Beyond Probiotics: A Functional Medicine Approach to Gut Healing
When most people think about gut health, probiotics are usually the first thing that comes to mind, and yes, they are important.
Probiotics can help balance your microbiome, which is foundational to digestion, nutrient absorption, immune defense, and even brain function. But what many don’t realize is that probiotics alone aren’t enough to restore and maintain true gut integrity.
Unfortunately, our gastrointestinal systems are under constant assault, from antibiotics and processed foods to stress, toxins, and hidden infections. Over time, this can wear down the gut lining, impair immune resilience, and create a condition known as increased intestinal permeability, or “leaky gut.”
When this protective intestinal barrier starts to break down, it allows unwanted substances like toxins, microbes, and undigested food particles to pass into the bloodstream. This can trigger an immune response and lead to chronic, usually low-grade inflammation throughout the body.
Over time, this inflammation can lead to a wide spectrum of health issues.
- Autoimmune conditions
- Seasonal allergies and asthma
- Mood and neurological disorders
- Skin issues
- Metabolic challenges like insulin resistance and weight gain
Supporting your gut integrity is a foundational step in addressing these conditions at their root.
The gut is incredibly resilient, and with the right support, it can heal.
In this article, I’ll walk you through the most effective supplements I use in my clinical practice to help patients calm inflammation, rebuild the gut lining, rebalance the microbiome, and support overall health.
Whether you’re navigating ongoing digestive issues or you are just looking to optimize wellness, these tools are essential to repair your gut.
Here is a breakdown of what is covered in the article:
- How gut inflammation impacts health – from food allergies to mood disorders
- Inflammatory triggers to avoid that can wreak havoc on your gut
- 12 supplements that support gut healing and optimal health
- Food and final thoughts
Before we explore gut health and the supplements that support it, I want to share a fascinating new study that offers insight into how the gut heals and why that’s so important when it comes to chronic health conditions.
According to research published in Gut homeostasis, injury, and healing: New therapeutic targets, the gut lining, also known as the gastrointestinal mucosa, is constantly balancing between injury and repair. This barrier plays a critical role in overall health, protecting the body from toxins, bacteria, and inflammation.
But when harmful factors like elevated acid, infections, medications (like NSAIDs), and environmental toxins overwhelm the gut’s protective mechanisms, it can lead to chronic injuries, such as ulcers or inflammatory bowel disease (IBD).
Over time, this breakdown in the barrier may contribute to broader health problems like autoimmunity, food sensitivities, and systemic inflammation.
The study highlights that while conventional treatments often focus on managing the symptoms (using antacids, steroids, or immunosuppressants), in Functional Medicine, we are looking to enhance the body’s ability to heal.
These include:
- Supporting mucus production and blood flow to protect the gut lining
- Strengthening tight junctions to prevent leaky gut
- Encouraging epithelial cell repair and migration to close wounds
- Targeting cellular repair mechanisms like FAK (focal adhesion kinase) and trefoil peptides, which play key roles in tissue regeneration
- Promoting angiogenesis (new blood vessel growth) and energy delivery to damaged tissue
The study also emphasizes the role of gut bacteria and nutrients, like short-chain fatty acids (SCFAs), amino acids (like glutamine), and phospholipids, in maintaining and restoring a healthy intestinal lining.
Your Intestinal Lining Matters More Than You Think
The gastrointestinal system is so much more than digestion. It’s a dynamic, intelligent interface between the outside world and your internal biology, home to trillions of microbes, a significant portion of your immune system, and a critical regulator of inflammation, detoxification, and even gene expression.
When the gut heals, the whole body can begin to restore balance.
When the gut barrier is injured or slow to heal, it doesn’t just cause bloating or discomfort. It can trigger widespread, chronic inflammation, disrupt immune function, and even contribute to chronic conditions over time.
The good news is your gut has an incredible ability to repair itself with the right support.
