Inflammatory Bowel Disease - Diet, Inflammation, and Microbiome

About 2 million people worldwide suffer from Inflammatory Bowel Disease (IBD). The development of IBD is still relatively unclear, but we know it involves many factors including genetics, environment, lifestyle, and the microbiota.  A Western lifestyle (eating junk and being sedentary) is also thought to play a major role in in the development of IBD. (R)

Quick Guide

  • Improvement in IBD symptoms have been seen when people eat semi-vegetarian and the Specific Carbohydrate Diet (SCD). The semi-vegetarian diet has more support behind it.

  • Gut bacteria seem to play a very large role in pathogenesis and symptoms

  • The research shows that probiotics help ulcerative patients more than Crohn's patients. VSL#3 is likely the best supported probiotic brand.

  • Vitamin D plays a role IBD

  • Fish oil supplementation has mixed results, but looks more promising for ulcerative colitis patients

  • Curcumin has been shown to improve symptoms in those with IBD

In-Depth Look

There are two types of inflammatory bowel disease (IBD); ulcerative colitis (UC) and Crohn’s disease (CD), both of which are chronic auto-immune conditions. (R)  Auto-immune conditions are disorders in which the body's immune system attack's its own healthy tissue. Ulcerative colitis and Crohn’s disease are similar, but different. The symptoms are fairly similar. Persons with IBD experience abdominal pain, persistent diarrhea, abdominal cramping, weight loss, rectal bleeding, fatigue, and other symptoms such as joint pain and skin conditions.

While ulcerative colitis and Crohn's disease are both chronic inflammatory diseases of the gastrointestinal tract, they are different in the areas in which they damage, how well they respond to diet, and the different mechanisms behind the development and inflammatory processes of each. Crohn’s disease can affect any part of the entire gastrointestinal tract, whereas ulcerative colitis is confined to the large intestine. (R) In general, Crohn’s patients have more relapse rates, surgeries, and worse prognosis than ulcerative colitis patients. (R)


T-Cell Activation


Courtesy of:

T-cell activation plays a major role in the immunological mechanisms behind IBD. (R)

Those with Crohn’s disease have a higher Type 1 T helper (Th1) response, and is mediated by higher levels of tumor necrosis factor-beta (TNF-beta), interferon-gamma (IFN)-γ), and Th17 cells. Its easiest to say that tumor necrosis factor (TNF), interferons (IFN), and interleukins (IL) are all involved in signalling some part of the immune system and mediate inflammation in some form or fashion. Ulcerative colitis patients are more Type 2 T helper (Th2) dominant, and mediated by higher levels of Th17 cells. (R) Without going in to too much detail, Th1 and Th2 are T-helper cells that "help" send signals in different immunological processes. They influence the immune system differently, and this is important because it helps us to understand the development, management, and have more precise targeted therapies. (Th1 cells produce interferon-gamma, interleukin-2 (IL2), and tumor necrosis factor-beta (TNF-beta). Th1 is responsible for what's known as cell-mediated immunity. Th2 cells produce IL-4, IL-5, IL-10, and IL-13, and is responsible for antibody production, eosinophil activation, and phagocyte-independent responses.) (R)  This is one reason why one thing might help someone feel better, but might make someone else feel worse. I will go into more detail about Th1/Th2 cells on a different post, because its fairly complex, and I myself would like to learn more about it.

Higher intakes of potassium are associated with lower risk of Crohn’s disease. Dietary potassium may mediate the effect of Th17 and development of Crohn’s disease. (R)


Semi-vegetarian Diet (SVD)

Semi-vegetarian, otherwise known as flexitarian, is a diet that is primarily vegetarian, but includes occasionally eating meat and fish. Semi-vegetarian diets have been shown to prevent symptomatic relapse in those with IBD. (R)

One study found that a 94% remission rate was maintained in Crohn’s disease patients who followed a semi-vegetarian diet compared with a 33% remission rate of those that followed an omnivorous diet. After 1 year, the semi-vegetarian diet group had a 100% remission rate, and 92% at 2 years.  The semi-vegetarian diet group also had lower levels of inflammatory C reactive protein (CRP). (R)

Diets high in refined carbohydrates, sugar, saturated fatty acids, omega-6s, and poor in healthier options like fruits and vegetables might be a critical trigger for IBD.  It has also been demonstrated that higher intakes of animal protein is associated with developing Crohn’s, while higher intakes of fruits and vegetables is inversely associated with Crohn’s. One review found that higher intakes of fat are associated with ulcerative colitis, and red meat is associated with an increased risk of developing Crohn's or ulcerative colitis. (R)

Clinical remission can be obtained when Crohn’s patients follow an elemental diet, or completely remove food from the gut by getting nutrient through total parenteral nutrition. Total parenteral nutrition is when nutrients are given through the vein, which bypasses the gastrointestinal system all together. When patients resume an omnivorous (meat and plant based) diet, there is a gradual rise in C reactive protein (CRP); which again is a marker of inflammation. (R)



According to NHS data on 170,776 subjects, an intake of 24.3 g of fiber a day reduces the risk of Crohn’s disease by 40%. Interestingly, soluble fiber gave the most benefit, while insoluble fiber didn’t actually affect disease risk. Also, fiber didn’t affect the risk of developing ulcerative colitis (R); which doesn’t make sense to me, but that’s what this data has shown.

