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Inflammatory Bowel Disease: Treatments for IBD Flares and Remission

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Inflammatory Bowel Disease: Treatments for IBD Flares and Remission

Inflammatory bowel disease (IBD) describes intestinal disorders involving chronic inflammation within the tissues of the digestive tract. Affecting three million American adults, an IBD diagnosis is associated with poorer quality of life, high rates of hospitalization, and increased risk of medical complications. The financial burden of IBD is significant; IBD medical costs account for nearly seven billion dollars annually. Early diagnosis and maintenance of disease remission are essential for preventing poor health outcomes and preserving the quality of life. (1)


What is IBD?

Often called an invisible illness, Inflammatory bowel disease (IBD) is chronic, recurrent episodes of inflammation within the gastrointestinal (GI) tract, which can lead to permanent damage of the intestines and severe complications over time.

IBD is subcategorized into Crohn's disease and ulcerative colitis (UC). The underlying cause of IBD is unknown, but the etiology of disease progression is understood to be a consequence of the interplay between genetics, environmental stimuli, and exaggerated immune response.

IBD Symptoms

IBD symptoms vary depending on the severity and location of inflammation and tend to occur episodically between periods of remission. Common symptoms include:

  • Persistent diarrhea
  • Rectal bleeding and/or bloody stools
  • Abdominal pain
  • Mouth sores
  • Weight loss
  • Fatigue

Complications of IBD

Possible complications of IBD include:

  • Malabsorption and resulting nutritional deficiencies
  • Anal fistulas: tunnels traveling from inside the anus to an opening on the skin around the anus
  • Strictures: narrowing of the intestines
  • Intestinal perforation or obstruction
  • Hemorrhage
  • Toxic megacolon: a life-threatening widening of the intestines
  • Inflammatory disorders of the eye
  • Skin disorders characterized by painful areas/lesions on the skin, commonly the legs
  • Increased risk of colon cancer, blood clots, gallstones, liver disease, arthritis, and osteoporosis

Difference Between Crohn's Disease & Ulcerative Colitis

Crohn's disease and ulcerative colitis are primarily differentiated by the location of inflammation and the depth of involvement in the bowel wall.


  • Crohn's disease can affect any part of the digestive tract, from mouth to anus; it generally affects the small intestine prior to the large intestine.
  • UC is limited to the colon; it begins in the rectum and can ascend up the large intestine.

Wall Involvement

  • Crohn's is defined by full-thickness transmural inflammation (present within all layers of the bowel wall).
  • UC is limited to the innermost lining of the intestine.

Lesion Pattern

  • Crohn's is characterized by patchy skip lesions, meaning that there are areas of healthy tissue between the affected areas of the gut.
  • UC lesions and inflammation are continuous.Functional Medicine Labs to Test for Root Cause of IBD

Functional Medicine Labs to Test for Root Cause of IBD

Blood Work

Laboratory testing serves to aid in the diagnosis of IBD, monitor disease activity, and screen for disease complications. These tests do not take the place of colonoscopy/endoscopy with biopsies for a definitive diagnosis of Crohn's or UC. Valuable blood work during the initial evaluation of IBD includes (2):

  • Complete blood count (CBC): evaluates for anemia, malnutrition, and infection
  • Comprehensive metabolic panel (CMP): evaluates for dehydration, malnutrition, and gallbladder/liver dysfunction
  • C-reactive protein (CRP) and erythrocyte sedimentation rate (ESR): quantify levels of systemic inflammation

Fecal Testing

A disturbance in the healthy balance of both bacterial and fungal intestinal colonies plays a role in the pathogenesis of IBD. Additionally, a comprehensive stool test includes additional fecal tests commonly ordered by a primary care physician or gastroenterologist to diagnose and quantify the severity of the disease:

  • Leukocytes: white blood cells indicate immune activity; presence and frank elevations within the GI tract can indicate IBD pathology
  • Calprotectin: signifies the presence of white blood cells and inflammation; this test is helpful to both quantify baseline disease severity and monitor patient response to treatment (2)
  • Lactoferrin: similar to calprotectin, this serves as another marker of inflammation and white blood cell activity in the intestines; lactoferrin is often elevated during IBD flares (2)

Saccharomyces cerevisiae Antibodies

Saccharomyces cerevisiae is a yeast found in various foods (bakers yeast). Immune proteins against this yeast, called anti-Saccharomyces cerevisiae antibodies (ASCA), are frequently present in people with IBD. ASCA is commonly ordered along with a test for perinuclear anti-neutrophil cytoplasmic antibody (pANCA) to differentiate between Crohn's and UC. ASCA is more common in Crohn's, while pANCA is more common in UC.  

