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Inflammatory Bowel Disease

Inflammatory Bowel Disease (IBD) consists primarily of Ulcerative Colitis (UC) and Crohn’s disease. Although distinctly different, both are considered autoimmune conditions that affect the bowel locally and other parts of the body systemically. Medical management is aimed at immune suppression. Surgical management is indicated when medical management fails and involves the removal of involved bowel. IBD does increase the chances of bowel cancer and should be monitored closely with endoscopy. 

An Integrative and Functional Medicine Approach to IBD

The development of IBD is a complex process that involves genetic predisposition, triggers from the environment, inflammatory mediators and an immune system response that results in the expression of disease. The goal is to investigate this complex puzzle and reverse the process as much as possible. Because each individual is unique, each disease process is unique and varies in presentation. Treatment plans must be customized based on individual symptoms and test results. IBD can be successfully reversed in many individuals. 

Many clinicians utilize specialized testing through Prometheus Therapeutics and Diagnostics. The Prometheus IBD sgi diagnostic panel combines Genetic testing with serology and inflammatory markers to predict prognostic accuracy.

Keeping a diet diary is useful in determining food intolerances and food triggers. If possible record  your diet for 7-14 days and bring this to your office visit with us for evaluation.

A Detailed History

An extensive medical history is necessary when trying to determine the causative and contributing factors that lead to inflammatory bowel disease. In functional medicine circles, we look at antecedents, triggers, and mediators. 


Antecedents are any factors, genetic or acquired, that predispose to illness. Antecedents do not cause disease but are essential to its formation. There are several antecedents distinctive to IBD:


  • Positive family history

  • Cesarean birth

  • Formula fed/lack of breast-feeding as an infant

  • Intolerance to cow’s milk

  • Allergic symptoms, asthma, rhinitis

  • Exposure to antibiotics

  • Gastrointestinal infections

  • Dietary factors

  • Abnormal gut permeability

  • Deficiency of Vitamin D

  • Second hand smoke exposure

  • Smoking (for Crohn's disease)

  • Oral contraceptive use

  • Hormone replacement therapy

  • Appendectomy (for Crohn's disease)

  • Treatment of acne with isotretinoin (Accutane)

Triggers are things that provoke an illness or the emergence of symptoms or an exacerbation of symptoms. Triggers do not cause disease in and of themselves; all triggers exert their effects through the activation of host-derived mediators. Important triggers include:


  • Certain Foods and food antigens (yeast, gluten)

  • Allergens

  • Drugs

  • Environmental toxins/industrial chemicals

  • Nonsteroidal anti-inflammatory drugs (NSAIDs)

  • Small bowel bacterial overgrowth (Crohn's)

  • Infectious agents

    • Clostridium difficile (UC)

    • Mycobacterium avium paratuberculosis (Crohn's)

    • Certain strains of E. coli associated with proinflammatory cytokine expression and decreased epithelial barrier function

    • Cytomegalovirus

    • Yersinia enterocolitica

    • Blastocystis

    • Campylobacter

    • Entamoeba histolytica

    • Salmonella

    • Plesiomonas shigelloides

    • Strongyloides stercoralis

  • Stressful life events

  • Adverse social interactions

  • Powerful memories

  • Depression


In chronic illnesses, multiple interacting triggers are often present, which leads to disease exacerbations. Understanding the importance of the gut microbiome as an immune regulator is paramount to reversing IBD.

Mediators are intermediaries that contribute to the manifestation of disease. Mediators vary in form and substance and oddly lack disease specificity. Examples of mediators include:


  • Biochemical (prostanoids and cytokines)

  • Social (reinforcement for staying ill)

  • Psychological (fear)

  • Cultural (beliefs about the nature of illness)


Common mediators include hormones, neurotransmitters, neuropeptides, free radicals, fear of pain or loss, poor self-esteem, learned helplessness, lack of relevant health information, and social isolation.  Secondary mediators are also important and include:


  • Nutritional deficiencies

    • Vitamin deficiencies (Vit E, D, A, C, B6, B12)

    • Calcium

    • Folate

    • Iron, ferritin

    • Hemoglobin

    • Albumin

    • Zinc

    • Beta-carotene

    • Magnesium

    • Selenium

  • Systemic effects of inflammation

    • Oxidative stress

    • Osteoporosis

    • Muscle wasting

    • Hypogonadism

    • Malnutrition

    • Depression

  • Iatrogenic factors (induced by medical management)

