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An Integrative & Functional Medicine Approach to Optimal Intestinal Health 

Hippocrates was an ancient Greek physician who is considered the father of medicine. He is quoted saying "All Disease Begins in the Gut," and we believe this is as true today as it was hundreds of years ago.

Healthy Gut
  • Proper nutrition substrates consisting of micronutrients and phytonutrients

  • Optimal pH and digestive enzymes

  • Healthy diverse microbiome

  • Intact intestinal epithelial barrier

  • Superior immune health

  • Autonomic balance


A Sick Gut
  • Poor diet

  • Dehydration

  • Interaction of Medications

  • Infections

  • Toxins (food, metals, molds)

  • Inadequate stomach acid and digestive enzymes

  • Dysbiosis (lack of bacterial balance)

  • Impaired intestinal permeability (leaky gut)

  • Alterened neuroendocrine balance and autonomic function

Irritable Bowel Syndrome (IBS)


IBS is a common disorder that affects the intestines, and can cause whole-body symptoms as well. The most common symptoms are cramping, abdominal pain, bloating, gas, diarrhea and constipation. It is often a chronic condition that waxes and wanes with no apparent reason. Nausea, fatigue, and insomnia are also common. Clinical studies show that altered gut bacteria (dysbiosis) can also contribute to weight gain and depression.

When to Suspect Digestive Dysfunction


  • Bloating or belching following a meal

  • Flatulence after eating

  • A sense of fullness after eating

  • Chronic intestinal infections

  • Undigested food in stool

  • Iron deficiency

  • Unintentional weight loss

  • Chronic diarrhea

The Integrative/Functional Medicine approach to IBS aims at discovering the root cause of the problem and treating it accordingly.  Rarely will treatment protocols be exactly the same for two different people, although the approach to diagnostic testing may be similar.  Tests are used to access digestion, food allergies, the microbiome, intestinal permeability, and inflammation. In Functional Medicine the “5R” framework outlines the goals of diagnosis and treatment:




What needs to be removed? Allergy testing may reveal foods in which an individual is allergic, sensitive, or intolerant. Pathogenic bacteria and yeast may be discovered on stool analysis and require treatment to eradicate. Environmental pollutants and contaminants may be an issue. Lastly physical and emotional stress may be contributing to poor overall health.




What needs to be replaced? Quality nutrient dense food is often lacking in the standard American diet and must be replaced. Stomach acid and digestive enzymes are critical to nutrient absorption and may need to be replaced. Dietary fiber is also critical to maintain stool consistency and is commonly prescribed.




This refers to the reintroduction of desirable GI microflora (prebiotics, probiotics, synbiotics) to obtain a more desirable balance to the intestinal milieu. Probiotic species of Bifidobacteria and Lactobacillus are important to maintain as well as the good yeast Saccharomyces boulardii.  Prebiotics are foods that maintain the good bacteria, like inulin, fructooligosaccharides (FOS) and various other soluble fibers. Synbiotics are combinations of prebiotics and probiotics. Ideally supplements are only used to reset the system, as these factors can be achieved with a healthy diet.




Repair is focused on providing nutritional support for healing and regeneration of the GI mucosa. Medical nutritional formulas contain specialized ingredients such as glutamine, amino acids, vitamins and phytonutrients. Botanicals like turmuric (curcumin), aloe, marshmallow, and ginger are known to promote gut healing. Nutritional anti-oxidants and anti-inflammatories like fish oil high in EPA/DHA may also be beneficial. Immune support in the form of immunoglobulins may be utilized as well.




Balance is aimed at providing stress reduction to the GI tract through mindful eating and better food choices. Overall stress-reduction techniques may include biofeedback via heart-rate variability, yoga, prayer, meditation, and breathing exercises. Often these modalities prove the most useful but are not given the same value as other treatments. We encourage a stress reduction practice.

The first step in figuring out the puzzle of IBS is to obtain a careful history that includes dietary choices, recent antibiotic exposure, and anything significant in the past that could contribute to GI dysfunction.


  • Diet diary

  • Travel history

  • Allergy history

  • Surgical history

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 a prescription 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 suffering from IBS and eliminates symptoms in up to 80% of patients.