The short chain fatty acids created through gut bacterial fermentation of fiber activates peroxisome proliferator-activated receptor gamma (PPAR γ), which has anti-inflammatory effects. (R) One benefit of short chain fatty acids is that they promote immune tolerance through increased production of T-regulatory cells. (R) If you have chronic inflammation and an overactive immune system, its a good thing to have an immune system become more tolerant.

During flare-ups, low fiber diets are recommended. The low FODMAP (fermentable oligo-, di-, mono-sachharides and polyols) diet has been shown to decrease abdominal pain, flatulence, and diarrhea in those with IBD. (R) FODMAPs are special kinds of fiber that many people have gastrointestinal issues with.



Iron increases the formation of free radicals and reactive oxygen species (ROS). These free radicals cause oxidative stress in the form of cellular injury, activation of NF-κB, and inflammation. Pathogenic bacteria also consume iron as a food source and flourish in the presence of it, which simply put increases inflammation and can throw off the balance of gut bacteria. The type of iron does make a difference. Heme iron, a type of iron found in red meat, has been found to increase the severity of colitis. The iron supplement iron (ferrous) sulfate has also been shown to cause inflammation. (R) You’ve probably experience some nausea and stomach aches after consuming iron supplements.


The Specific Carbohydrate Diet (SCD)

The Specific Carbohydrate Diet (SCD) has been shown to decrease inflammatory markers and increase mucosal healing in Crohn’s disease patients. (R)  Its a pretty restrictive diet. Basically, all grains and some starches are removed from the diet, honey is the only allowed sugar, and fermented yogurt is the only dairy allowed.  Be careful with the fermented foods on the SCD, if you have a mast cell activation disorder, you’ll likely feel a lot worse because the SCD promotes the consumption of high histamine foods like bone broth.

The theory of the SCD is that monosaccharides are easily absorbed, while di- and poly-saccharides require brush border enzymes to be fully digested. Brush border enzymes are located on the outside of the intestine where food particles and nutrients are absorbed. Those with injured guts will have less digestive enzymatic activity, which would then allow the di- and poly-saccharides to reach and feed the gut bacteria, causing dysbiosis, overgrowths, overproduction of mucus, and inflammation. Removing di- and poly-saccharides from the diet should alleviate these symptoms. (R)

The SCD at a glance

Here's the foods permitted:

Carbs/sugars: glucose, fructose, galactose (honey is allowed)

Fresh fruits and vegetables (except for potatoes and yams)

Legumes: examples are lentils and split peas, but not soybeans or chickpeas

Fresh, unprocessed meats

Dairy: Lactose free milk, yogurt, and cheese

*Read Breaking the Vicious Cycle for more information



Our intestines contain trillions of microorganisms.  We call these creatures in our guts the microbiota.  Healthy gut bacteria do all kinds of good things for us, like digest fiber and produce short chain fatty acids, protect against injury, regulate fat metabolism, synthesize vitamins like vitamin K and B12, cause intestinal motility, and regulate our immune systems. They also protect us against harmful pathogens that can be detrimental to our health. Those with IBD have less diverse populations of gut bacteria than normal healthy individuals; 25% less diverse actually. (R)

The genome of the microbiota is 100 times that of our own body, and these microscopic beings can alter how our bodies function, both good and bad. When the balance of good and bad bacteria is disrupted, we call that dysbiosis.  One critical concern with dysbiosis is that it can decrease the integrity of the tight junctions holding the cells of the intestinal mucosa together, which causes the gut to become more permeable and allow substances and pathogens to enter in places where they shouldn’t be. This, simply put, leads to inflammation. Those with IBD have a stronger inflammatory response to foreign stuff (antigens). The large intestine contains the most bacteria, and the small contains some, but not much. (R) Many journal articles and reviews have found that Crohn’s and ulcerative colitis are both related to dysbiosis. (R)

High fat and sugar diets over long term have been shown to change the microbiota unfavorably. In mice, a diet high in saturated fat and low in polyunsaturated fat induces dysbiosis and leads to inflammation mediated by Th1 cells.  It has been shown that high fat diets and/or sugar can create dysbiosis and lead to increased production of harmful endotoxins. (R)

The bacteria in our guts eat and ferment some of the foods we eat. Bacterial fermentation of carbohydrates produces short chain fatty acids, which is very healthy for the cells of our colon, and they have other benefits as well.  On the other hand, bacterial fermentation of protein residues creates harmful substances. (R) Animal protein and fat rich diets have been shown to cause a decrease in good, healthy, beneficial bacteria. (R)

Probiotics doesn’t seem to have much effect on Crohn’s disease, but ulcerative colitis is more responsive to probiotics.  S. boulardii is the only strain that has been shown to benefit Crohn’s disease patients.