    • Mesalamine induced folic acid deficiency

    • Steroid induced metabolic, dermatologic, ocular, and neuropsychiatric disturbances

    • Biologic therapy induced cancers

  • Psychosocial factors

    • Lower quality of life

    • Lower sense of well-being

    • Decreased social support

    • Increased levels of stress and anxiety

    • Increased unemployment 

Seeking and Gathering Information in IBD:

The diagnosis and management of IBD aims at getting to the root of the problem. In addition to routine labs, endoscopy, and medical imaging, a more detailed work up is sought that may look specifically at the following factors: 


  • Digestion/Absorption

    • Hypochlorhydira (to little stomach acid)

    • Food intolerance

    • Villous Atrophy (Celiac disease)

    • Pancreatic insufficiency (lack of digestive enzymes)

    • Small Intestinal Bacterial Overgrowth (SIBO)

  • Inflammation/Immunity/Infection

    • Food sensitivity (IgG) and Allergy (IgE)

    • Neutrophilic inflammation (Infection, IBD, Cancer)

    • Eosinophilic Inflammation

    • Infection (Bacterial, viral, parasitic)

    • Gluten Sensitive Enteropathy (Celiac)

  • Gut Bacterial Flora/Dysbiosis

    • Beneficial bacteria

    • Opportunistic bacteria

    • Infectious baceria

    • SIBO

    • Candidiasis (yeast infection)

  • Intestinal Permeability/Leaky gut

    • Food intolerance

    • Parasites

    • Dysbiosis

    • Autoimmune manifestations

Dysbiosis-overpopulation of bad bacteria and to few good bacteria
Leaky Gut-compromised intestinal permeability, lack of protective barrier
Immune system dysregulation-in response to abnromal absorption of large food particles and toxins
Specialized Testing: Some tests are valuable, while others are simply supportive. Not every patient requires testing. We find that comprehensive stool analysis, parasitology and complete nutritioanl evaluations are the most helpful tests to guide specific dietary and supplement therapies.

Comprehensive Digestive Stool Analysis: This is a home test kit that is collected over 1-3 days. It provides information about bacterial balance, digestive function, and dysbiosis. If pathogenic bacteria and yeast are detected sensitivities are given to antibiotics and herbals. Inflammatory markers and parasitology is also reported. We use test kits from Genova Diagnostics and Doctors Data Inc.


Parasitology Testing: It is estimated that 1 in 6 persons harbor parasites. It is estimated that 23% of persons with IBS symptoms have parasites.  More than 130 parasites have been found in Americans, with Blastocystis hominis being the most common. Parasites have unusual life cycles and can be difficult to detect. For this reason, we use double testing with two separate labs, generally Genova or Doctors Data and Bio Health Laboratory.


Celiac Disease: Antibody tests are utilized including tTG-IgA, and EMA-IgA. Total serum IgA is also useful. In IgA deficiency, Ig-G testing must be used, or genetic testing of HLA-DQ2 and HLA-DQ8. Antibody testing is only accurate when a patient is on a gluten-containing diet. Genetic testing does not require gluten.


Candida Testing: Organic acid urine testing is a handy non-invasive way to check for by-products of cellular metabolism, digestion, and the metabolism of the gut microbes and yeast. Genova’s metabolic analysis urine test also measures neurotransmitters, vitamins, and mitochondrial metabolites.


Small Intestinal Bacterial Overgrowth: This is a hydrogen breath test that measures breath levels of hydrogen or methane to determine whether there is a bacterial infection in the small intestine.


Lactose Intolerance Test: this is a breath test in which hydrogen and methane is measures after ingestion of a lactose solution.


Intestinal Permeability Testing:  This is a urine test taken at baseline and then in intervals after drinking a mannitol/lactulose mixture.


Nutritional Evaluation Testing: The NutraEval test from Genova is a comprehensive nutritional evaluation that includes a metabolic anaylsis, amino acid profile, essential and metabolic fatty acid profile, oxidative stress markers, and an elemental analysis of toxic exposures.


