How to Heal Inflammatory Bowel Diseases Like Crohn’s Disease

The bacteria in your gut play crucial roles in your health, and your diet can significantly alter your gut microbiome. Sugar nourishes health-harming bacteria, yeast and fungi in your gut, which may actually harm you more than its impact on insulin resistance.

By eating a healthy diet, you allow beneficial gut bacteria to flourish. They then perform the real “magic” of nourishing  your health. You may have noticed that probiotics are now featured in articles relating to all sorts of health problems, including obesity, diabetes, depression and heart disease.

As explained by Russian neurologist Dr. Natasha Campbell-McBride, creator of the GAPS diet, a woman’s gut flora can also influence the health of her child, and if your child’s gut flora is compromised from birth, he may be at an increased risk of neurological and behavioral problems, as well as vaccine damage.

Naturally, imbalances in your gut microbiome are most readily associated with gut problems, ranging from mild discomforts to severe inflammatory bowel diseases (IBD) such as Crohn’s disease and ulcerative colitis.

IBD — A Common Problem With Potentially Serious Consequences

Crohn’s disease and ulcerative colitis are collectively known as IBD. An estimated 1.6 million Americans struggle with IBD, and 70,000 new cases of IBD are diagnosed in the U.S. each year.1 Both of these conditions are characterized by symptoms such as:

  • Frequent diarrhea, abdominal cramps and severe pain
  • Rectal bleeding
  • Weight loss
  • Fatigue
  • Nausea and fever

Ulcerative colitis and Crohn’s disease are autoimmune diseases that can have serious consequences if left unaddressed. The symptoms associated with these conditions are caused by inflammation in your intestines, which also increases your risk of intestinal blockages, abscesses, bowel perforation and colon cancer.

IBD Raises Your Risk of Bone Diseases

IBD is also associated with malabsorption and malnutrition, which can result in bone fractures and bone diseases such as osteopenia and osteoporosis.2 In fact, gut inflammation appears to be an important contributor to bone loss.3

Researchers have also found that leaky gut, which allows microbes and other foreign particles to enter your bloodstream, is strongly associated with joint problems such as rheumatoid arthritis.4,5 As explained by a globally recognized leader in the field of functional and integrative medicine, Chris Kresser, in a recent article on this topic:6

“[Your] immune system is intricately involved in the regulation of bone metabolism and physiology. Immune cells that are activated by microbes in the gut can migrate to bone and directly regulate bone remodeling via osteoclast-inducing factor, RANKL and other bone-active molecules.7

Increased levels of activated innate immune cells have been shown to increase expression of the signaling molecule TNFα in bone marrow. TNFα stimulates stems cells in the bone marrow to differentiate into osteoclasts.

This tips the normal balance of bone resorption and formation, resulting in higher levels of bone breakdown and lower bone density.8,9

Bacteria and Fungi Linked to Crohn’s Disease

Many lifestyle factors can contribute to inflammation in your intestines. Not surprisingly, research suggests bacteria and fungi are involved:

Previous research has linked Crohn’s disease to the presence of a bacterium called Mycobacterium paratuberculosis, which prevents white blood cells from killing E. coli bacteria known to be present in increased numbers within Crohn’s disease infected tissue. One route of exposure to this Mycobacteria is cow’s milk.10,11

One study found that Mycobacterium avium paratuberculosis (MAP) was present in about 92 percent of patients with Crohn’s disease, compared to 26 percent of patients in a control group. MAP is present in about 2 percent of commercial pasteurized milk.

So, not only does pasteurization kill the beneficial bacteria available in milk, but it leaves potentially harmful organisms alive and well. There are good reasons to limit milk consumption altogether (as it is high in natural sugars that can promote insulin resistance and prevent nutritional ketosis).

But if you do drink milk and if you struggle with IBD, raw milk from healthy grass-fed cows is FAR preferable to pasteurized milk from cows raised in concentrated animal feeding operations (CAFOs). Raw grass-fed milk can be quite healing when you have IBD.

Former World Health Organization expert Dr. A.V. Costantini found that people with Crohn’s often have aflatoxin, a mycotoxin made by Aspergillus molds, in their blood.

