“All disease begins in the gut”
― Hippocrates
The gut isn’t just where digestion happens, its central to almost every aspect of our health, from our immune system to neurological function, and often referred to as our “second brain.” When balanced, it lays the groundwork for health. When out of balance, dysfunction and disease follow.
Another enduring truth from Hippocrates, “Let food be thy medicine,” is something our modern society is just now understanding. The foods we eat have the power to either nourish and heal or harm and disrupt the intricate systems that keep us well. Healing begins on the plate with the choices we make each day.
To restore gut health, we focus on
- Using Food as Medicine
- Killing harmful bacteria
- Fortifying tight functions
- Fostering the proliferation of beneficial bacteria
- Repairing the damaged tissue of the mucous membrane
- Regularity to flush out what the body wants to excrete
- Increasing nutrient absorption
Healing the gut begins with a diet that removes irritants, incorporates healing foods, and nourishes the microbiome. Here’s how food can function as medicine.
Eat Anti-Inflammatory Foods
Reduce systemic and gut inflammation by incorporating:
- Fruits: Include berries (antioxidants), apples (quercetin), and cherries (anthocyanins).
- Vegetables: Incorporate carrots, spinach, red bell peppers, and sweet potatoes for their vitamins and beta-carotene.
- Nuts and Seeds: Walnuts, almonds, Brazil nuts, cashews, chia seeds, and flaxseeds.
- Whole Grains: Oats, quinoa, and barley offer anti-inflammatory benefits and promote gut health.
Remove Inflammatory Foods
Just as some food can nourish and heal our body, some food and food-like substances can inflame the gut lining, disrupt the microbiome, and trigger systemic inflammation, all of which undermine the body’s ability to heal itself.
Common Gut Irritants to Eliminate
- Processed Foods and Additives: Processed foods are often loaded with preservatives, artificial sweeteners, colors, and emulsifiers that disrupt gut flora and weaken the gut lining.
- Sugar and Refined Carbohydrates:Sugar and refined carbs feed harmful bacteria and yeast (like Candida), creating an imbalance in the microbiome. This can lead to dysbiosis and inflammation.
- Industrial Seed Oils: Oils like soybean, canola, and corn are high in omega-6 fatty acids, which promote inflammation when consumed in excess. Instead, use anti-inflammatory fats like grass-fed butter and olive oil.
- Consider going Gluten-Free: Gluten can increase gut permeability by triggering the release of zonulin, a protein that weakens tight junctions in the gut lining. This is especially problematic for individuals with autoimmune conditions or sensitivities.
- Consider Dairy: Dairy can be inflammatory for many people, especially if they have lactose intolerance or casein sensitivity. It may exacerbate gut irritation and contribute to symptoms like bloating and gas.
Fiber-Rich Foods
Fiber is essential for feeding beneficial bacteria, which ferment it into short-chain fatty acids like butyrate, a key nutrient for gut epithelial cells.
- Legumes: Lentils, chickpeas, and beans encourage microbial diversity.
- Fruits and Vegetables: Bananas, apples, leafy greens, and artichokes.
- Whole Grains: Oats, millet, and quinoa help maintain a balanced microbiome.
Probiotic-Rich Foods
Probiotic-rich foods replenish beneficial bacteria, promoting gut harmony and resilience.
- Yogurt: Choose unsweetened varieties with live cultures.
- Fermented Vegetables: Sauerkraut, kimchi, and pickles (unpasteurized).
- Kefir and Kombucha: Fermented beverages rich in probiotics and enzymes.
- Miso and Tempeh: Fermented soy products that deliver probiotics and protein.
Prebiotic Foods
Prebiotics serve as the fuel for probiotics, promoting their growth and activity.
- Vegetables: Garlic, onions, and leeks*contain inulin, a natural prebiotic.
- Fruits: Bananas and apples provide fermentable fibers.
- Whole Grains: Chicory root, asparagus, and oats are excellent sources.
*for a sneaky way to get vegetables in your kids’ diets, try Dr. Cowan’s Garden with powdered vegetables including leeks, low oxalate greens, beets and more, to slowly add to their favorite meals.
Digestive Enzymes
Digestive enzymes from food help break down nutrients, reduce gut stress, and support microbial balance.
- Pineapple. Contains bromelain, a protease that aids digestion.
- PapayOffers papain, another protein-digesting enzyme.
- Mango. Also rich in papain.
- Broccoli Sprouts. Enzyme rich due to germination.
- Raw Honey.Provides amylase and protease.
- Ground Flax Seeds. Rich in lipase.
