What is the protocol for gut healing in Functional Medicine (FM)?

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Last updated: May 24, 2025View editorial policy

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From the Guidelines

A functional medicine gut healing protocol should prioritize gut-directed hypnotherapy as a key component, given its strong evidence base for short-term and long-term efficacy in managing irritable bowel syndrome (IBS) symptoms, as demonstrated in a meta-analysis of 6 RCTs recruiting 639 patients 1.

Key Components of the Protocol

  • Diet: An elimination diet for 4-6 weeks, removing common inflammatory foods like gluten, dairy, processed sugar, alcohol, and artificial additives, while focusing on nutrient-dense whole foods including vegetables, lean proteins, healthy fats, and fermented foods.
  • Supplements: Incorporate gut-supporting supplements such as a high-quality probiotic (25-50 billion CFU daily), L-glutamine (5-10g daily), digestive enzymes with meals, and zinc carnosine (75mg twice daily) to support the intestinal lining and restore beneficial gut bacteria.
  • Stress Management: Address stress through daily mindfulness practices like meditation or deep breathing for 10-15 minutes, and consider gut-directed hypnotherapy, which has been shown to modulate the gut-brain axis and improve symptoms in patients with IBS 1.
  • Lifestyle: Ensure adequate sleep (7-9 hours nightly) and regular moderate exercise (30 minutes most days), and stay hydrated with 2-3 liters of filtered water daily.

Implementation and Monitoring

  • Start with the elimination diet and supplement regimen, and gradually introduce gut-directed hypnotherapy sessions, which can be individualized or group-based, depending on the patient's needs and preferences.
  • Monitor symptoms and adjust the protocol as needed, with regular follow-up appointments to assess progress and make any necessary changes.
  • After the initial healing phase, gradually reintroduce eliminated foods one at a time to identify specific triggers, and maintain a personalized diet that continues to support gut health long-term.

From the Research

Functional Medicine Gut Healing Protocol

The functional medicine approach to gut healing involves a combination of lifestyle interventions, dietary changes, and supplementation. Some key components of this protocol include:

  • Diet: A balanced diet rich in fruits, vegetables, and whole grains can help support gut health 2
  • Omega-3 fatty acids: These have been shown to have prebiotic effects and can help alter the gut microbiome composition 3, 4, 5, 6
  • Prebiotics: Non-digestible fibers that can help feed the good bacteria in the gut, promoting a healthy gut microbiome 3, 4
  • Probiotics: Live bacteria and yeasts that can help support gut health and boost the immune system 4
  • Stress reduction: High levels of stress can negatively impact gut health, making stress reduction techniques like meditation and yoga important components of a gut healing protocol 2
  • Supplements: Certain supplements like omega-3 fatty acids, prebiotics, and probiotics can be useful in supporting gut health, but it's essential to consult with a healthcare professional before adding any new supplements to your regimen 3, 4, 5, 6

Key Nutrients for Gut Health

Some key nutrients that can support gut health include:

  • Omega-3 fatty acids: Specifically EPA and DHA, which have been shown to have prebiotic effects and support gut health 3, 4, 5, 6
  • Fiber: A high-fiber diet can help support the growth of beneficial gut bacteria 2, 4
  • Polyphenols: These compounds, found in foods like fruits, vegetables, and whole grains, can help support gut health and reduce inflammation 4

Supplementation Guidelines

When it comes to supplementation, it's essential to follow guidelines and consult with a healthcare professional. Some general guidelines include:

  • Omega-3 fatty acids: Aim for 1,000-1,500 mg per day of combined EPA and DHA, in the form of triglycerides, for at least 12 weeks 6
  • Prebiotics: Choose a well-characterized prebiotic like inulin, and follow the recommended dosage 3
  • Probiotics: Select a probiotic supplement with multiple strains and follow the recommended dosage 4

References

Guideline

Guideline Directed Topic Overview

Dr.Oracle Medical Advisory Board & Editors, 2025

Research

Integrative Approaches to Managing Gut Health.

Current gastroenterology reports, 2024

Research

Omega-3 fatty acids in nutrition and supplementation.

Ceska a Slovenska farmacie : casopis Ceske farmaceuticke spolecnosti a Slovenske farmaceuticke spolecnosti, 2025

Professional Medical Disclaimer

This information is intended for healthcare professionals. Any medical decision-making should rely on clinical judgment and independently verified information. The content provided herein does not replace professional discretion and should be considered supplementary to established clinical guidelines. Healthcare providers should verify all information against primary literature and current practice standards before application in patient care. Dr.Oracle assumes no liability for clinical decisions based on this content.

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