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A Functional Medicine Constipation Protocol: Testing, Nutrition, and Supplements

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A Functional Medicine Constipation Protocol: Testing, Nutrition, and Supplements

Constipation is a common functional gastrointestinal disorder in children and adults, affecting 20% of the general population. Chronic constipation compromises the quality of life, social functioning, and the ability to perform activities of daily living. Conventional treatment options for constipation include fiber supplements and prescription stool softeners, laxatives, and motility agents, and patients often depend on these agents long-term for normal bowel function.

Functional medicine doctors are trained in understanding the physiologic mechanisms underlying normal bowel habits and are equipped with specialty testing that can identify commonly overlooked contributors to functional constipation. This article will explain functional constipation and a functional medicine approach to its evaluation and treatment.


What is Functional Constipation?

Functional constipation is a functional gastrointestinal disorder (FGID) that presents as persistent, difficult, infrequent, and seemingly incomplete evacuation. Unlike other types of constipation, and like other FGIDs, functional constipation has no identifiable cause and lacks observable changes to gastrointestinal (GI) anatomy. Functional constipation is often the consequence of behavioral and environmental factors, to be discussed in more detail later in this article.

Per the Rome IV Criteria, functional constipation is diagnosed when at least two of the following symptoms have been present for at least three months:

  • Straining during more than 25% of defecations
  • Lumpy or hard stools more than 25% of defecations
  • A sensation of incomplete evacuation in more than 25% of defecations
  • A feeling of anorectal obstruction/blockage in more than 25% of defecations
  • Manual maneuvers are required to facilitate more than 25% of defecations (e.g., digital evacuation, support of the pelvic floor)
  • Fewer than three spontaneous bowel movements weekly
  • Loose stools are rarely present without the use of laxatives
  • Insufficient criteria to meet the diagnosis of irritable bowel syndrome (IBS)

Functional Constipation Signs & Symptoms

Common symptoms of chronic, functional constipation include (1, 2):

  • Infrequent bowel movements
  • Straining during bowel movements
  • Hard, dry, or lumpy stools
  • Painful passing of bowel movements
  • A sensation of incomplete evacuation after bowel movements
  • Abdominal pain
  • Gas, bloating, and abdominal distension
  • Hemorrhoids, anal fissures, and rectal bleeding

Children, especially infants, may have difficulty communicating they are constipated. Therefore, watching for bowel and behavioral patterns consistent with chronic constipation in the pediatric population is important. The following symptoms, along with those listed above, can indicate functional constipation in children (3):

  • Going several days without a bowel movement
  • Rectal bleeding
  • Fecal incontinence in toilet-trained children
  • Irritability
  • Crossing legs, clenching buttocks, or making faces to try to hold in stool
  • Fear of having a bowel movement

What Causes Functional Constipation?

When conventional labs and imaging rule out secondary causes of chronic constipation, patients are diagnosed with functional constipation. Functional constipation can be categorized into normal-transit constipation, slow-transit constipation, and evacuation disorders. There isn't a firm consensus on why these constipation subtypes develop; however, it is understood to be at least partially impacted by behavioral habits, nervous system dysfunction, and diet. (4)

Diets characterized by a high intake of processed foods and animal products and insufficient fiber, such as the Standard American Diet (SAD), are associated with FGIDs. Additionally, poor food quality associated with SAD increases the risk of micronutrient deficiencies, like vitamin C, magnesium, and potassium, associated with higher rates of constipation. (5)

Food sensitivities contribute to the development of leaky gut, GI inflammation, and dysbiosis, all of which frequently manifest as constipation. Gluten and dairy, common food culprits responsible for food sensitivities, are typically eaten in large amounts by people following SAD. (6, 7)

Fiber is a plant component that is resistant to digestion by human enzymes. Soluble and insoluble fiber supports digestive function through various mechanisms. First, it acts as a prebiotic for the colonic microbiota, which produces short-chain fatty acids (SCFAs) through fiber fermentation. SCFAs are an important energy source for intestinal cells but also support the function of the nerves supplying the GI tract, increasing gut motility. Fiber can hydrate and bulk stool, supporting fecal consistency and transit through the GI tract. Diets that lack fiber are associated with increased colonic transit times and chronic constipation. (8, 9)

Lifestyle factors, such as a sedentary lifestyle, chronic stress, poor eating hygiene, and habitual delayed defecation, can contribute to dysbiosis and neurological dysfunction of the enteric and parasympathetic nervous systems. This can result in altered GI motor and immune function, blood flow, and mucosal and digestive secretions, negatively impacting digestive and GI function. (10, 11)

Functional Medicine Labs to Test for Root Cause of Functional Constipation

Functional medicine labs help practitioners personalize treatment options for their patients. Below are some of the most common labs ordered for patients with functional constipation.

