The 4 Stages of Gut Healing
Learn how to support your gut needs at each stage of change
The stages of gut healing are inspired by the “4Rs” of gut healing from the functional medicine model: Remove, replace, reinoculate, repair
A few days ago, I came across a headline that 40% of the global population struggles with functional gastrointestinal disorders (FGID). Those interviewed also shared that these disorders, including conditions such as irritable bowel and chronic constipation, disrupt their lives on an ongoing basis.
Five years ago, I was in this group myself. What started as a slight bloating after eating gradually grew into multiple food sensitivities, brain fog, and arthritis. What I learned very quickly is that a GI issue is very different than a broken bone which can be set back into place and healed within weeks - it requires a journey with multiple stages and iterations. When you emerge from it, you will likely want to eat and live very differently than you did before.
Today, my gut is healthy and I enjoy a diet and lifestyle that keeps my body and mind feeling clear, but it was a long journey. It was only once I became certified as a Nutritional Therapy Practitioner (NTP) that I began to understand why gut healing is so complex and how supporting it can be broken into approachable stages. When I discovered the “4R” approach to gut healing derived from functional medicine, a lightbulb moment went off in my head: the approach described all of the stages that I passed through rebuild a healthy gut.
So here are the “Four Stages of Gut Healing,” inspired by functional medicine’s “4Rs,” with a few additions from my own experience:
Stage 1: Remove
The first stage of healing is one that most people understand intuitively: stop putting anything into your body that leaves it damaged or inflamed. When I first realized that chronic inflammation was linked to my diet and lifestyle, I cut out alcohol, processed foods, and seed oils from my diet (e..g corn, soy, canola). While this step makes a huge difference for most people, for some, even more is required.
Where “Remove” gets more challenging is when it comes to identifying individual food sensitivities. While most people are aware of food allergies (e.g. peanuts) or intolerances (e.g. lactose intolerance), food sensitivities arise when a person’s gut lining becomes damaged and their immune system starts reacting to normal food particles passing into the bloodstream. People may develop sensitivities to common foods such as eggs, gluten, or even carrots and oats. By taking a blood test for IgG antibody activity, you can learn which foods your immune system is reacting to.
Beyond removing foods or beverages, it’s sometimes necessary to remove pathogens from the gut as well. After a multi-year struggle with Candida overgrowth and parasites in my gut, I learned that a comprehensive testing (e.g. stool, urine) is incredibly helpful in determining exactly what is stressing your gut so you can combine diet and lifestyle changes with medication when it’s needed.
Stage 2: Replace
One of the challenges of healing the gut is that it’s not only responsible for digestion, but also for nutrient absorption. That means when it is damaged, it struggles both to break down food for energy and to get the nutrients needed for its own repair.
When your stomach and small intestines are damaged or not functioning optimally, they may not be able to produce enough stomach acid and pancreatic enzymes to fully break down food or to absorb the nutrients needed for their own repair.
The “Replace” stage is about giving your gut what it often cannot give itself for digestion and healing: digestive enzymes, additional hydrochloric acid, and nutrients that are often deficient in those with digestive issues (e.g. vitamin B12, zinc, fat soluble vitamins) being the most common.
Stage 3: Reinoculate
Your gut is both home to, and shaped by, its microbiome. The bacteria, fungi, and viruses that populate a healthy gut help protect the gut lining, maintain the chemical conditions of the gut, keep out pathogens, and produce vitamins and compounds your body can’t produce on its own.
When your gut is damaged, one of the most critical steps in healing it is to reintroduce a community to it that supports normal digestion and maintains stability against other microorganisms. Though research has yet to arrive on any concept of an “ideal” microbiome, it is clear that high diversity is positive.
The “Reinoculation” stage generally involves taking probiotics, eating fermented foods, and introducing various sources of dietary fiber to help a new microbial community take root. It’s important to note that reinoculation takes time and while it’s not a substitute for dietary improvements, it can nudge microbiome towards a better state.
Stage 4: Repair
When all other conditions are met, your gut is ready for full repair. In general, your gut needs a few fundamental things to heal: energy, nutrients, and time. One of the most common gut healing aids, L-glutamine, provides a direct energy source for the cells lining the gut and helps support healing of the gut’s mucosal layer. Extended time between meals, or even fasting periods, are also important to give the gut a break from digestion so it can repair itself.
Finally, one of the best ways to support repair is by identifying and reducing sources of stress. Your body heals best when the nervous system is in a parasympathetic, or “rest-and-digest,” state. Therefore, finding ways to calm your body and mind - whether meditation, relaxation, or gratitude - will support your gut in both healing and digestion.