Food Sensitivities

Intestinal permeability, leaky gut, has been associated with Crohn's disease. Additionally, food intolerances are often reported by patients with IBD as driving triggers for GI symptoms and IBD flares. A food sensitivity test can help identify dietary triggers perpetuating GI inflammation and IBD symptoms.

Small Intestinal Bacterial Overgrowth (SIBO)

SIBO is a form of intestinal dysbiosis in which the overgrowth of bacteria in the small intestine causes digestive symptoms like bloating, abdominal pain, and changes in bowel habits. This systematic meta-analysis calculated a SIBO prevalence rate of 22.3% in IBD patients, and in another study, those who were treated for SIBO reported decreased severity of IBD symptoms. SIBO can be diagnosed by an at-home breath test ordered by a practitioner.

Other Beneficial Labs to Order

Micronutrient Testing

Small intestinal inflammation, damage, and dietary restrictions can impair the ability to digest and absorb essential nutrients through diet. Common deficiencies in people with IBD are iron, vitamin B12, folate, zinc, and vitamin D. A micronutrient test can detect deficient and suboptimal nutrient levels in the blood. Suboptimal and frankly deficient nutrient status can contribute to symptoms like fatigue, impair intestinal healing, and increase the risk for secondary diseases.

Health Screenings

People with IBD are at higher risk for osteoporosis due to calcium and vitamin D deficiencies, chronic systemic inflammation, and side effects of steroid treatments. Initial screening for osteoporosis with a DEXA scan at the time of IBD diagnosis is recommended and periodically thereafter, as advised by your doctor.

The risk of colon cancer increases by 0.5% every year after ten years of the disease. Screening colonoscopy for colorectal cancer is recommended 8-10 years after initial IBD diagnosis, followed by surveillance colonoscopy at intervals recommended by your doctor.

Functional Medicine Treatment for IBD

Treatment goals will differ slightly depending on whether you are experiencing an active IBD flare or are in disease remission. While the focus of IBD flare treatment is symptom management and induction of disease remission, long-term management will emphasize addressing the underlying triggers of IBD to prevent future flares.

This article will not discuss conventional treatment options such as anti-inflammatory, immunosuppressant, biologic, and antibiotic medications. It is important to understand that these can be beneficial aspects of a successful integrative treatment protocol.

IBD Flare Treatment


Making dietary modifications to eliminate inflammatory triggers and allow the bowels time to rest is a critical aspect of flare management. Common IBD trigger foods that should be avoided include (3):

  • Hard-to-digest foods high in insoluble fiber: fruits with skin and seeds, raw green vegetables, whole nuts, whole grains
  • Lactose
  • Refined sugars
  • Fried foods
  • Alcohol and caffeine
  • Yeast
  • Gluten

A low-residue diet that reduces dietary fiber helps relieve abdominal pain and diarrhea by limiting the amount of matter traveling through the intestines.

The elemental diet is a medical protocol consisting of a liquid formula of macro- and micronutrients broken down into their simplest form for easy digestion. It ensures comprehensive nutritional support that may otherwise be missing with other elimination diets. Many published clinical studies show that elemental diets effectively manage impaired bowel function.

Herbs & Supplements

Nutraceutical and botanical products that palliate GI symptoms and reduce intestinal inflammation should be incorporated into an acute IBD treatment plan. Well-researched options include:  

  • Peppermint Oil: Peppermint acts as an antispasmodic and can help calm the digestive tract muscles. It is effective at treating IBS-like digestive symptoms, primarily pain and bloating.
  • Aloe vera gel's anti-inflammatory mechanisms have been researched and safely applied to various health conditions. A small clinical trial utilizing aloe vera in the treatment of UC resulted in significant reductions in disease activity after one month of treatment (4).
  • Boswellia serrata (Indian frankincense) modulates inflammation by inhibiting the formation of inflammatory mediators (5). A 2001 study found that Boswellia was as effective as mesalamine, a common anti-inflammatory medication used in the treatment of IBD, at the end of an eight-week trial.
  • Wormwood (Artemisia absinthium) is an herb that has historically been used to treat IBD. Its ability to decrease inflammatory proteins and its antimicrobial properties are likely the mechanisms behind its ability to support healthy bowel function. Although limited, the available data through clinical trials supports its ability to achieve and maintain remission and improve symptom scores for patients with IBD. (5)
  • Curcumin is a naturally occurring chemical found in turmeric. It has been shown to reduce inflammation and treat ulcerative colitis when used with mesalamine therapy.

