She would let herself get very hungry and then be too weak to eat. She didn’t report drinking alcohol. Roxanne’s grandmother said she had colitis, although it was diagnosed as irritable bowel syndrome.

Roxanne had been under extreme levels of stress for the past year. A 5-year-long, stressful relationship had ended seven months earlier and she had been in psychotherapy. When she was under stress, it affected her eating habits and diet choices. At the time of her case, she was not employed, having sufficient independent wealth to cover her costs. Also at the time of her initial presentation, the floors in her home were being remodeled and her house was chaotic.

Roxanne would get epidural steroid injections for back and neck pain.  She was under chiropractic care. She had had ablation done on lumbar vertebra 3-5. Roxanne had a hysterectomy three years earlier due to endometriosis, which had been troubling her four years before that. She had been taking hormone replacement therapy (estradiol) since the hysterectomy.

Antibiotics, Diarrhea, and Recurrent Clostridioides difficile Infections


Since 2015, Roxanne had had six test-positive infections with Clostridum difficile (now known as Clostridioides difficile) and with it, multiple rounds of vancomycin antibiotics. She had also been treated with vancomycin antibiotics for “probable” C. difficile at least four times. Each time she was given a very long vancomycin taper. Within a few doses she would feel better and the C. difficile symptoms would disappear. But if she would get antibiotics for any another reason later on, the C. difficile would come back, and the cycle of infection and antibiotics would continue.

Roxanne’s downward spiral started with a hospital emergency room visit, which was believed to be due to a skin Staphylococcus infection (not confirmed). The wound was lanced and she was given the antibiotic clindamycin. She said it made her “dog-sick” after a few days, but she finished the antibiotic course anyway. She then was diagnosed with C. difficile and it took her months to overcome it. She lost a lot of weight, going down to 117 pounds, and felt that she was on death’s doorstep.

Roxanne’s previous colonoscopies over three years had been normal except for a couple of hyperplastic polyps. Her gastroenterologist had told her at one point that she had post-infectious irritable bowel syndrome, but otherwise had not diagnosed her with either irritable bowel syndrome or inflammatory bowel syndrome (IBD). He diagnosed her with: change in bowel habit (787.99 -R19.4), diarrhea (787.91), and Clostridioides difficile infection (A04.72), generalized abdominal pain (789.07-R1.84), and personal history of colon polyps (V12.72 – Z86.010).

During the current flare-up, Roxanne’s test showed a high fecal lactoferrin, positive C. difficile genes, but negative C. difficile toxins. Fecal lactoferrin is a marker of gut inflammation. Roxanne’s gastroenterologist assumed Roxanne had another C. difficile infection given her history and the high lactoferrin and ordered a long vancomycin taper to last 5-6 weeks, as well as a colonoscopy.

Colonoscopy Results Point to Crohn’s Disease

Roxanne’s colonoscopy showed inflammation of the colon suggestive of Crohn’s disease. Her exam showed moderate aphthous ulceration in the ascending and transverse colon suspicious for Crohn’s disease. Other findings included sigmoid diverticulosis, erythema in the rectum, a sliding small hiatal hernia in the esophagus; non-erosive gastritis in the stomach; and erosions and erythema of the mucosa in the duodenal bulb. The terminal ileum was normal.

Her gastroenterologist said the high levels of inflammation in the colon made him suspect Crohn’s. The doctor that did the colonoscopy diagnosed her with Crohn’s disease and said this was the actual cause of her current problems, not C. difficile.

Her team recommended that she begin Remicade (infliximab) for treating her Crohn’s. This biologic medication blocks TNF-alpha, an inflammatory cytokine, to suppress inflammation. Her doctor suggested that if she immediately started on Remicade, she likely would no longer have trouble with C. difficile infections. He believed Crohn’s was making her susceptible to C. diff or imitating it, which was why her tests were sometimes negative.

The diagnosis reaffirmed Roxanne’s desire to seek other experts for her colon inflammation. She wanted to keep immune-suppressing medications and surgeries as a last resort for treating her Crohn’s disease. She found an integrative and functional medicine practitioner in her area who ran a GI-MAP stool test and a battery of other tests.


GI-MAP Stool Test Results for Crohn’s Disease


The GI-MAP stool test is popular among integrative and functional medicine practitioners to detect infections, microbiome disturbances, inflammation, and immune dysfunction in the gut. It uses quantitative PCR to measure genomic material of a wide array of pathogens, opportunists, and commensals in stool.

Roxanne’s GI-MAP stool test showed no Clostridioides difficile, nor any other pathogens in her stool.

Roxanne’s commensal bacteria were very low, consistent with recent antibiotic treatments.


