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A Functional Medicine IBS-C Protocol: Testing, Differential Diagnosis, and Treatment

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A Functional Medicine IBS-C Protocol: Testing, Differential Diagnosis, and Treatment

Irritable bowel syndrome (IBS) is the most common functional gastrointestinal disorder (FGID), with a global prevalence of 12-30%. In the United States, IBS affects up to 45 million people and is responsible for 600,000 office and emergency room visits annually (1, 2). Despite these high numbers, less than 50% of IBS sufferers seek medical help, and 63-84% of those that do experience minimal or no response to conventional treatment options (2).

IBS with predominant constipation (IBS-C) is a subtype of IBS that accounts for more than a third of diagnosed IBS cases. This article will discuss a functional medicine approach and treatment protocol that can be implemented for patients seeking alternative options for IBS management.


What is IBS-C?

IBS-C is the constipation-predominant subtype of IBS. IBS is an FGID related to incohesive brain and gut signaling, which causes intestinal hypersensitivity and dysmotility, leading to abdominal pain associated with changes in stool frequency and appearance. Stated simply, IBS-C is chronic abdominal pain with constipation. (3)

IBS-C Symptoms

The hallmark symptoms of IBS-C are abdominal pain and constipation. Constipation can be described as fewer than three bowel movements weekly; stools that are hard, dry, lumpy, difficult, or painful to pass; or a feeling of incomplete evacuation. To have IBS, a patient must have symptoms that meet the ROME IV criteria, which state abdominal pain must be present at least once weekly for three months and associated with at least two of the following: related to defecation, a change in stool frequency, and a change in stool appearance. (3)

What Causes IBS-C?

Like all FGIDs, there is not a single cause of IBS-C; instead, it is understood to be related to various factors that disrupt normal immune function and gastrointestinal motility. Evidence suggests that such factors may include genetics, infection, dysbiosis, abdominal surgeries, stress, alcohol, and smoking. These factors appear to cultivate a proinflammatory and hypersensitive intestinal environment, which causes slowed gastrointestinal motility (i.e., constipation) and pain. (4-6)

Differential Diagnosis for IBS-C

The characteristic gastrointestinal symptoms of IBS-C overlap with many other conditions. Part of the role of the functional medical provider, therefore, is to construct a comprehensive differential diagnosis to rule out other conditions contributing to and masquerading as IBS. Conditions such as intestinal methanogen overgrowth (IMO), intestinal fungal overgrowth, celiac disease, hypothyroidism, food sensitivities, anxiety, and depression present with IBS-like symptoms and constipation, so they should be appropriately assessed for during the diagnostic process.

Functional Medicine Labs to Test for Root Cause of IBS-C

Standard labs, like a CBC, CMP, and celiac panel, are beneficial in the initial diagnostic process of IBS digestive symptoms but typically result unremarkably. Functional medicine labs go beyond traditional lab markers and can help assess for contributing factors to IBS and constipation that are often overlooked in the conventional setting. Some of the most frequently utilized specialty labs to consider for patients with IBS-C are described below.

Comprehensive Stool Test

Conventional stool testing typically encompasses the inflammatory marker calprotectin and a pathogenic screening profile. A comprehensive stool test goes beyond these two markers for a more thorough evaluation of gut health, digestive function, inflammation, large intestinal dysbiosis, and fungal overgrowth. Subtle variations in the gut microbiome and digestion can alter the gut-brain axis and cause IBS symptoms.

SIBO/IMO Breath Test

A SIBO/IMO breath test measures gaseous bacterial fermentation metabolites exhaled through the lungs. It is estimated that up to 80% of IBS patients have an underlying SIBO. IMO is a subtype of SIBO characterized by an overgrowth of methane-producing microorganisms. Methane gas has been shown to directly slow intestinal transit and cause constipation, strongly linking it to IBS-C. A peak methane level of at least 10 ppm at any point during a SIBO breath test is diagnostic for IMO per the North American Consensus guidelines.

Food Sensitivities

Food sensitivities and allergies may play a role in GI symptoms for some people with IBS, so a comprehensive serum food antigen profile can help identify dietary triggers related to immune activation and IBS pathology.