- Apple Cider Vinegar. Stimulates the production of digestive enzymes.
The gut microbiome is a delicate ecosystem made up of trillions of microorganisms, including beneficial bacteria that help regulate digestion, support immune function and maintain gut health. Harmful bacteria are naturally present in small amounts throughout our body, but in a healthy system, these bacteria are kept in check. However, the microbiome can be thrown out of balance by the overgrowth of harmful bacteria known as dysbiosis, which can lead to a variety of issues, including inflammation, infection, and disruption of nutrient absorption. Addressing this imbalance often involves:
Antimicrobial Treatments: Utilizing herbal or pharmaceutical antimicrobials to reduce populations of pathogenic bacteria.
Restrict Sugars and Refined Carbohydrates: Harmful bacteria and yeast thrive on sugars and refined carbs. Cutting out sugary snacks, sodas, and processed foods can starve these microbes.
Increase Fiber-Rich Foods: Insoluble fibers in vegetables, whole grains, and legumes help sweep out waste and potentially harmful microbes.
Incorporate Antimicrobial Foods: Garlic, onions, ginger, and turmeric have natural antimicrobial properties and can help inhibit harmful bacteria.
Supplemental Support: Using herbs like cat’s claw, caprylic acid, berberine, and oregano oil, which have natural antibacterial properties, to help suppress harmful bacteria without disrupting beneficial microbes.
Tight junctions are the gatekeepers of the gut lining, controlling what passes from the small intestine into the bloodstream. When tight junctions become loose, often referred to as “leaky gut,” harmful substances like toxins and pathogens can enter the bloodstream, leading to systemic inflammation and a host of symptoms.
Zinc Carnosine: Zinc is critical for modulating inflammatory cytokines that can disrupt tight junction proteins, maintaining the structural integrity of the gut barrier.
Dietary Sources:
- Animal-based: Oysters, red meat (beef, lamb), poultry (dark meat), and seafood.
- Plant-based: Pumpkin seeds, chickpeas, lentils, cashews, quinoa, and whole grains.
Butyrate: Butyrate is the primary energy source for intestinal epithelial cells (colocytes) and strengthens tight junctions, reduces inflammation, and serves as an anti-inflammatory agent
Direct Dietary Sources: Grass-fed butter and ghee.
Indirect Dietary Sources: Fiber-rich foods like oats, barley, bananas, and legumes (chickpeas, lentils) that promote butyrate production through gut fermentation.
Glycine: Glycine is a building block for collagen, which supports the structural integrity of the gut lining and tight junctions. It also has anti-inflammatory properties and serves as an inhibitory neurotransmitter in the brain, reducing stress and promoting mental clarity.
Dietary Sources: High-protein foods such as fish, meat, poultry, eggs, and dairy.
A healthy gut flora is essential for maintaining proper digestion, synthesizing key vitamins, regulating immune function, and protecting the body against harmful pathogens.
Probiotics
These “good bacteria” play a crucial role in nurturing your microbiome, helping you feel better from the inside out. While dietary sources are excellent for maintaining gut health, probiotic supplements can provide targeted support for specific needs, such as during illness, after antibiotics, or for managing conditions like PANS/PANDAS or histamine intolerance.
Choosing the Right Probiotic
Strain Specificity.
Not all probiotics are created equal. The effectiveness of a probiotic depends on the specific strain(s) used, as different strains have unique properties and target different issues. Look for clinically studied strains proven to support the specific condition you’re addressing.
Be aware that terms like Lactobacillus, Bifidobacterium, or Saccharomyces refer to genera. You must look for the full strain name (Lactobacillus rhamnosus GG).
Examples of Strain-Specific Benefits.
- Lactobacillus rhamnosus GG: Reduces intestinal permeability (“leaky gut”), inflammation, and supports immune modulation.
- Bifidobacterium longum: Reduces inflammation, repairs gut tissue, and supports mental health via the gut-brain axis.
- Lactobacillus plantarum: Calms gut inflammation, promotes anti-inflammatory pathways, and aids in butyrate production.
- Saccharomyces boulardii: A beneficial yeast that binds toxins, mycotoxins and pathogens, making it ideal for detoxification and recovery after antibiotics.
Multi-Strain Formulas.
A combination of strains can promote diversity and offer broader benefits by promoting microbial diversity in the gut.
Spore-Based Probiotics.
These probiotics encase beneficial bacterial strains in a tough, natural protective coating that allows them to withstand extreme conditions, including heat, oxygen, stomach acid, and bile. This coating ensures that the bacteria arrive alive and active in the intestines, where they can thrive and effectively support gut health.