Prescription Diets for IBD

Food is the best medicine for reversing and controlling inflammatory bowel disease. We frequently recommend the following:


  • Elimination Diet

  • Specific Carbohydrate Diet

  • FODMAP Diet

  • Candida Diet

Elimination Diet


The elimination diet is a whole food healthy diet that allows fruits, vegetables and organic healthy proteins (wild-caught fish and poultry). This is an excellent diet that is used to determine food allergies and sensitivities. The “common culprit” foods are eliminated for a period of time, and then gradually added back to see if symptoms arise. This is an excellent diet for those unclear about the diagnosis of IBD, as well as an excelllent detox from the standard American diet.

Specific Carbohydrate Diet


The Specific Carbohydrate Diet (SCD) was designed for patients with Ulcerative Colitis and Crohn’s disease. The allowed carbohydrates are monosaccharaides that are easily absorbed by the intestines. Adhering to this diet produces excellent results in those who suffer from IBD. For more information please visit the following web sites:





FODMAP is an acronym that stands for:

Fermentable – meaning they are broken down (fermented) by bacteria in the largebowel

Oligosaccharides – “oligo” means “few” and “saccharide” means sugar. These molecules made up of individual sugars joined together in a chain

Disaccharides – “di” means two. This is a double sugar molecule.

Monosaccharides – “mono” means single. This is a single-sugar molecule.


Polyols – these are sugar alcohols (however don’t lead to intoxication!)


The FODMAP diet is ideal for decreasing small bowel bacterial overgrowth. It is good for patients who have had their right colon removed and J-pouch patients. Search for more information at




Candida Diet


The candida diet restricts carbohydrates in order to starve off yeast and some bacterial pathogens. Allowed foods include vegetables that grow above the ground, proteins, yogurt, fats, and oils.

Healing Foods


  • Organic Bone Broth

  • Organic Chicken Stock

  • Dahl with Turmeric and Ginger

Medical Foods & Prescription Supplements

Clinical studies support several supplements in treating and reversing IBD. There are many other useful supplements depending on individual patient laboratory profiles, and each patient should be treated accordingly.


Anti-Inflammatory Medical Food- Medical food powders are formulated to provide  macro- and micro-nutrient support for patients with compromised intestinal function. Many products also contain healing anti-inflammatory herbs and immunoglobulin’s.


Probiotics- Clinical studies have shown that multi-strain probiotics aid in achieving remission in IBD. VSL#3 is quoted in most studies and can be found at VSL#3 is an eight-strain probiotic that does come in a prescription form, which some insurance companies cover. There are many other multi-strain probiotics on the market as well.


Fish Oil-The anti-inflammatory properties of the omega-3 fatty acids EPA and DHA found in fish oil has been shown to de crease inflammation in IBD. The dose of EPA/DHA should be 1500mg taken twice a day. It is helpful to look for formulas that have high levels of EPA/DHA.


Vitamin D- Vitamin D is often found to be low in patients with IBD. 25-hydroxy vitamin D is easy measured through standard laboratory testing. Reference ranges from 20-100 ng/mL are standard for “normal,” but we like to correct vitamin D deficiency until it is well above 50 ng/mL.


Curcumin-Curcumin is the active ingredient in turmeric, a popular spice found in curry and mustard.  Curcumin has been shown to improve patient symptoms and allow decreases in the use of steroids.


Boswellia- (Boswellia  serrata) is also known as Indian frankincense and is a gum resin from the bark of the boswellia tree.  It contains anti-inflammatory properties and has been used for arthritis, and many forms of colitis.  The dose for IBD is 350-400 mg of 65% boswellic acids up to three times a day. Boswellia may interact with antibiotics, NSAID’s, sedatives, and chemotherapy drugs and should be used only under physician supervision.


Dr. Pennington recommends specialty medical foods and supplements from professional nutraceutical manufacturers. She uses companies such as Metagenics, Thorne Research, Xymogen, and Pure Encapsulations.  Based on patient test results and individual needs the following products may be recommended:

Stress Management

Stress is an important trigger that must not be overlooked in the management of IBD. Studies have shown that emotional stress contributes to IBD flares. Stress managment may include:


  • Breathing exercises (pranayama) 

  • Meditation

  • Prayer

  • Yoga

  • Pet therapy

  • Massage

  • Acupuncture

IBD Treatment Summary

When it comes to IBD, one size does not fit all. Individualized treatment strategies should be used based on your specific needs.


  • Detailed history

  • Specific Labratory Tests

  • Prescription Diet

  • Lifestyle Changes

  • Stress Reduction

  • Targeted Nutriceuticals and Supplements

  • Individualized Care Plan

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