Research12 seems to confirm the potential role of aflatoxin in Crohn’s, as disease activity in patients with Crohn’s was lower while they followed a yeast-free diet, specifically avoiding baker’s and brewer’s yeasts.

Researchers have also linked Crohn’s to a lack of the healthy bacteria Bifidobacterium and Bacteriodes and the concurrent reduction in short-chain fatty acids (SCFAs).13

SCFAs are produced by gut microbes that ferment dietary fiber, so making sure you’re getting enough fiber in your diet is an important part of the treatment equation.

Most recently, researchers found that Crohn’s patients have higher amounts of the bacteria Serratia marcescens and E. coli in their intestines, along with the fungus Candida tropicalis.14,15

Experiments revealed that these three microorganisms interact to create an inflammatory biofilm that in turn produces the symptoms of Crohn’s.

Gut Bacteria Have a Powerful Influence on Your Immune Responses

Recent research also shows that gastrointestinal (GI) bacteria may be responsible for overactive immune responses, ranging from celiac disease to food allergies and food sensitivities.

According to estimates by the World Health Organization (WHO), 1 to 3 percent of all adults and between 4 and 6 percent of all children worldwide are allergic to at least 1 of 70 allergenic foods.

Foods associated with the most severe reactions include gluten, seafood, eggs, peanuts, soy, milk and nuts.16 As reported by the American Society for Microbiology (ASM):17

“Allergies are caused by an overactive immune response to a foreign particle or protein that the body mistakes as a threat.

There are a few theories on why this happens, but the Hygiene Hypothesis is the most prevalent, and posits that the root of increasing allergy rates is due to modern access to antimicrobials and an obsession with disinfectants.

Being ‘too clean’ has ultimately led to too little microbial colonization early in life. Microbes are necessary for the development of a normal immune system (and thus, a normal immune response to non-pathogens).

Children born with low levels of Bifidobacteria have a higher risk of developing allergies. The presence of certain gut bacteria during infancy is important for several reasons.

Not only do they influence health by themselves, but they also interact with other microbes to produce T-cell maturation in infants.18 Without this interaction, the child is left with reduced immune function.19 As noted by ASM:

‘… [C]olonization by microbes both early-on and later in life appears to be extremely important in preventing allergies, but is a hard pill to swallow for a generation raised to believe that cleaner is better, and sterile is best.'”

Dos and Don’ts When You Have Crohn’s Disease

Addressing Crohn’s disease involves two strategies: Avoiding things that disrupt your gut microbiome, and implementing dietary strategies that nourish beneficial microbes. Your gut bacteria are very vulnerable to lifestyle and environmental factors, including the following, which are best avoided as much as possible:

Refined sugar and processed fructose Refined grains, especially those containing gluten Processed foods (common food additives such as emulsifiers have been linked to Crohn’s disease and ulcerative colitis specifically) Antibiotics (including antibiotics given to livestock for food production)
Chlorinated and fluoridated water Antibacterial soaps Agricultural chemicals and pesticides Pasteurized dairy

All of these factors throw your gut flora out of balance. While some of these factors are pervasive and can be difficult to avoid, it’s not impossible. Simply altering your diet to avoid processed foods and focusing on real foods (ideally locally grown organics) will make a big dent, as it will dramatically reduce the amount of sugar you consume, and automatically limit your exposure to antibiotics and agricultural chemicals.

Signs and Symptoms of Imbalanced Gut Flora

How can you tell whether your health is already starting to suffer from a lack of healthy bacteria in your digestive system?  The following symptoms are all signs that unhealthy bacteria have taken over too much real estate in your gut, and that you probably need to take action — even in the absence of an IBD diagnosis:

Gas and bloating Constipation or diarrhea Fatigue
Nausea Headaches Sugar cravings, and cravings for refined carb foods

Specific Foods That Help Prevent and Heal IBD

Reseeding your gut with probiotics should be high on your list. Traditionally fermented and cultured foods (provided they’ve not undergone any kind of pasteurization) are loaded with beneficial, healthy bacteria, and are easy to make from scratch.