The test showed that Roxanne had overgrowth of opportunistic bacteria called Klebsiella species and Klebsiella pneumoniae. This bacteria can cause Crohn’s colitis.4

Roxanne’s stool test showed a low fecal calprotectin. Calprotectin is a gold standard marker for inflammation in the gut lining. It’s normally a differentiator between IBS and IBD. In someone with inflammatory bowel disease it should be very high, especially during a flare-up. It was surprising that Roxanne’s calprotectin was normal. Other markers of digestive health were mostly normal and no occult blood was detected in her stool specimen.

Other testing (not shown here) revealed high thyroid hormone and high testosterone levels. Blood lead levels were normal.

Crohn’s Treatment with Diet and Digestive Support Supplements

Roxanne was diagnosed with insufficiency dysbiosis, or a lack of good bacteria. She had opportunistic bacterial overgrowth. Her integrative and functional medicine practitioner prescribed digestive enzymes such as GluDaZyme by Metabolic Maintenance (1 cap with meals), probiotics at 100 B CFUs twice daily, and antimicrobial herbs for dysbiosis, such as Happy Belly from Metabolic Maintenance (two caps three times daily). She was to follow this treatment for four months.

Roxanne began a low-allergen, anti-inflammatory diet for Crohn’s disease. Her clinician recommended avoiding white bread, rice, pasta, gluten, dairy, sugar, and soy. She suggested avoiding corn, but said rice noodles were okay as a pasta substitute. She was advised to eat more healthy animal proteins. Her doctor told her to read labels and check everything for gluten. The clinician asked her to wean herself off of coffee, if possible, especially to avoid dairy creamer. After a number of months of food elimination, Roxanne would be able to reintroduce the foods one at a time and monitor for gut symptoms.

To feed and grow her good gut bacteria, the practitioner told her to increase bananas, asparagus, garlic, apples, legumes, kefir, flaxseed, leeks, and onions. She was encouraged to eat more fermented foods, cruciferous vegetables (like broccoli, cauliflower), and to eat more fiber to build good colon bacteria.

Roxanne felt the bread removal would be the biggest challenge for her. Roxanne said, “My brain has been begging my body to ask my brain to please eat healthier for a long time. The idea that I could feel normal again is a good motivator.” She avoided ultra-processed junk food, basically anything in a box or a bag.

Healthier Bowels, No Abdominal Pain, and Feeling Great with an Integrative and Functional Medicine Treatment for Crohn’s


Within 11 days of starting her supplements and dietary changes, Roxanne said that she “had a normal stool for the first time in forever.” This was even after having coffee!


She said the first week of diet changes and supplements was super difficult but she was starting to get the hang of eating and taking pills, eating and taking pills. She was enjoying lots of salads and vegetables. She noted that she didn’t feel as stressed about her ex-boyfriend and thought her brain might be clearing up, too.

She was no longer taking dicyclomine and hyoscyamine for abdominal cramps. She didn’t need them anymore. Stools continued to get more normal or formed, instead of liquid.

“I feel SO much better! I can’t believe I let myself get into such a state with food and how easy (and agonizingly difficult) it is to eat good food. That bread was a killer.”

During this time, Roxanne was under a lot of pressure from her gastroenterology team, totaling about 4-5 practitioners. They wanted her to begin Remicade as soon as possible for her Crohn’s disease. They insisted that she go back in to be monitored because of her serious condition. However, she was very reluctant to begin Remicade infusions and wanted to see if she could cure her Crohn’s disease without medications.

After a month of her Crohn’s treatment protocol, Roxanne said she felt 75% better. She noticed, “If I don’t eat well, like eat all my meals and supplements, I don’t feel as good the next morning.” When she would cheat on her diet, she would feel symptoms coming back. So, she was following her protocol as closely as she could, with occasional cheats of a slice of cheesecake or gluten-free thin mints. She remarked, “Good food is starting to taste good. It’s not so bad after all.” She said she was starting to enjoy the taste of fruit.

She was gradually losing weight and was happy about it. She noticed that she was eating a lot of food but casually dropping a pound here and there. She weighed 145 pounds. Her goal was to weight 135 pounds, which was a healthy weight with good muscle mass for her.

She was thrilled because she felt so much better. She had almost no abdominal pain except for one or two spots, where her gastroenterology team said the most intestinal damage was. And even for those spots, she said, the pain was faint.

Roxanne said she was avoiding the “bread-rice-pasta monster” and staying away from the cookies and the bakery at the grocery store. Otherwise, all of the foods she ate before her treatment were acceptable for her diet.

After four months of a functional medicine treatment, Roxanne said she was feeling great! She no longer had any abdominal pain whatsoever. She was still taking her probiotics, digestive enzymes, and antimicrobial herbs. She was down to 139 pounds and jokingly commented, “I feel awesome and I look pretty damn good, too.” She was successfully following her elimination diet (also known as an exclusion diet), but still cheated with dairy. She noticed that if she ate foods that she shouldn’t, she would feel bad and her stool would be loose or liquid the next day. She tried hard not to cheat on her diet.