Stress Panel

An HPA Profile measures hormones and neurotransmitters to assess for adrenal gland and nervous system function. Chronic stress and intestinal dysbiosis negatively influence mood, creating a perpetual cycle between stress, depression, and digestive symptoms. Specialty testing helps identify specific imbalances in the gut-brain axis so that targeted therapies can be implemented to optimize the stress response and neurotransmitter production.

Thyroid Panel

Subclinical and overt hypothyroidism can slow gastrointestinal motility, manifesting as constipation. A comprehensive thyroid panel assesses the brain-thyroid axis by measuring multiple hormones and immune proteins implicated in thyroid health and function, allowing for a more accurate screening and early detection of thyroid disease.

Conventional Treatment for IBS-C

Conventional therapy goals for IBS-C include symptom palliation to improve patient quality of life. Dietary modifications, gut-related psychotherapies, and medications that encourage regular bowel movements and decrease abdominal pain are common first-line treatment recommendations. (7, 8)

Functional Medicine Treatment Protocol for IBS-C

While a functional medicine doctor may recommend prescription medications for fast-acting relief of symptoms, they do not address the root cause of IBS. Additionally, they can worsen IBS-C symptoms when used for prolonged periods. Functional medicine doctors use lab findings to create personalized treatment plans that correct imbalances underlying visceral hypersensitivity and slowed gastrointestinal motility, emphasizing dietary modifications, mind-body techniques for stress relief, and dietary supplements to support digestion and gut function.

Therapeutic Diet and Nutrition Considerations for IBS-C

Given the prevalence of food sensitivities in the IBS population, dietary modifications should almost always be considered in patients with IBS. Foundational nutritional habits that do not include restriction can go a long way in supporting gastrointestinal health. These include eating slowly, chewing food thoroughly before swallowing, and listening to hunger and satiety signals. (3)

Adding fiber to the diet also supports healthy bowel movements by nourishing beneficial Lactobacillus and Bifidobacterium gut bacteria and improving stool consistency. Bacterial fermentation of fiber produces short-chain fatty acids (SCFAs), which can interact with the nervous system to decrease pain signals. Non-fermentable fibers, such as psyllium, oats, and partially hydrolyzed guar gum, are usually best tolerated by those with IBS.

For some patients, a therapeutic 6-8 week elimination diet may be warranted to reduce exposure to triggering foods stimulating overactive immune responses and causing digestive symptoms. If available, the elimination diet should be tailored to a patient's food sensitivity lab results. Otherwise, a low FODMAP diet has been shown to reduce IBS symptoms in 75% of IBS patients. Patients should be instructed to rechallenge foods back into the diet to test their tolerance; foods that do not trigger symptoms can be safely reintroduced into their regular diet.

Supplements Protocol for IBS-C

Dietary and herbal supplements can be prescribed to expedite gut healing, support digestion, and palliate IBS symptoms. Below is a sample protocol that can be recommended to patients with IBS-C.

Digestive Enzymes

Digestive enzyme insufficiency can contribute to food sensitivities, intestinal inflammation, and altered bowel habits. Supplemental digestive enzymes can be taken with meals to support the normal digestion of foods into their absorbable building blocks. A digestive enzyme formula should be chosen based on the patient's lab results and clinical symptoms but may include hydrochloric acid, amylases, proteases, lactase, lipase, and ox bile. Reductions in bloating, gas, and abdominal pain have been observed in patients taking digestive enzymes (9, 10).

Dose: one serving size (per label) at the beginning of each meal

Duration: 3-12 months


IBgard® is a nonprescription encapsulated peppermint oil that is available over the counter. Peppermint oil promotes bacterial balance in the gut, supports healthy digestion, and relaxes small intestinal muscles to manage gastrointestinal symptoms, including cramping, bloating, constipation, and gas. Supplementation with IBgard® results in nearly a 19% reduction in the total IBS symptom score within 24 hours after the first dose.