Lifestyle Changes

Smoking cessation is imperative for those with Crohn's disease. Tobacco doubles the risk of developing Crohn's and is associated with a more severe form of the disease.

High levels of stress can contribute to IBD symptoms and trigger flares. Identifying stress triggers and learning to eliminate and/or healthfully cope with them is an essential aspect of IBD treatment.

Long-Term Treatment for IBD


The importance of correcting nutritional deficiencies cannot be overstated. Nutrient deficiencies can alter gastrointestinal structure and function, resulting in a vicious cycle of intestinal impairment and poor nutritional status. A varied and healthy diet that includes dietary fiber and a higher ratio of omega-3 to omega-6 fatty acids is recommended to prevent malnutrition and reduce the risk of disease relapse (3).

Some patients may continue to eliminate identified food sensitivities/triggers to maintain remission. This study found that the most common offending foods for patients with Crohn's disease are wheat, yeast (especially if ASCA-positive), and dairy.

Additional diets that have been shown to improve quality of life and reduce GI symptoms in IBD patients are the low-FODMAP diet and Specific Carbohydrate Diet (SCD).

Herbs & Supplements

Common supplements utilized to address intestinal dysbiosis and heal the intestinal barrier include:

  • Herbal antimicrobials (such as oregano and berberine) have been shown to be just as effective as pharmaceutical antibiotic therapy in treating SIBO.
  • Repopulating the microbiome with healthy probiotic organisms, especially those in the Lactobacillus and Bifidobacterium species, has been shown to be beneficial in the treatment of IBD.
  • L-Glutamine is an amino acid that supports healthy intestinal cell proliferation, reduces intestinal permeability, and decreases intestinal inflammation.
  • The continued use of botanical inflammation modulators, like aloe and Boswellia, prevents inflammatory episodes and prolongs disease remission.  
  • Turmeric (Curcuma longa) contains the strong anti-inflammatory compound curcumin. Safe to use long-term, curcumin mediates colonic inflammation. In addition, it also has anticoagulant and liver-protective effects that can provide additional support to those at risk for cardiovascular and liver complications. (4, 5)
  • Vitamin D deficiency may be a contributing factor to IBD development. Supplementation with vitamin D supports proper immune regulation within the intestinal mucosa and supports bone health.

Lifestyle Changes

Implementing healthy lifestyle habits to reduce and manage stress decreases GI symptoms and inflammation and prevents IBD flares. Routine exercise, acupuncture, massage, and cognitive behavioral therapy (CBT) can all be utilized in a holistic IBD treatment plan.  


Inflammatory bowel disease, encompassing Crohn's disease and ulcerative colitis, is a debilitating intestinal disease characterized by chronic episodic inflammation. Taking into consideration its multifactorial etiology, a functional medicine approach to IBD treatment dives into the root causes of disease while palliating symptoms to optimize treatment success, improve patient quality of life, and prevent unwanted complications.

The information provided is not intended to be a substitute for professional medical advice. Always consult with your doctor or other qualified healthcare provider before taking any dietary supplement or making any changes to your diet or exercise routine.
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Lab Tests in This Article

1. Dahlhamer, J. M. (2016). Prevalence of Inflammatory Bowel Disease Among Adults Aged ≥18 Years — United States, 2015 | MMWR.

2. Veauthier, B., & Hornecker, J. R. (2018). Crohn’s Disease: Diagnosis and Management. Am Fam Physician, 98(11), 661–669.

3. What Should I Eat? (n.d.). Crohn’s & Colitis Foundation.

4. Wan, P. (2014). Advances in treatment of ulcerative colitis with herbs: From bench to bedside. World Journal of Gastroenterology, 20(39), 14099.

5. Triantafyllidi, A., Xanthos, T., Papalois, A., et al. (2015). Herbal and plant therapy in patients with inflammatory bowel disease. Annals of Gastroenterology, 28(2), 210–220.

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