To make kefir, for example, all you need to do is add half a packet of kefir starter granules to a quart of raw grass-fed milk and leave out at room temperature for one to three days. To learn more about fermenting vegetables, see my previous article, “Tips for Fermenting at Home.” Besides fermented veggies, raw milk, kefir and/or raw milk yogurt, other specific foods that are important if you struggle with IBD include:

Blueberries. Rich in antioxidants, vitamins and fiber, research has shown blueberries can help alleviate and protect against intestinal inflammation such as ulcerative colitis.20,21 Blueberries’ protective effect on IBD is two-fold. First, blueberries are rich in polyphenols, which have both antimicrobial and antioxidant effects. When combined with probiotics, the combo not only reduces inflammation-inducing bacteria, but also increases the amount of health-promoting Lactobacilla.

Moreover, the fiber in blueberries is not highly degraded in your large intestines. What this means is that substances that can cause inflammation are kept from contacting the lining of your intestines. Instead, they are embedded in the blueberry fiber, where they do not cause harm, and are then transported out of your body during elimination.

Blueberries may also be protective against colon cancer, courtesy of an antioxidant compound called pterostilbene.22 This compound inhibits genes involved in inflammation, which is thought to be a risk factor for colon cancer. Blueberries are also a good source of ellagic acid, which is known to block metabolic pathways that may lead to cancer.

Coconut oil is another beneficial addition to your diet if you have IBD. The anti-inflammatory and healing effects of coconut oil have been shown to soothe inflammation and help heal injury in the digestive tract. Coconut oil also has antimicrobial properties that promote intestinal health by killing troublesome microorganisms, including Candida yeast, that may cause chronic inflammation.

Caprylic acid, a medium-chain triglyceride (MCT oil) with eight carbons (which is why it’s also known as C8) is also a potent antifungal. Dr. Leon Chaitow, author of “Candida Albicans: Could Yeast Be Your Problem?” recommends it in lieu of antifungal drugs for Candida overgrowth. (Caprylic acid also readily converts to ketones, which are a very efficient and healthy fuel for your body.)

Animal-based omega-3 is another absolutely essential element of preventing and controlling IBD. The omega-3 fats in krill oil, EPA and DHA, have immune-boosting qualities along with anti-inflammatory properties proven to benefit disorders of the gut, including Crohn’s disease and ulcerative colitis.23

Fiber-rich foods, such as organic psyllium seed husk, flax hemp and chia seeds, berries, vegetables such as broccoli and Brussels sprouts, root vegetables and tubers, raw nuts and beans, help nourish beneficial microbes in your gut. Aim for 50 grams of fiber per 1,000 calories consumed.

Supplementing with organic psyllium husk can help bring you closer to this ideal amount. Just make sure that the psyllium is organic, as non-organic psyllium is typically severely contaminated with pesticides.

The Importance of Vitamin D

Last but certainly not least, make sure your vitamin D level is in a healthy, therapeutic range of 40 to 60 nanograms per milliliter (ng/ml). Vitamin D has been shown to be an important part of the treatment puzzle if you have Crohn’s disease. Low vitamin D levels are associated with an increased risk of Crohn’s, and correcting your vitamin D deficiency has been shown to improve symptoms of the disease.24

Researchers have also found a “significant interaction between vitamin D levels and Crohn’s Disease susceptibility, as well as a significant association between vitamin D levels and genotype.”25

In this study, blood levels of vitamin D levels were found to be significantly lower in patients with Crohn’s disease. Of the seven DNA sequence variations examined for effects, two variants showed a significant association with vitamin D levels in those with Crohn’s; four variants were associated with vitamin D levels among controls.

In short, they found that vitamin D can affect genetic expression associated with Crohn’s disease, and make matters either better or worse, depending on whether you have enough of it or not. One of the reasons that vitamin D may work for inflammatory bowel disease is that it helps your body produce over 200 antimicrobial peptides that help fight all sorts of infections, including those that might trigger IBD.

Remember the ideal way to optimize your vitamin D level is to expose a significant amount of your skin to the sun around solar noon. Vitamin D is a steroid hormone and is a marker for ultraviolet B (UVB) exposure.