Ulcerative colitis (UC) is a form of inflammatory bowel disease (IBD) that causes inflammation in the colon and rectum, including ulcerations and bleeding in the intestinal lining as well as a thickening and narrowing of the colonic wall. UC symptoms are also manifested outside of the gut and may include fever, joint pain, and mouth ulcers. If the disease reaches a progressive state, ulcerative colitis can lead to cancer and bowel obstruction and may ultimately require surgery.

Ulcerative colitis is a digestive autoimmune disease, where the immune system wages war against the body’s healthy tissue, leading to chronic inflammation. Many individuals with UC have a concomitant (or associated) autoimmune disorder like thyroid or celiac disease.

The cause of ulcerative colitis is unknown but emerging evidence shows that gut bacteria play a primary role in the development of the disease.

Symptoms of ulcerative colitis include:

  • Abdominal pain
  • Bloating
  • Blood in the stool
  • Diarrhea
  • Mouth ulcers
  • Nodules on the skin (pyoderma gangrenosum and erythema nodosum)
  • Nutrient malabsorption
  • Undigested food particles in the stool
  • Weight loss


UC is also associated with irritable bowel syndrome (IBS) as a potential cause of IBS symptoms. Leaky gut may exasperate ulcerative colitis.

Gut Bacteria

The exact cause of ulcerative colitis (UC) is unknown, yet gut bacteria are strongly associated with autoimmune diseases like UC. Lifestyle behaviors that lead to sub-optimal gut bacteria are:

  • Antibacterial products
  • Antibiotic use
  • C-section
  • Environment that’s too clean
  • Lack of childhood exposure to germs
  • Poor diet high in fat, starch, and sugar


These risk factors may increase an individual’s susceptibility to disease by suppressing the natural development of the immune system, allowing pathogenic bacteria to proliferate destroying the integrity of intestinal lining, and killing off good bacteria.


Antibiotic use is strongly associated with IBD. Antibiotics wipe out large amounts of bacteria and create a typical gut bacteria profile that is seen in IBD patients: an overall decrease in diversity of gut bacteria, higher levels of pathogenic species, and lower levels of protective ones. Being treated with antibiotics in your first year of life is associated with a threefold increase in risk for IBD, compared to children who haven’t received antibiotics.


Although the vast majority of people with UC don’t have a family history of the disease or a genetic susceptibility, more than one hundred gene mutations are associated with IBD disease, and those with Eastern European Ashkenazi Jewish descent have a four- to five-fold increased risk of developing IBD. Yet not everyone who is genetically susceptible develops the disease; an environmental trigger must be present that unmasks the genetic risk and leads to symptoms. This environmental trigger most often involves gut bacteria as described above.

Diagnosing ulcerative colitis begins with a close look at health history and symptoms. If history and symptoms indicate UC as a possible cause of your digestive distress, medical tests that can help in confirming a diagnosis include:

  • Blood tests: blood is tested for anemia and/or infection, both signs of UC
  • Stool tests: a stool sample is tested for white blood cells, a sign of UC
  • Scopes: a flexible sigmoidoscopy, in which a small tube with a camera on its end is inserted through the rectum to look for inflammation in the sigmoid colon. If inflammation is apparent, a colonoscopy is often administered, and biopsies taken
  • CT scan: an imaging test that looks at the abdominal and pelvic regions to investigate signs of inflammation

Lifestyle Modifications

An integrative approach that includes nutritional intervention and stress reduction works well for treating individuals with ulcerative colitis. A modified Paleo diet in combination with high-dose prescription-strength probiotics has been extraordinarily successful for accomplishing IBD remission and reducing or eliminating the need for toxic medications. A gluten free diet is also recommended. Most UC patients show significant improvements in their inflammation and symptoms when removing gluten (as well as refined sugars) from their diets.

Studies show that not only can diet and exercise improve symptoms and allow a reduction or discontinuation of drugs, but it can also lead to actual healing of the inflammation in the gut. Studies also infer that these changes are most likely mediated through alterations in gut bacteria.

Bottom line in treating ulcerative colitis: one of the most powerful tools in preventing and treating our modern plagues is the food we eat, since that’s what determines which bacteria grow in our gut garden. Check out the Lifestyle guidelines outlined in Dr. Chutkan’s books, Gutbliss and The Microbiome Solution for a step-by-step roadmap for implementing these changes in your own life, balancing your microbiome, and creating long-lasting good health along the way.


Occasionally, a patient whose disease is so severe, cooling things down with stronger conventional therapy first is recommended before embarking on the slower pace of dietary change. Some patients are just too sick and need faster-acting and more potent drugs. Even then, the goal is always to transition off those drugs as quickly as possible once the inflammation has improved, and to try to maintain the results with diet and lifestyle whenever possible.


Because gut bacteria may play a large roll in ulcerative colitis, a robust probiotic is helpful in rehabbing your microbiome and controlling your UC symptoms.

Fecal Microbiota Transplant (FMT)

More and more evidence points to the role of microbial imbalance and reduced microbial diversity in the pathogenesis of IBD. Early studies utilizing FMT to treat ulcerative colitis show amelioration of symptoms as well as the possibility of sustained remission and even cure. Large case series demonstrate improvement in symptoms and cessation of medications in 76% of patients, and remission in 63%.

Unlike C. diff where the response to FMT is rapid – a few days in most and just hours in some – with ulcerative colitis it takes longer for symptoms to improve, and the improvement may increase over time, as the microbiome gradually shifts towards normalcy.

Clinical data exists to support the use of FMT in treating UC, although FMT is not first line therapy for UC and should only be considered after standard treatments, including significant dietary modification and probiotics, have proved ineffective.

For chronic autoimmune illnesses like ulcerative colitis, you may need to do an initial series of daily FMT for 1-2 weeks, then a regimen of one to three times a week indefinitely, or at least for several months. Remember that most of the bacteria you’re transplanting don’t take up residence in the colon – they just pass through, although they may reproduce while in your digestive tract. So although some people are able to achieve lasting changes in their microbial composition and then stop treatment, for most autoimmune diseases, FMT represents a chronic form of therapy that needs to be administered regularly. The good news is that for some patients with IBD, the effects of FMT continue to improve over time, as the microbial changes slowly take root.