In functional medicine, we focus on getting to the root cause. And when it comes to gut health, that means nourishing the intestinal lining, calming inflammation, and supporting your body’s natural healing process.
Before we get into some of my favorite supplements for gut repair, let’s take a look at how common gut issues can show up and how they’re connected to the rest of your health.
Gut Inflammation, What You Need to Know
When your gut is inflamed, it usually means your gut integrity has been compromised. The delicate intestinal lining and the microbial ecosystem that help protect it have been disrupted.
Your gut lining isn’t just a wall. It’s an intelligent interface between your body and the outside world. It works closely with your microbiome, the trillions of beneficial bacteria that play a critical role in digestion, immune balance, nutrient absorption, and keeping inflammation in check.
There’s also a lesser-known player that’s just as important—ACE2, short for angiotensin-converting enzyme 2. This is a protein found throughout the body, including in the gut. In the intestines, ACE2 helps maintain balance by supporting amino acid absorption, strengthening the gut barrier, and calming inflammation.
When ACE2 function is disrupted, whether from stress, infections, or chronic inflammation, it can weaken the gut lining, upset the microbiome, and increase the risk of gut and whole-body inflammation.
Together, your gut lining, microbiome, and ACE2 activity are designed to let the good stuff in, like nutrients, while keeping harmful substances like toxins, pathogens, and partially digested food out.
But when the microbiome becomes imbalanced and ACE2 isn’t functioning well, the gut barrier can become too permeable. This allows things that don’t belong in your bloodstream to slip through.
Your immune system sees those substances as threats and reacts. When this happens over time, the immune system stays on high alert, which can lead to chronic, body-wide inflammation.
Maintaining gut integrity is one of the most important things you can do to support your health, not just for digestion, but for your immune system, hormones, metabolism, and even your brain.
Here’s how gut inflammation may show up:
- Autoimmune conditions
A disrupted gut microbiome and an inflamed gut lining can confuse the immune system, leading it to attack the body’s own tissues. This is often seen in conditions like Hashimoto’s, lupus, multiple sclerosis, and rheumatoid arthritis.
- Mood and cognitive symptoms
Gut inflammation can impair neurotransmitter production and affect the blood-brain barrier. This may lead to anxiety, depression, brain fog, and even cognitive decline.
- Allergies and sensitivities
A leaky gut can let allergens and food proteins into the bloodstream, increasing the risk of eczema, asthma, seasonal allergies, and food intolerances.
- Metabolic issues
Chronic inflammation and an imbalanced microbiome can disrupt blood sugar regulation, leading to weight gain, insulin resistance, and eventually metabolic syndrome or type 2 diabetes.
- Skin problems
The gut-skin connection is real. Conditions like acne, rosacea, and eczema often improve when gut inflammation is reduced and microbial balance is restored.
Gut inflammation rarely stays in the gut. That’s why in functional medicine, we almost always start with the gut. By restoring the gut lining and rebalancing the microbiome, you’re not just supporting digestion, you’re creating a powerful foundation for long-term health, vitality, and disease prevention.
What Triggers Gut Inflammation?
Inflammatory triggers are everywhere in today’s modern life, and they can quietly wreak havoc on your gut lining and microbiome over time. Some of the most common include:
High-Inflammatory Foods
Processed foods, refined sugars, and industrial seed oils (like canola, soybean, corn, and sunflower oil) can have a damaging effect on your gut and overall health.
These oils are commonly used in packaged and restaurant foods and are often highly refined, oxidized, and stripped of any beneficial nutrients during processing. They are typically high in omega-6 fatty acids, which, in excess, can drive inflammation throughout the body and disrupt the delicate balance of your gut microbiome.
When consumed regularly, seed oils can:
- Promote gut inflammation
- Disrupt tight junctions and contribute to leaky gut
- Feed harmful bacteria and suppress beneficial microbes
- Impair cell membrane health and nutrient absorption
- Contribute to blood sugar instability when combined with refined carbs
To make matters worse, these processed foods often lack the vitamins, minerals, and healthy fats your gut cells need to repair, regenerate, and function optimally.