Dose: 2 capsules 1-3 times daily

Duration: As needed/Ongoing

Motility Activator™

Motility Activator™ is Integrative Therapeutics' patented combination of artichoke and ginger. Ginger is a traditional herb often used to support digestion and soothe upper intestinal inflammation. The prokinetic actions of gingerol, one of ginger's botanical compounds, is often forgotten. Gingerol accelerates gastric emptying and prevents bacterial accumulation in the small intestine by stimulating the small intestine's migrating motor complex. This formula can promote bowel regularity and reduce IBS symptoms, like gas, bloating, and abdominal discomfort. (11)

Dose: 1-2 capsules twice daily

Duration: 3-6 months


Atrantil is a botanical formula made of three polyphenols (quebracho, horse chestnut, and peppermint) that is clinically proven to reduce abdominal pain, bloating, and constipation and target methanogen-producers, treating IMO and re-establishing a healthy microbiome for gut function.

Dose: 2 capsules three times daily

Duration: 6-12 weeks

Zenbiome™ DUAL

Probiotics are live microorganisms that support the gut by balancing the microbiome. Research supports using Bifidobacterium and Lactobacillus as safe and effective options for treating IBS (12, 13). Zenbiome™ DUAL is a probiotic by Microbiome Labs that combines two strains of Bifidobacterium longum to optimize the gut-brain axis and support optimal gastrointestinal function and mood self-regulation.

Dose: 2 capsules daily

Duration: 3-6 months

When to Retest Labs

Depending on the chronicity of IBS symptoms, recovery time can vary between patients as underlying imbalances are corrected. It is not uncommon for patients to experience symptom improvement soon after implementing dietary, lifestyle, and supplemental changes. To allow time for the treatment protocol to work, retesting is typically performed 3-6 months after initiation of the plan to objectively observe patient response to interventions.



IBS-C is a functional gastrointestinal disorder characterized by the hallmark symptoms of abdominal pain and constipation. Symptoms can be debilitating and significantly impact the quality of life, and, unfortunately, conventional treatment protocols don't always elicit desired patient outcomes. A functional medicine approach to IBS-C offers a holistic evaluation and appreciation of the interconnectedness of the gastrointestinal, immune, and nervous systems that play into IBS etiology. A personalized treatment plan can correct identified imbalances to encourage the return to optimal gut functioning and resolution of symptoms.

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. Henry, K. (2022, October 31). IBS vs IBD: Know The Symptoms. Rupa Health.

3. Cloyd, J. (2022, December 15). IBS-C: Diagnosis and Natural Treatments Options. Rupa Health.

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5. National Institute of Diabetes and Digestive and Kidney Diseases. (2020, January 12). Symptoms & Causes of Irritable Bowel Syndrome. National Institute of Diabetes and Digestive and Kidney Diseases.

6. Cloyd, J. (2023, March 20). Top 5 Functional Medicine Labs for IBS-C Patients. Rupa Health.

7. Wilkins, T., Pepitone, C., Biju, A., et al. (2012). Diagnosis and management of IBS in adults. American Family Physician, 86(5), 419–426.

8. Lacy, B.E., Pimentel, M., Brenner, D.M., et al. (2021). ACG Clinical Guideline: Management of Irritable Bowel Syndrome. American Journal of Gastroenterology, 116(1), 17–44.

9. Spagnuolo, R., Cosco, C., Mancina, R.M., et al. (2017). Beta-glucan, inositol and digestive enzymes improve quality of life of patients with inflammatory bowel disease and irritable bowel syndrome. European Review for Medical and Pharmacological Sciences, 21(2 Suppl), 102–107.

10. Ciacci, C., Franceschi, F., Purchiaroni, F. et al. (2011). Effect of beta-glucan, inositol and digestive enzymes in GI symptoms of patients with IBS. European Review for Medical and Pharmacological Sciences, 15(6), 637–643.

11. Bodagh, M.N., Maleki, I., & Hekmatdoost, A. (2018). Ginger in Gastrointestinal disorders: a Systematic Review of Clinical Trials. Food Science & Nutrition, 7(1), 96–108.

12. Yuan, F., Ni, H., Asche, C.V., et al. (2017). Efficacy of Bifidobacterium infantis 35624in patients with irritable bowel syndrome: a meta-analysis. Current Medical Research and Opinion, 33(7), 1191–1197.

13. Tiequn, B., Guanqun, C., & Shuo, Z. (2015). Therapeutic Effects of Lactobacillus in Treating Irritable Bowel Syndrome: A Meta-analysis. Internal Medicine, 54(3), 243–249.

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