Follow-up Colonoscopy Showed No More Crohn’s Disease Inflammation


Six months after starting a functional medicine treatment for Crohn’s disease, Roxanne’s colonoscopy showed that there was no sign of Crohn’s disease anymore. There was no evidence of active colitis or of microscopic colitis. There was normal mucosa throughout the colon and in the terminal ileum. However, there was still mild diverticulosis of the sigmoid colon and small internal hemorrhoids. The gastroenterologist told her she no longer had Crohn’s disease. She recommended that Roxanne return for her next colonoscopy in five years to follow up on her history of colon polyps.



In this case, a 45-year-old woman who ate a standard American diet high in ultra-processed foods was caught in a downward spiral of C. difficile infection, antibiotics, diarrhea, and abdominal pain with an eventual diagnosis of colon inflammation and Crohn’s colitis. In an effort to avoid conventional treatments, she sought out an integrative and functional medicine approach to Crohn’s. Stool test results showed a depleted gut microbiome and opportunistic bacterial infection, especially high for Klebsiella species. She adopted a Crohn’s diet free of gluten, dairy, soy, corn, and sugar. She took herbal antibiotics, probiotics, and digestive enzymes. These diet changes and supplements led to rapid improvements. Stools became more formed, abdominal pain faded away, and medications were no longer needed. Follow-up colonoscopy showed that inflammation in the colon was greatly improved. She no longer had a Crohn’s diagnosis and was told to return for monitoring in five years.

Gut Microbiome Changes in Inflammatory Bowel Disease

Commensal gut bacteria

Roxanne had a long history of antibiotic use. After a Staph infection and an antibiotic treatment, she developed a Clostridioides difficile infection that recurred at least six times. The sheer amount of antibiotics she took, and continued taking every time she had a C. difficile infection, likely killed much of her beneficial bacteria and left her vulnerable to reinfection. The gut microbiome is well known to provide “colonization resistance,” or to prevent pathogenic infections. Roxanne had lost these defenses.

Good gut bacteria play a fundamental role in the development of inflammatory bowel disease.5 Antibiotics, which kill beneficial bacteria, can influence inflammatory bowel disease.6 Imbalances in the microbiome and reduced gut microbe diversity have been seen in patients with IBD, as well as an aberrant response to otherwise normal gut bacteria.7

Clostidioides difficile in IBD

C. difficile is a bacterium that lives in the human gut. It is a common hospital-acquired infection. Antibiotics are the most likely trigger for developing a C. difficile infection.8 People may have no symptoms, varying degrees of diarrhea, and even life-threatening colitis or death.9 C. difficile is a common complication of IBD and can lead to flare-ups of IBD.8 It has similar symptoms to IBD and like IBD, it disturbs the gut microbiome.

Testing for C. difficile has limitations and there is no single test adequate for diagnosing and confirming C. difficile infection. This explains why Roxanne’s practitioners struggled to diagnose her recurrent C. difficile infections. In IBD patients who have C. difficile infection, treatments may not work and it increases the risk of hospitalization, surgery, and death. Vancomycin is the first-line treatment for managing C. difficile infection in IBD.8

Because Roxanne was positive for C. difficile so many times, it’s possible she had been carrying it for years. While symptoms would go away with 5–6-week treatments with vancomycin, it’s possible that the organism wasn’t fully eradicated. However, C. difficile was not detected on the GI-MAP test, suggesting that the vancomycin treatment she had been on at the time effectively killed C. difficile.

Roxanne’s gastroenterology team had repeatedly treated and suspected C. difficile, but her case suggests that there was much more involved. The GI-MAP stool test showed significant bacterial overgrowth in Roxanne’s gut, even though she was taking vancomycin. It suggests that microbes in her gut like Pseudomonas and Klebsiella were resistant to that antibiotic.4,10 These are easily missed by conventional tests.

Opportunistic bacteria Klebsiella and Pseudomonas

GI-MAP testing showed an extreme overgrowth of Klebsiella species and Klebsiella pneumoniae. Klebsiella pneumoniae has been implicated as a causative agent of IBD.4 It has been identified as having a key role in Crohn’s disease gut and joint tissue damage.11 Klebsiella may have been an explanation why recurrent antibiotic treatment (for C. difficile) could not resolve Roxanne’s gut symptoms. This pathogen is commonly isolated from the GI tract of individuals with IBD.4,11 Furthermore, IgG antibodies to Klebsiella pneumoniae serotypes are commonly elevated in UC and Crohn’s patients.12