Replacing inflammatory oils with healthy fats like extra virgin olive oil, coconut oil, and omega-3-rich sources such as wild-caught fish can help calm inflammation and support the healing of the gut lining.
Foods that You are Sensitive to or Allergic to
Some foods that are generally considered healthy can actually cause inflammation if your body reacts to them. When you eat foods you’re allergic or sensitive to, it can overstimulate the immune system, irritate the gut lining, and weaken the barrier that normally keeps harmful substances out. Over time, this can contribute to leaky gut and systemic inflammation.
Gluten is one of the most common culprits, and many people react to it without even realizing it. One reason has to do with how wheat is processed in the United States. Most conventional wheat is sprayed with glyphosate, a toxic herbicide that isn’t just used to kill weeds. It’s also applied as a drying agent just before harvest.
Glyphosate has been shown to disrupt the microbiome, damage the intestinal lining, and increase inflammation in the body. Even if you don’t have a known allergy, gluten exposure—especially from conventional sources—may still be affecting your gut health.
If you have celiac disease or non-celiac gluten sensitivity, avoiding gluten meticulously is essential to protect your gut and prevent ongoing inflammation.
Dairy is another example. Beyond the natural proteins that some people are sensitive to, modern dairy is often highly processed, pasteurized at high temperatures, and may contain added hormones or antibiotic residues. These changes can alter how the body responds and increase the likelihood of inflammation.
Other common reactive foods include soy, corn, eggs (for some individuals), and nightshades. When the gut is already inflamed or leaky, reactions to these foods can be amplified, making it even more important to identify and remove inflammatory triggers while you work to restore gut integrity.
If you are curious about whether you are consuming a food that you may be reacting to, consider a food allergy test. All labs are not equally accurate. Depending on the patient, I’ll usually consider using the Vibrant Wellness Food Sensitivity Test or ALCAT.
Chronic Stress
How Chronic Stress Affects Your Gut
You’ve probably heard of the gut-brain axis – the powerful, two-way connection between your brain and digestive system. But what many people don’t realize is just how directly chronic stress can affect gut health.
When you’re under ongoing stress, your body shifts into survival mode. This can reduce the production of digestive enzymes, decrease blood flow to the digestive tract, slow down motility (how food moves through your digestive tract), and disrupt the balance of your microbiome.
Stress also weakens the intestinal lining, leading to leaky gut. And perhaps most importantly, chronic stress can impair your body’s natural ability to repair and heal the gut lining.
If you’re focusing on healing your gut but not addressing your stress, it may be the missing piece in your recovery. One of the best ways to alleviate stress is to meditate, use neurofeedback, and/or a vagus nerve stimulator. Learn more here.
Medications
Certain medications, especially antibiotics, NSAIDs (like ibuprofen), acid-blockers (like PPIs), and even oral contraceptives, can disrupt the microbiome and damage the gut lining. Antibiotics, in particular, can wipe out beneficial bacteria, creating space for opportunistic pathogens like yeast to overgrow.
Environmental Toxins
Environmental toxins are all around us, and they can have a major impact on your gut health.
Toxicants such as pesticides, heavy metals, mold toxins, and endocrine-disrupting chemicals (like BPA, phthalates, and parabens) can damage the cells that line your gut, disrupt your microbiome, and trigger inflammation. Over time, they can weaken the barrier that protects your body from unwanted substances, leading to a leaky gut.
But that’s just one part of the picture.
These toxins also place extra stress on your detox systems, especially your liver. When your body is constantly working to process and eliminate environmental exposures, it can slow down your ability to clear other waste, like inflammatory byproducts and hormone metabolites. This added toxic burden can leave your body more inflamed, your gut more vulnerable, and your healing process slower.
Some chemicals, like glyphosate, have been shown to harm beneficial gut bacteria while allowing more harmful strains to grow. This throws off your microbial balance and makes it even harder for your gut to stay resilient.