Spore-Based Probiotics for PANS/PANDAS Kids
Just Thrive Probiotic
- Contains Bacillus subtilis, Bacillus clausii,and Bacillus coagulans.
- Supports gut balance, detoxification, and inflammation reduction.
MegaSporeBiotic by Microbiome Labs
- A spore-based formula containing Bacillus subtilis, Bacillus clausii,and Bacillus coagulans.
- Promotesmicrobial diversity, reduces endotoxins, and supports gut resilience.
- These are available as gummies
Klaire Labs Saccharomyces boulardii
- Targets toxins, restores gut balance, binds mycotoxins and supports recovery after antibiotics or illness.
Probiotics
Key Prebiotic Foods and Compounds
- Garlic, Onions, and Leeks: Rich in inulin, promoting beneficial bacteria growth.
- Bananas: Provide resistant starch, fermenting into gut-healing SCFAs like butyrate.
- Inulin: Found in chicory root, asparagus, and artichokes; supports microbiome balance and butyrate production.
- FOS (Fructooligosaccharides): Found in fruits and vegetables, feeding beneficial strains like Bifidobacterium.
- Pectins and Beta-Glucans: Soluble fibers in apples, oats, and citrus fruits that support microbial diversity.
Prebiotic Supplements
Key Prebiotic Foods and Compounds
- Stimulates beneficial bacteria (Bifidobacteria, Lactobacillus).
- Enhances SCFA production for gut integrity and boosts immune function.
- Gentle on sensitive guts; ideal for children with conditions like PANS/PANDAS.
- How to Use: Mix into smoothies or soft foods like applesauce
Dandelion Root
- Prebiotic-rich in inulin, encouraging beneficial bacteria.
- Supports liver detoxification, reducing gut stress by processing and removing toxins.
Digestive Enzymes
Digestive enzymes play an often-overlooked role, breaking down food into absorbable nutrients, they reduce the burden on your gut, limiting the undigested material that could otherwise feed harmful bacteria and contribute to imbalances.
When to Use: (these should not be taken long term)
- After antibiotics to restore balance.
- For chronic gut conditions like SIBO or IBD.
- To ease food sensitivities, including gluten or dairy.
- During stress, when enzyme reserves are depleted.
Restorative Interventions
Aloe Vera
Aloe vera also forms a protective coating over the gut lining, which promotes epithelial repair and regrowth, enhancing the integrity of the mucosal barrier. Additionally, it helps balance stomach acidity by reducing irritation caused by excessive acid production. Its antimicrobial properties selectively target harmful bacteria without disrupting the balance of beneficial gut flora. For individuals exposed to mold, aloe vera stimulates bile production, aiding liver detoxification, and binds toxins to facilitate safe elimination from the body.
Slippery Elm
Slippery elm creates a mucilaginous coating in the gut, forming a protective barrier that shields the lining from irritants and fosters healing. This action reduces inflammation, promotes epithelial cell regeneration, and supports tissue repair. Slippery elm also encourages the production of mucus, which helps restore the gut’s natural defense layer for added protection.
Slippery Elm is an endangered plant, so whether or not to use it, is an ethical choice. Licorice is a substitute many herbalists use, instead of slippery elm.
L-Glutamine
L-glutamine serves as a fuel source for epithelial cells, the building blocks of the gut barrier, enabling them to repair damage and regenerate effectively. L-glutamine strengthens the overall integrity of the gut, making it more resilient to stress and damage. It also plays a key role in reducing inflammation within the gut, protecting tissues from the harmful effects of chronic inflammatory conditions and promoting a balanced, healthy gut environment.
Omega-3 Fatty Acids
Omega-3s, found in fish oil and flaxseeds, are renowned for reducing inflammation and promoting tissue repair.
Supports Epithelial Healing: Reduces inflammation to speed mucosal repair.
Enhances Gut Resilience: Improves the gut’s structural integrity and reduces systemic inflammation.
Incorporate fatty fish like salmon into your diet or take high-quality fish oil supplements.
Vitamins A and D: Critical for Mucosal Healing
These fat-soluble vitamins are essential for restoring and maintaining the gut lining.
Vitamin A: Enhances epithelial regeneration and promotes mucus production.
Vitamin D: Modulates immune responses and supports barrier repair.
Colostrum: “Liquid Gold” for Gut Repair
Colostrum, the nutrient-rich first milk, is packed with compounds that support the healing of the gut lining.
Promotes Cellular Regeneration: Rich in epithelial growth factor (EGF) to stimulate repair of intestinal cells.