Roxanne showed high Pseudomonas species in her stool. Pseudomonas species can be opportunistic pathogens, causing epidemic diarrhea, rectal abscess, and necrotizing enterocolitis in the gut.  Though not detected in her case, the individual species Pseudomonas aeruginosa can cause antibiotic-associated diarrhea in immune-compromised patients. It can cause diarrhea, rectal bleeding, and elevated inflammatory markers. It is often seen together with Clostridioides difficile.10

Dietary Considerations for Crohn’s and Ulcerative Colitis

Diet can play a significant role in inflammatory bowel diseases. It is estimated that we eat almost one ton (or 2,000 pounds) of food each year. Patients with IBD often benefit when they go off of allergenic foods and eat more whole foods, fiber, and avoid sugar. The standard American diet can encourage inflammation, imbalance gut bacteria, and change the mucosa causing intestinal permeability (or leaky gut).

Roxanne ate a standard American diet with lots of dairy and bread products, such as blueberry waffles and bagels. She had cravings for sweets. Her practitioner had her avoid gluten, dairy, soy, corn, sugar, and rice. She was motivated to make significant changes in her diet and was pleasantly surprised by the results. In my experience, most people who cut out gluten and bread products feel happier, more energetic, have less digestive problems, and may even lose 10 pounds. Indeed, diet changes may have helped to reduce Roxanne’s gut inflammation and pain. She had an immediate improvement (<11 days) with the treatment plan, suggesting that foods may have played a big part in putting her Crohn’s into remission.

Toxins, Stress, Hormones, and Inflammatory Bowel Disease

Inflammatory bowel disease involves genetic and environmental factors. Clearly, a history of antibiotics and pathogenic infections had greatly harmed Roxanne’s gut. But these changes were not happening in a vacuum. Roxanne may have had a genetic predisposition. Her grandmother had gut problems, either colitis or irritable bowel syndrome. Roxanne had struggled with endometriosis, a condition associated with hormone imbalance. Roxanne complained of extreme stress for the previous year. Genetics, stress, and hormones are all known potential triggers for inflammatory bowel disease.6 Finally, Roxanne was having her home remodeled at the time of this case. She may have been getting toxic or allergenic exposures during the renovation that served as the “final straw,” sending her into an acute inflammatory state.

Colonoscopy Findings and Limitations

For three years prior, Roxanne had shown normal colonoscopy results except for polyps. Her gastroenterologist had maintained for years prior that she did not have irritable bowel syndrome or inflammatory bowel syndrome. However, Roxanne’s initial colonoscopy featured in this case showed moderate aphthous ulceration in the ascending and transverse colon, leading to a Crohn’s disease diagnosis.

One of the limitations of this case study is Roxanne had only recently been diagnosed with Crohn’s disease. The diagnosis is based only on an observation of inflammation, not on root cause. While her fecal lactoferrin was high, her calprotectin result on the GI-MAP was normal. Calprotectin can identify IBD and hers was not suggesting any significant intestinal inflammation, even though she was in a flare (with diarrhea 10-15 times daily, pain, and fatigue). Nonetheless, after six months of treatment with diet and supplements, there was normal mucosa throughout the ascending and transverse colon. Whether Roxanne was headed for a firm diagnosis of Crohn’s with many years of medications and/or surgery will never be known for sure.

Another limitation of this case study is we did not see a follow-up GI-MAP. We observed rapid and dramatic improvement in Roxanne’s clinical symptoms, as well as in the six-month follow-up colonoscopy results. However, we do not know if the diet, antimicrobial, and digestive enzyme treatments actually lowered Klebsiella species or Pseudomonas species. We do not know if microbiome-building treatments indeed increased commensal bacteria.



Chronic diseases can have multiple causes. This is why functional medicine uses a systems biology approach to chronic illnesses. It looks for and addresses root causes of disease, instead of only treating the symptoms. From an integrative and functional medicine perspective, the absolute most important areas to investigate in IBD are: diet, food sensitivities and allergies, the gut microbiome, other infections, nutrition, and leaky gut. Addressing Klebsiella, Pseudomonas, inflammatory foods, and building the microbiome helped to turn around a woman’s case of Crohn’s disease diarrhea, infections, and antibiotics. This case is consistent with other reports in the medical literature showing that inflammatory bowel disease can be successfully treated with a 5-R protocol. Roxanne’s story shows that an integrative and functional medicine approach to Crohn’s disease can be effective for reducing intestinal inflammation, pain, and diarrhea, and these improvements were documented using colonoscopy techniques.

Potential Root Causes of Crohn’s Disease and Ulcerative Colitis

  • Diet
  • Food sensitivities and allergies
  • Gut microbiome imbalances
  • Gut or systemic infections
  • Malnutrition
  • Intestinal permeability (leaky gut)

Treatments and Testing Used in This Case


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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.