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Functional Gastrointestinal Disorders: Diagnosis and Treatment

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Functional Gastrointestinal Disorders: Diagnosis and Treatment

Functional gastrointestinal disorders (FGIDs) are a diverse group of conditions characterized by chronic or recurrent symptoms related to the gastrointestinal (GI) tract. These disorders affect up to 40% of people, are often associated with a marked impact on quality of life, and can lead to significant psychological distress and functional impairment. In addition, FGIDs are associated with a significant economic burden due to direct and indirect costs.

A growing body of evidence suggests that FGIDs are associated with alterations in the gut microbiota, GI motility and permeability, immune dysfunction, and neurological abnormalities, including increased visceral sensitivity of the GI tract. However, the exact nature of these alterations remains to be fully elucidated. The management of FGIDs typically involves a multimodal approach, including lifestyle modification, dietary modification, and pharmacotherapy. In some cases, psychological therapies may also be indicated. If you or a loved one suffer from these disorders, this article can help you understand functional medicine approaches to treating FGIDs so that you can heal and thrive.


Functional GI Disorders Overview

​​Functional gastrointestinal disorders (FGIDs) are conditions characterized by chronic disruptions in gastrointestinal function. Unlike other GI disorders, they lack observable changes to GI anatomy (like ulcers, strictures, or other findings on endoscopy and colonoscopy). The symptoms associated with FGIDs cannot be explained by another diagnosable GI disorder. FGIDs include irritable bowel syndrome (IBS), functional dyspepsia (FD), abdominal migraine, functional abdominal pain not otherwise specified (NOS), and functional constipation (FC).

Common Symptoms Of Functional GI Disorders

The symptoms of FGIDs vary based on which type of FGID someone is experiencing, but in general, they all involve abdominal discomfort, changes in stool habits and form, and digestion issues. Specific symptoms associated with each FGID include

Irritable Bowel Syndrome (IBS)

ROME IV criteria for IBS state that symptoms of abdominal pain have to have occurred for at least one day per week, every week, for the past three months. Additionally, the symptoms above must be characterized by at least 2 of the following symptoms:

  • Abdominal pain is related to bowel movements.
  • Abdominal pain is associated with a change in stool frequency.
  • Abdominal pain is associated with a change in the form or appearance of stool.

Functional Dyspepsia

ROME IV criteria for functional dyspepsia includes

  • Frequent and bothersome sensations of fullness after eating
  • A bothersome sensation of early satiety
  • Stomach pain or burning that is unrelated to bowel movements

Abdominal Migraines

Symptoms are characterized by episodes of intense central abdominal pain associated with at least two of the following

  • Nausea
  • Vomiting
  • Headache
  • Photophobia (light sensitivity)
  • Pallor (looking pale)
  • Anorexia (lack of appetite)

Functional Abdominal Pain Not Otherwise Specified

Abdominal pain can be constant or intermittent but occurs at least four times a month. It cannot be explained by another medical condition or physiologic condition like eating or menstruation.

Functional Constipation

At least once a month, people with constipation experience:

  • Two or fewer bowel movements per week
  • History of excessive stool retention
  • History of hard or painful bowel movements
  • History of large bowel movements
  • Large fecal masses in the rectum or that obstruct the toilet

What Causes Functional GI Disorders

There is no singular cause of FGIDs. Instead, various factors contribute to the development of functional gastrointestinal disorders. There is a growing body of evidence to suggest that FGIDs are associated with alterations in the gut microbiota (including infection), GI dysmotility and permeability, immune dysfunction, and neurological abnormalities, including increased visceral sensitivity of the GI tract. Researchers have established a link between stress, allergic disorders, gastrointestinal infections, abdominal surgeries with the development of FGIDs.

Functional Medicine Diagnosing of Functional GI Disorders (FGIDs)

FGIDs can only be diagnosed once all diagnosable medical conditions have been ruled out. Tests that can help a physician rule out medical disorders so that a FGID diagnosis can be made include

Ruling Out Celiac Disease

Symptoms of celiac disease can mimic those of FGIDs, including altered bowel habits like diarrhea and stomach pain. Testing for celiac disease typically includes antibodies to t-TG2, endomysial, and deamidated gliadin peptide, the Wheat Zoomer (IgE, IgG, IgA), Elisa LRA Gluten Panel (IgG, IgM, IgA), and Genova Diagnostics Celiac and Gluten Sensitivity Panel (IgG & IgA).