Comprehensive Gut Assessment

Screening for intestinal dysbiosis, infections, and signs of leaky gut with a comprehensive stool analysis is often a functional medicine doctor's first step in working up functional constipation. This extensive assessment of GI health and function measures markers of digestion and absorption, intestinal inflammation, SCFAs, and a complete profiling of the microorganisms living in the large intestine.

Yeast overgrowth is just as likely to cause constipation as imbalances in gut bacteria. Most functional stool tests screen for large intestinal yeast overgrowth; however, they may not catch yeast overgrowing in the upper portions of the digestive tract. Some providers consider the organic acids test (OAT) the most accurate assessment for yeast overgrowth in the body by measuring the metabolic byproducts of yeast instead of relying on stool culture.

A SIBO breath test is used to diagnose small intestinal bacterial overgrowth (SIBO) and intestinal methanogen overgrowth (IMO). These conditions are associated with bacterial overgrowth within the small intestinal and methanogenic overgrowth throughout the GI tract. IMO is more highly associated with constipation-type presentations, although some cases of SIBO can present with mild constipation or mixed stool types.

Food sensitivities can be diagnosed through a blood test that measures antibodies against specific food proteins. Identifying food sensitivities as a cause of leaky gut and constipation can be helpful, especially when personalizing nutritional therapies and elimination diets to alleviate constipation.

Micronutrient Panel

A comprehensive micronutrient panel screens for functional and overt nutrient imbalances that can contribute to constipation and other digestive symptoms. Similar to food sensitivities, these results help target nutritional and supplemental therapies to a patient's nutritional needs.

Stress Panel

Chronic stress causes changes to the hypothalamic-pituitary-adrenal (HPA) axis and cortisol levels. Elevated salivary cortisol and/or dysfunctional cortisol secretion patterns can reflect the predominance of the sympathetic nervous system and reduced GI function.

Chronic stress and elevated cortisol can directly influence the thyroid gland and the secretion of thyroid hormones. Constipation is a common manifestation of subclinical and overt hypothyroidism. Ordering TSH alone to screen for thyroid disease can miss cases of thyroid dysfunction, so ordering a complete thyroid panel is helpful for patients with chronic constipation.


Functional Medicine Treatment Protocol for Functional Constipation

Because functional medicine emphasizes personalizing treatment plans per the patient's lab results and preferences, every protocol will vary slightly. The outline below summarizes general evidence-based nutritional and supplemental recommendations to consider when aiming to reduce intestinal permeability, promote intestinal motility, and support a healthy gut microbiome.

Additional modalities to consider in a treatment protocol for functional constipation include acupuncture, pelvic floor physical therapy, and bowel retraining. These are beneficial in retraining the neuromuscular system of the GI tract and pelvic floor and toning the parasympathetic nervous system to encourage regular bowel habits.

Therapeutic Diet and Nutrition Considerations for Functional Constipation

Avoiding the Standard American Diet in favor of a Mediterranean-type diet can help reduce the risk of functional constipation. With the Mediterranean diet, foods encouraged include whole grains, fruits, vegetables, beans, herbs and spices, nuts, olive oil, fatty fish, and dairy.

Customization of this diet is encouraged depending on food allergies and sensitivities. A short-term dietary elimination of identified food sensitivities should be implemented for 4-6 weeks. After this, the patient should be instructed to reintroduce foods into the diet individually. Each reintroduction should occur over three days, as follows:

  • Day 1: Eat one portion of food three times
  • Days 2-3: Re-eliminate the challenged food, and observe for changes in bowel patterns

If the patient does not experience constipation after this three-day challenge, they can be instructed to reincorporate that food into their diet. Any foods that cause constipation, or trigger any other adverse reactions, should continue to be avoided.

Because low-fiber diets contribute to constipation, ensuring adequate daily fiber intake is essential in any constipation protocol. Foods contain a mix of soluble and insoluble fibers. Soluble fiber dissolves in water, creating a gel-like substance, whereas insoluble fiber remains more intact as it passes through the digestive system. Both types of fiber can ease constipation, and getting at least 25 grams of fiber daily is recommended. Research shows that the effects of fiber can be amplified by staying well hydrated, ensuring daily water intake of 1.5-2 liters daily. (12, 13)

Supplements Protocol for Functional Constipation

The following supplements can be prescribed to patients to encourage bowel regularity and correct imbalances contributing to constipation.