Supporting your detox pathways and reducing toxic exposures are key steps in protecting your gut and your long-term health.
Download my free guide, How to Be Safe in a Toxic World.
Gut Dysbiosis and Yeast Overgrowth
When the balance of your gut microbiome is disrupted and harmful microbes start to outnumber the beneficial ones, it’s known as dysbiosis. As mentioned, an imbalance in the microbiome can weaken the gut lining and increase inflammation.
One common form of dysbiosis is yeast overgrowth, especially Candida. While Candida is a normal part of the gut microbiome, it can become problematic when it grows out of balance.
A high-sugar diet is one of the most common drivers. Excess sugar feeds yeast and other unwanted microbes, allowing them to multiply and crowd out beneficial bacteria. This can lead to a wide range of symptoms, including bloating, brain fog, sugar cravings, fatigue, skin issues, and acid reflux.
Over time, if not addressed, yeast overgrowth and microbial imbalance can further damage gut integrity and contribute to chronic inflammation.
Restoring balance to the microbiome and limiting the foods that fuel the overgrowth is a foundational part of gut healing and whole-body health. If you are suffering from any of these symptoms, ask your doctor to test for yeast overgrowth, or consider my DIY GI MAPS test.
To learn more about how to improve gut health, read How to Improve Digestive Symptoms and Restore Gut Health.
12 Supplements that Help to Heal the Gut
The first step in gut healing is identifying and removing these inflammatory triggers, whether that’s through food allergy tests, an elimination diet, reducing toxin exposures, managing your stress, or working with your provider to adjust medications when appropriate.
Then, through the strategic use of diet and gut-supportive supplements, you can begin to repair the gut lining, restore microbial balance, and create the conditions for long-term health and resilience.
Here are 12 of my go-to gut health supplements, along with how they work:
1. Probiotics
Probiotics are beneficial bacteria that help bring balance back to your gut. They support healthy digestion, crowd out harmful microbes, and help keep the gut lining strong.
But their benefits go beyond digestion. Probiotics also play an important role in calming inflammation, supporting the immune system, and even improving mood, focus, and mental clarity—thanks to the connection between the gut and the brain.
Certain strains, especially from the Lactobacillus family, have been shown to reduce inflammation by lowering harmful immune signals and increasing protective, anti-inflammatory ones. Adding the right probiotics can help your gut and immune system stay balanced and more resilient.
- Daily Probiotics includes Lactobacillus acidophilus, Bifidobacterium longum, and Lactobacillus plantarum
2. Prebiotics
Prebiotics are special types of fiber that your body can’t digest, but your beneficial gut bacteria can. Think of prebiotics as nourishment for your microbiome. They help good bacteria grow and thrive, improving microbial diversity and supporting a healthier, more balanced gut.
When these microbes are well-fed, they produce short-chain fatty acids like butyrate, which help strengthen the gut lining, reduce inflammation, and support immune function.
You can get prebiotics naturally from foods like garlic, onions, leeks, asparagus, artichokes, and bananas. Including these in your diet regularly helps create an environment where your good bacteria can flourish.
- Exceed Greens + Reds also makes it easy to boost your prebiotic intake, especially on busy days or when your diet could use extra support. It includes a powerful blend of plant fibers, organic greens, and polyphenol-rich reds that feed beneficial microbes while delivering antioxidants, phytonutrients, and gut-nourishing compounds.
Together, food-based and supplemental prebiotics help lay the foundation for better digestion, stronger immunity, and overall vitality.
3. Digestive Enzymes
Digestive enzymes like protease, lipase, amylase, and cellulase help break down food into nutrients you can actually absorb and use. These enzymes are naturally produced in the pancreas and small intestine, but factors like stress, aging, inflammation, or poor gut health can reduce their production, leading to bloating, gas, and nutrient deficiencies.