Ruling Out IBD

It's important to rule out inflammatory bowel disease (IBD) before diagnosing a functional GI disorder. Colonoscopies are the gold standard for diagnosing IBD. Inflammatory blood and stool test markers commonly associated with IBD include fecal or serum calprotectin, fecal lactoferrin, and serum C-reactive protein (CRP).

p-ANCA and ASCA antibodies are often used to assess the disease state in IBD, and PEI (pancreatic exocrine insufficiency) is also associated with IBD.

FIT (fecal immunochemical testing)

FIT can screen for structural issues in the colon that cause bleeding. It can be run independently or as part of more comprehensive functional medicine tests like the GI Comprehensive Profile.

SIBO Testing

A SIBO breath test can rule out small intestinal bacterial overgrowth as a cause of gastrointestinal dysfunction and pain.

FGID Root Cause Testing

To find the root cause of FGIDs, a doctor may order some or all of the following tests.

  • Complete Blood Count: A CBC can help detect issues with the immune system or nutrient deficiencies that can contribute to gut distress.
  • Comprehensive Stool Profiles: Stool profiles can detect several possible GI disorders, including pancreatic enzyme insufficiency, microbial and fungal overgrowth, and hydrochloric acid deficiencies. It can also detect infections like H. pylori, parasites, campylobacter, and more.
  • Food Sensitivities testing can help determine if a patient reacts to a specific food, which could worsen FGID symptoms.
  • Food allergy testing is also helpful since allergic disorders are linked to functional gastrointestinal issues.
  • Pancreatic insufficiency testing: Pancreatic insufficiency (PEI) can cause many symptoms associated with FGID. A Fecal Elastase-1 test can be used to diagnose PEI. Values under 200 are considered diagnostic for pancreatic exocrine insufficiency.
  • Iron and ferritin rule out iron storage diseases like hemochromatosis, which can impact pancreatic function and result in digestion issues.
  • Salivary Cortisol: Measuring cortisol levels throughout the day can help detect abnormal responses to stress that may affect FGID symptoms.
  • Diabetes Testing: A1C testing can be used to screen for diabetes, which can affect digestion and result in conditions like gastroparesis that can mimic FGIDs.
  • Thyroid Testing: thyroid conditions can worsen FGID symptoms like constipation.

Functional Medicine Treatment for Functional GI Disorders

A functional medicine approach to treating functional gastrointestinal disorders always focuses on healing the root cause. If blood sugar issues are present, for example, a functional medicine approach to normalizing blood sugar may help to improve GI symptoms. If the problem is SIBO or dysbiosis, treating the microbiome may improve FGID.

However, various treatments have been shown to improve FGIDs in general. These include psychotherapy, regular exercise, and probiotic supplementation. Nutritional approaches can help improve symptoms of FGIDs, including removing atypical allergens like wheat and adopting a whole foods eating pattern. People with diarrhea should avoid caffeine, and people with dyspepsia should avoid overindulging in alcohol.

Mind-body-spirit approaches can also help to improve symptoms of FGIDs, including gut-directed hypnotherapy and cognitive behavioral therapy. Interestingly, a placebo can improve symptoms in 41% of children with FGIDs.

Coping with Functional GI Disorders

Living with FGID symptoms can be difficult and painful if they're not controlled. There's evidence, for example, that chronic pain from conditions like FGID can impact school performance and learning children. FGIDs also have a bidirectional relationship with mood disorders, including anxiety, and can worsen mental health issues.

An integrative care team that includes a primary care clinician, gastroenterologist, nutritionist or registered dietitian, functional medicine doctor, therapist, and more can help people living with FGIDs get to the root cause.


Functional gastrointestinal disorders (FGIDs) are associated with symptoms that include stomach pain, bowel changes, dyspepsia or indigestion, and more. A functional medicine approach to functional gastrointestinal disorders can help people to find and treat the root cause of the GI issues so that they can heal and thrive.

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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