Magnesium Oxide

Low magnesium status is associated with a higher prevalence of constipation. Magnesium oxide has a laxative effect by pulling water into the bowels and stimulating intestinal contractions.

Dose: 400-800 mg nightly before bed

Duration: 1-2 weeks, or as needed


Various species, strains, and doses of probiotics have demonstrated efficacy in increasing the number of weekly bowel movements in patients with constipation, as much as 40% in some studies. Bifidobacterium and Lactobacillus spp. are most commonly tested in clinical trials. (14, 15)

Dose: 1-10 billion CFU

Duration: at least one month


Biocidin is a formula combining 18 botanical extracts and essential oils that acts as a broad-spectrum, natural antimicrobial to treat dysbiosis and improve bowel regularity. Natural antimicrobial herbs, such as berberine, thyme, oregano, and garlic, have effectively treated bacterial infections (including SIBO) and fungal overgrowth.

Dose: Take two capsules three times daily

Duration: 6 weeks


Enteromend is a formula containing L-glutamine, partially hydrolyzed guar gum (PHGG), aloe vera, curcumin, and frankincense. This botanical, amino acid, and prebiotic formula supports gut health by reducing intestinal mucus membrane inflammation and colonic permeability, supporting bowel regularity, and fueling the healthy bacteria of the gut microbiome.

Dose: Mix one scoop in water twice daily

Duration: 4-6 weeks

When to Retest Labs

Complete resolution of chronic constipation can take time; however, with an effective treatment protocol, positive shifts in cellular metabolism and GI function can be seen as soon as 4-6 weeks after initiation.



Functional constipation is a chronic, debilitating gastrointestinal condition characterized by infrequent and difficult-to-pass bowel movements without an identifiable pathological underlying cause. Functional medicine doctors understand that functional gastrointestinal disorders are multifactorial in origin, typically associated with alterations in the healthy gut microbiota, intestinal infections, and neurological dysfunction. Using specialty testing to uncover contributing causes to digestive dysfunction and personalize treatment plans, it is possible to improve bowel function and quality of life for those living with chronic constipation without dependence on pharmacotherapy.

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


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2. Sweetnich, J. (2023, February 16). 4 Medical Conditions That Can Cause Constipation. Rupa Health.

3. Blake, K. (2023, April 6). A Functional Medicine Approach to Treating Constipation in Children. Rupa Health.

4. What is Functional Constipation? (2017, February 21). WebMD.

5. Rollet, M., Bohn, T., & Fardaei, M. (2021). Association between Dietary Factors and Constipation in Adults Living in Luxembourg and Taking Part in the ORISCAV-LUX 2 Survey. Nutrients, 14(1), 122.

6. Concerned About Constipation? National Institute on Aging.

7. Greenan, S. (2021, November 17). The 8 Most Common Signs Of A Food Sensitivity. Rupa Health.

8. Forootan, M., Bagheri, N., & Darvishi, M. (2018). Chronic constipation. Medicine, 97(20), e10631.

9. Bellini, M., Tonarelli, S., Barracca, F., et al. (2021). Chronic Constipation: Is a Nutritional Approach Reasonable? Nutrients, 13(10), 3386.

10. Harvard Health. (2021, February 15). Common causes of constipation.

11. Massey, P. (2022, September 27). Stress and Constipation: What’s the Link? GoodRx.

12. Anti, M., Pignataro, G., Armuzzi, A., et al. (1998). Water supplementation enhances the effect of high-fiber diet on stool frequency and laxative consumption in adult patients with functional constipation. PubMed, 45(21), 727–732.

13. Cloyd, J. (2023, March 22). 10 Differential Diagnoses for Your Constipation Patients. Rupa Health.

14. Ibarra, A., Latreille-Barbier, M., Donazzolo, Y., et al. (2018). Effects of 28-day Bifidobacterium animalis subsp. lactis HN019 supplementation on colonic transit time and gastrointestinal symptoms in adults with functional constipation: A double-blind, randomized, placebo-controlled, and dose-ranging trial. Gut Microbes, 9(3), 236–251.

15. Martínez-Martínez, M.L., Calabuig-Tolsá, R., & Cauli, O. (2017). The effect of probiotics as a treatment for constipation in elderly people: A systematic review. Archives of Gerontology and Geriatrics, 71, 142–149.

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