Low stomach acid, or hypocholrhydria causes the following symptoms:


  • Bloating, belching, burning, and flatulence after meals

  • Fullness after eating

  • Diarrhea or constipation

  • Food allergies

  • Nausea after taking supplements

  • Itching around the rectum




Sometimes low stomach acid is mistaken for acid reflux because the symptoms are similar. People treated with acid-blocking agents long term may eventually suffer from the effects of low stomach acid.  Proton-pump inhibitors (Dexilant, Nexium, Prevacid, Prilosec, Zegerid, Protonix, Aciphex) are intended for short-term use for acid reflux disease. Proton pump inhibitors are associated with electrolyte abnormalities, pneumonia, interstitial cystitis, Clostridium difficile colitis, and hip fractures. These medications must be weaned slowly to prevent rebound gastritis caused by the hormone gastrin, which becomes high in response to the stomach’s low acid content. We recommend deglycerized (DGL) licorice to treat mild reflux disease, as there are virtually no side effects, and it can be taken while one is weaning off acid lowering medications.  Many DGL products also contain marshmallow, slippery elm, and aloe vera to soothe the stomach and promote barrier function. Low stomach can be encountered with aging. Taking an acid supplement is an easy way to determine if this is the case, and much easier than trying to measure the acid in the stomach with pH probes.

Low Bile Salts

Symptoms of Bile Insufficiency:


  • Diarrhea

  • Abdominal pain

  • Gas and bloating

  • Water retention


  • No gallbladder/gallbladder disease

  • Liver disease

  • Thyroid issues

  • Small bowel removal

Bile is a soap-like substance made from cholesterol by the liver and stored in the gallbladder. Bile salts emulsify the fats from our food so that our lipase enzymes can digest fats and fat-soluable vitamins. People who have had their gallbladders removed do not concentrte bile salts. People who have liver or gallbladder disease or who have had their distal small bowel removed often beneit from taking extra bile salts. Testing for fats in the stool is a good indicator of bile acid insufficiency.

Low Digestive Enzymes

The most common digestive enzyme insufficiencies:


Lactose Intolerance: A large majority of the world's population is lactose intolerant due to a lack of the enzyme lactase.

Gluten Intolerance: People with Celiac disease cannot digest gliaden, the protein found in wheat, due to a lack of protetin-splitting enzymes.

Fructose intolerance:



Digestion starts when we chew food, by the enzyme amylase, found in saliva. Food mixed with stomach acid triggers the pancreas to secrete several enzymes. There are separate enzymes for digesting fats, carbohydrates, proteins, pectins, and phytic acid.  The fat-splitting enzymes are called lipases, the carbohydrate-splitting enzymes are called amylases, and the protein-splitting enzymes are called proteases. Pectinase enzymes break down pectins found in fruits. Phytase enzymes help to break down phytic acid found in grains and beans. Digestive enzymes are found in food, with raw foods containing the most viable enzymes. Cooked, packaged, and processed foods are enzyme depleted. Many people have enzyme deficiencies and studies show that 50% of people over age 50 have enzyme deficiencies.  Comprehensive stool analysis, as well as Nutritional Evaluations, helps determine if enzyme deficiencies exist. Supplemental proteolytic enzymes can improve protein digestion and limit the quantity of antigens that leak into the bloodstream, thus reducing food allergies.



Benefits of dietary fiber:


  • Improvement in bowel function

  • Prevents hemorrhoids and anal fissures

  • Prevents obesity

  • Keeps intestinal pH in balance

  • Normalize cholesterol

  • Reduces heart disease

  • Reduces high blood pressure

  • Reduces cancer incidence

Dietary fiber consumption is often inadequate. Soluble fiber found in fruits, beans, barley, rice, and flaxseed helps to bind bile acids, regulates cholesterol and blood glucose levels, and keeps our intestinal pH in balance. Insoluble fiber found in bran, vegetables, whole grains and carrots helps keep bowel movements regular and normalizes peristalsis. Insoluble fiber is fermented in our large intestines by beneficial bacteria to produce butyrate and other short-chain fatty acids that provide fuel and cell-maintenance in the colon.