When digestion isn’t complete, food particles can ferment in the gut, creating discomfort and disrupting the microbiome. Supplementing with a broad-spectrum digestive enzyme can support more efficient digestion, reduce the burden on your gut, and help your body absorb nutrients more effectively.
Adding enzymes with meals can be especially helpful during times of stress, healing, or when transitioning to a more nutrient-dense diet.
4. Betaine HCl & Pepsin
Stomach acid is crucial for breaking down proteins and killing harmful pathogens. Many people have low stomach acid, especially with age or stress. Betaine HCl and pepsin help restore proper acidity in the stomach, improving digestion and nutrient absorption.
5. L-Glutamine & L-Glutamic Acid
These amino acids are fuel for the cells of your intestinal lining. They support gut repair, reduce inflammation, and help tighten the junctions between gut cells, which are critical for healing leaky gut.
6. Slippery Elm & Marshmallow Root
These soothing herbs coat the digestive tract and help calm inflammation. Their mucilaginous properties make them excellent for easing irritation and supporting mucosal healing, especially in those with IBS, reflux, or IBD.
7. Magnesium Glycinate
Magnesium supports muscle relaxation, including in the intestines. Magnesium glycinate can gently promote bowel regularity, ease constipation, and support the nervous system’s influence on digestion. Most people are deficient when I test their levels
8. Aloe Vera Extract
Aloe vera is anti-inflammatory and calming to the gut lining. It supports the healing of inflamed tissue and promotes healthy bowel movements when used in its properly purified form (free of aloin).
9. Butyrate
This short-chain fatty acid fuels colon cells, strengthens the gut barrier, and regulates immune responses. It also supports healthy bowel motility and may improve comfort in those with bloating or IBS.
10. Immunoglobulin G (IgG)
IgG binds to and neutralizes harmful microbes, toxins, and antigens in the gut. It’s especially helpful after gut infections or in cases of food sensitivities and leaky gut, supporting immune modulation and gut lining protection.
11. BPC-157
This healing peptide has been shown to accelerate repair in the gastrointestinal tract and may reduce inflammation in conditions like IBD. It helps restore tissue integrity and supports overall gut resilience.
12. N-Acetyl Glucosamine (NAG)
NAG plays a structural role in the protective mucosal lining of the intestines. It supports barrier function, gut lining regeneration, and may benefit those with inflammatory gut conditions or autoimmunity.
Functional Formulas for Gut Healing
To simplify your routine, some of my favorites include:
- Exceed Greens + Reds Superfood Powder: Prebiotics, probiotics, and digestive enzymes.
- Daily Probiotics: Four researched strains totaling 30 billion CFU per capsule.
- GI Defend Powder: L-Glutamine, NAG, and Aloe Vera Leaf Gel Extract.
- IgG Pro Powder: Immunoglobulin G for immune and gut barrier support.
- Pancreatic Enzymes Plus: Aids in the digestion of protein, carbohydrates, and fats.
- Body Protection Compound (BPC-157): A peptide formula to support tissue repair.
Want to Understand Your Gut More Deeply?
If you’re ready for a more personalized approach, I highly recommend the GI-MAP test. This comprehensive stool analysis evaluates your microbiome composition, markers of inflammation and digestion, and detects potential pathogens.
It provides a window into what’s happening inside your gut, so you can take targeted action to support healing.
You can explore DIY lab testing options here.
Food and Final Thoughts
Supplements can be incredibly helpful for healing the gut, but food is the foundation. What you eat every day has a powerful impact on lowering inflammation, nourishing your microbiome, and rebuilding a healthy gut lining.
If your diet is high in ultra-processed foods and low in nutrient-dense meals, even the best supplements will have limited impact. Real healing begins with what’s on your plate.
Your gut is central to your overall health. By nurturing it with the right foods, reducing harmful exposures, and incorporating targeted supplements, you can support healing from the inside out.
References:
Probiotics: Shaping the gut immunological responses
Probiotics and gut microbiota modulation: implications for skin health and disease management