VSL#3 is a probiotic mixture that has been shown to be superior to placebo for improving symptoms in patients with ulcerative colitis. Lactobacillus GG has also been shown to have similar efficacy as 2400 mg/day of mesalamine. Fermented milk has been shown to improve ulcerative colitis patients vs a placebo. (R)



A higher intake of linoleic acid (omega-6) which is found more concentrated in red meat, cooking oils and margarines is associated with an increased risk of developing ulcerative colitis. (R)

Eating fast food is a risk factor (obviously). (R)

Higher intakes of alpha-linolenic acid (omega-3) is associated with a lower risk of developing ulcerative colitis. (R)

Magnesium, vitamin C and fruits are associated with decreased risk, while retinol (active form of vitamin A) is positively associated with risk. (R)

Titanium dioxide, aluminum silicates, and talc are linked to risk of Crohn’s disease.  Carrageenan injures enterocytes in animal models similar to what is observed in IBD in humans. (R)

Water is linked to IBD…because it can carry pathogens like Helicobacter pylori. (R)

Muscle loss is major concern in those with IBD. Bone loss (osteopenia) is too, due to the malabsorption of calcium and vitamin D.  Bone loss is also a side effect of long-term use of corticosteroids. (R)

Anemia is also pretty common in IBD patients, and its usually iron-deficiency anemia. Vitamin deficiencies can also be a concern, especially if resections of the gut have occurred. (R)

Malnutrition and being underweight is common in those with IBD. (R) Tracking calories to make sure you’re eating enough is a really good idea.

Gluten-free diets improve symptoms and decrease the severity of flares in those with IBD. (R)

An old study from 1965 found that dairy free diets have been shown to improve symptoms and relapse rates in patients with ulcerative colitis. (R)

Ulcerative colitis patients who consume less sulfur containing amino acids have been shown to improve the disease. Hydrogen sulphide decreases the utilization of butyrate. (R)


Vitamin D

Those with Crohn’s disease have lower levels of vitamin D, and lower levels of vitamin D are also correlated with an increase in disease activity. Vitamin D has immune regulating and anti-inflammatory roles. Inflammatory TNF-α downregulates the vitamin D receptor, which furthers inflammation more. (R) Vitamin D (1200 IU daily) has been shown to lower rates of relapse in those with Crohn’s disease compared to placebo. (R)


Fish Oil


The studies on fish oil are somewhat mixed, and I will be writing a detailed post on whether fish oil is actually safe, soon.  A 12 month randomized controlled trial did find that fish oil reduced the need for corticosteroids in ulcerative colitis patients. (R) So there's that. Most of the studies I came across showed a little benefit in patients with ulcerative colitis, but not much or any at all in Crohn's patients.



Curcumin, it’s a pretty cool supplement.  It’s derived from turmeric, and has anti-oxidant, anti-inflammatory, anti-cancer, and neuroprotective properties.  The main mechanisms behind curcumin’s beneficial effects are the suppression of the inflammatory NF-κB, IL-1 and TNF-α. Curcumin has been shown to reduce symptoms and inflammation in both Crohn’s disease and ulcerative colitis patients. (R) It has also been shown at 2 g/day to reduce relapse rates compared to placebo at 6 months (4% to 18%), but no statistically significant difference was seen after 12 months (22% to 32%).  There was still less relapse in the curcumin group, but not “significant”. Some adverse effects were seen such as abdominal bulging, nausea, transient hypertension, and transient increase in the number of stools. (R) There are always side effects to consider, and one in particular that bothers me about curcumin is that it decreases the enzyme diamine oxidase (DAO), which breaks down histamine. If you get itchy and feel worse taking curcumin, this might be an indication that you have an issue with histamine or a possible mast cell activation disorder.

A small study found that all 5 patients with ulcerative colitis improved after supplementation with curcumin, and 4 out of the 5 decreased or eliminated their medication. (R) In a larger randomized, placebo controlled study, 8 out of the 39 in the control group relapsed after 6 months, while only 2 out of the 43 in the curcumin group relapsed. Then, both groups were given only placebo and no curcumin was distributed.  They found that the original curcumin group became just as bad as the original placebo group when they weren’t receiving curcumin even though they thought they were getting it. A great study, truly showing the power of curcumin. (R)

Disclaimer: Always check with your doctor before trying any of the supplements or diet strategies discussed.