The Microbiome and Dysbiosis

The gut microbiome is made up of trillions of bacteria that live in the gastrointestinal tract and together provide the same metabolic capacity as the human liver. A healthy microbiome is biologically diverse and provides the structural framework for optimal digestion, nutrition, immunity, and metabolic processes. When this delicate balance is disrupted it is termed dysbiosis, and symptoms of impaired digestion, nutrition, and immunity soon follow. Comprehensive stool analysis can identify the major bacterial colonies in the stool and guide probiotic supplementation to correct and rebalance the microbiome.

Common Symptoms and Diseases Associated with Dysbiosis:

  • Arthritis

  • Asthma

  • Autoimmune Disease

  • Bad breath

  • Belching

  • Bloating

  • Bowel urgency

  • Celiac disease

  • Constipation

  • Cramping

  • Acne

  • Depression/Anxiety

  • Diarrhea

  • Digestive Infections

  • Fatigue

  • Fibromyalgia

  • Food allergies/intolerances

  • Foul-smelling stools

  • Indigestion

  • Gas

  • Gastritis

  • Inflammatory Bowel Disease

  • Interstitial cystitis

  • Irritable Bowel Syndrome

  • Itching of the vagina/anus

  • Mucus or blood in stool

  • Nausea after taking supplements

  • Rectal itching

  • Restless leg syndrome

  • Sinus congestion

  • Skin conditions

  • Undigested Food in Stool

  • Weight loss or Obesity/Malabsorption

There are many causes of dysbiosis but by far the most common is antibiotic use. While antibiotics are meant to kill “bad” bacteria they often wipe out significant colonies of “good” bacteria and lead to an overgrowth of “potentially bad” bacteria. Antacids and Proton-pump inhibitors act by blocking stomach acid, which is the first line of defense against bad bacteria, and long term antacid therapy frequently leads to dysbiosis. A poor diet high in fat, sugar, and processed foods act to feed the “bad” bacteria and starve the “good bacteria” leading to dysbiosis. Dysbiosis can be corrected through dietary changes, pre-biotics, and probiotics.



Candida is a type of fungus that can cause a yeast infection in the gastrointestinal tract. It is an opportunistic infection commonly triggered by antibiotics, too many sweets, alcohol, birth control pills, or steroids.  Once candidiasis is established it can cause:

  • abdominal bloating

  • anxiety

  • constipation

  • depression

  • fatigue

  • food sensitivities

  • foggy thinking

  • insomnia

  • low blood sugar

  • recurring vaginal or bladder infections

  • enviornmental sensitivities

Stress Reduction

During times of rest, digestion is at its best. Stress results in chemical neurotransmitters that send signals to the GI tract to slow down GI secretions and motility. In chronic stress, digestion can shut down or be severely compromised. Stress and emotions play a big part in many digestive disorders including IBS. The following techniques are recommended daily:


  • Breathing techniques (pranayama)

  • Meditation

  • Prayer

  • Spending time in nature

  • Gardening

  • Yoga

  • Time with pets

  • Relaxing hobbies

Small Intestinal Bacterial Overgrowth (SIBO)


An overgrowth of bacteria can occur in the small bowel when there is poor acid production from the stomach or an insufficient amount of pancreatic enzymes function. Some studies report that 78% of people with IBS had underlying SIBO. People with fibromyalgia also have been found to have SIBO, and when treated, nearly 50% of them no longer meet the symptom criteria for fibromyalgia. SIBO is also seen in diabetics, gastric bypass surgery patients, and patients with inflammatory bowel disease. SIBO triggers an immune response that stimulates the enteric nervous system causing gas, bloating, abdominal discomfort, diarrhea, constipation, or alternating diarrhea and constipation. Bacterial overgrowth causes rapid fermentation of carbohydrate sugars, which can be detected on a hydrogen breath test. The treatment of SIBO involves antibiotics. Rifaxamin is an antibiotic that works locally in the digestive tract, without systemic side effects, and is commonly used to treat SIBO. The probiotic VSL#3 is also used to provide adequate numbers of healthy bacteria. Many clinicians also prescribe a special diet called FODMAP, which is an acronym that stands for Fermentable Oligosaccharides, Disaccharides, Monosaccharides and Polyols. The FODMAP diet is ideal for decreasing bacterial overgrowth.

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