Provides Immune Support: Contains immunoglobulins (IgG, IgA) to neutralize pathogens and reduce gut stress.
Peptides
These bioactive compounds are short chains of amino acids that work by signaling the body to accelerate healing, reduce inflammation, and regenerate tissues.
Key Peptides for Gut Health
BPC-157
- Repairs and strengthens the intestinal lining, addressing conditions like leaky gut
- Reduces inflammation in the gut and systemic tissues.
- Promotes angiogenesis (formation of new blood vessels) to enhance nutrient delivery to damaged areas.
Thymosin Beta-4 (TB4)
- Accelerates tissue regeneration, especially in inflamed or damaged gut tissues.
- Reduces fibrosis (scarring), promoting long-term gut health.
- Calms chronic inflammation, supporting overall mucosal integrity.
Sourcing Peptides Safely
Peptides are highly specialized treatments that should only be obtained from reputable, verified sources to ensure purity, safety, and effectiveness.
Other Supports
Epi-Integrity: A supplement designed to support epithelial integrity and repair.
Maintaining proper gut motility—the efficient movement of food through the digestive tract—prevents waste and toxins from lingering, supports nutrient absorption, and ensures effective detoxification.
Ways to Support Gut Motility
- Herbal Interventions
- Iberogast: A blend of herbs clinically shown to enhance motility and ease digestive discomfort.
- Ginger: This natural prokinetic stimulates digestion, reduces inflammation, and soothes the gut lining.
- Dietary Fiber
Both soluble and insoluble fibers bulk up stool and regulate bowel movements.
Sources: Flaxseeds, psyllium, and leafy greens.
- Hydration
Drinking adequate water ensures smooth stool passage and prevents constipation. - Movement and Exercise
Physical activity stimulates intestinal contractions, promoting healthy motility.
Herbal Laxatives for Constipation
They should be used thoughtfully, as certain types may cause dependency or irritation if overused.
Stimulating Laxatives
Stimulating laxatives trigger intestinal muscle contractions, helping stool move through the colon. These are effective for occasional relief but should not be used long-term.
- Aloe Vera: Aloe vera gelsoothes the gut lining and reduces inflammation.
- Senna: Contains sennosides that irritate the bowel lining to induce contractions. Effective for short-term use but potentially harsh.
- Cascara Sagrada: Promotes intestinal movement but should be used cautiously due to its potency.
Bulk-Forming Laxatives
These fiber-based laxatives absorb water in the intestine, creating soft, bulky stools that are easier to pass. Bulk-forming options are gentler and suitable for regular use without the risk of dependency.
- Psyllium Husk: Psyllium is one of the most effective fibers for creating stool bulk and easing passage.
- Flaxseed: Rich in soluble and insoluble fibers, flaxseed gently bulks stool
- Fenugreek: High in fiber, fenugreek seeds act as a mild laxative and soothe the intestinal lining.
While digestion breaks food into absorbable components, the actual absorption of these nutrients into the bloodstream and cells is the next step in the process.
Strategies to Increase Nutrient Absorption
Digestive Enzymes
Enzymes like protease, amylase, and lipase break down food into its absorbable components—amino acids, fatty acids, and simple sugars. This reduces the burden on the gut, improves absorption, and minimizes undigested material that can feed harmful bacteria.
Stomach Acid Support
Adequate stomach acid (hydrochloric acid, HCl) is critical for protein digestion and the activation of enzymes like pepsin. Many people with gut issues, especially those with leaky gut or infections, have low stomach acid, impairing nutrient breakdown.
- Incorporate apple cider vinegar (1 tsp diluted in water) before meals to gently improve acid levels and digestion.
Support Bile Production and Flow
Bile is essential for breaking down fats and absorbing fat-soluble vitamins A, D, E, and K. Poor bile flow, often seen in individuals with gallbladder dysfunction, compromises fat digestion and nutrient absorption.
- Include bitter herbs like dandelion rootto stimulate bile production. If bile flow is impaired or the gallbladder has been removed, consider ox bile supplements for additional support.
Humic & Fulvic Acid
They improve nutrient absorption at the cellular level by acting as a natural chelator and transporter. They bind to vitamins, minerals, and trace elements in the digestive tract, increasing their bioavailability and ensuring they are efficiently delivered to cells.
- Increase cellular permeability, allowing nutrients like magnesium, zinc, and calcium to cross cell membranes more effectively.
- Restore electrolyte balanceto support energy production and hydration.
- Optimize digestive efficiencyby enhancing nutrient uptake, which is particularly important for individuals with malabsorption issues.