Introduction
Your gut plays a crucial role in your overall health, affecting digestion, immunity, mood, oxidative stress, toxin absorption/removal, and skin health. If your digestive system is out of balance, you may experience bloating, constipation, diarrhea, food sensitivities, intolerances, chronic inflammation, acne, hormone imbalances and more. Fortunately, functional medicine offers an integrative approach to restoring gut health utilizing targeted supplements and essential nutrients. In this guide, we’ll explore the ultimate gut health toolkit, featuring the best probiotics, digestive enzymes, and gut-healing supplements we recommend. Of course you can head to our shop to explore all of our recommendations, from books, to cookware, to supplements here.
1. Probiotics: The Foundation of Gut Health
Probiotics are beneficial bacteria that help maintain a balanced gut microbiome. They support digestion, enhance immune function, and help with mental health. When out of balanced digestive symptoms occur. Probiotics are considered 'good' however, some people with conditions like small intestinal bacterial overgrowth (SIBO) may need to avoid these initially as probiotics can exacerbate the condition.
Best Probiotics for Gut Health:
Lactobacillus and Bifidobacterium strains – Support digestion and reduce bloating.
Saccharomyces boulardii – Helps prevent diarrhea and supports gut healing. This is actually a beneficial yeast.
Spore-based probiotics – Bacillus species. More resilient and effective for gut repopulation.
Favorites: Integrative Therapeutics ProBiome 50.
2. Digestive Enzymes, Bile Acids, and HCL: Optimize Nutrient Absorption
If you experience bloating, gas, or discomfort after meals, you may have low digestive enzyme levels or hypochlorhydria (low stomach acid). Digestive enzymes and hydrochloric acid (HCl) break down food into absorbable nutrients, helping prevent bloating and indigestion. Bile acids aid in the digestion of fats, help absorp nutrients, like vitamin A, and have antimicrobial properties that help prevent conditions like SIBO. This is why gallbladder removal can be detrimental to the gut and long term health; many patients complain of diarrhea post cholescystectomy as they can only minimally emulsify fats with limited concentrated bile acids (normally the gallbladder stores and concentrates bile acids from the liver).
Key Digestive Enzymes to Look For:
Protease – Helps break down proteins.
Lipase – Aids in fat digestion.
Amylase – Assists in carbohydrate breakdown.
Lactase – Supports dairy digestion.
HCl - activates digestive enzymes (pepsinogen to pepsin), lowers stomach acid pH, kills pathogenic bacteria, aids in digestion of food
Bile Acids - from cholic acid and chenodeoxycholic acid from the liver and deoxycholic acid and lithocholic acid from bacteria in the colon. Emulsify fats and help nutrient absorption (vitamins D,E,A,K).
Favorites: Thorne Advanced Digestive Enzymes.
3. L-Glutamine: Healing the Gut Lining
L-glutamine is an amino acid that plays a vital role in repairing the gut lining and reducing intestinal permeability (leaky gut). It supports gut integrity, making it essential for those struggling with bloating, food sensitivities, or IBS.
How L-Glutamine Helps:
Supports gut barrier function
Reduces inflammation
Enhances nutrient absorption
Favorites: Jarrow Formulas L-Glutamine
4. Collagen and Bone Broth: Strengthening the Gut Barrier
Collagen is rich in amino acids like glycine and proline, which help repair and strengthen the gut lining. Similarly, bone broth is rich in minerals, nutrients, and collagen to aid in gut repair and maintenance. Regular intake can aid in reducing gut inflammation and improving digestion. Anxious individuals may need to use caution or glutamate sensitive persons as bone broth may worsen anxiety.
Benefits for Gut Health:
Supports gut lining integrity
Promotes healthy skin and joints
Reduces inflammation in the digestive tract
Favorites: Sports Research Collagen Peptides
5. Prebiotics: Fuel for Good Bacteria
Prebiotics are non-digestible fibers that feed beneficial gut bacteria, helping them grow. They work in synergy with probiotics to maintain a healthy gut microbiome.
Top Prebiotic Foods & Supplements:
Chicory root
Berries, asparagus, pistachios, almonds, cashews, garlic & onions, green bananas
Acacia fiber & inulin supplements
6. Gut-Healing Superfoods & Lifestyle Tips
Let's not forget that along with supplementation, lifestyle and dietary habits play a crucial role in gut health. If you remain stressed your gut cannot heal effectively due to numerous factors like persistent cortisol elevations. If you are not hydrated you will not effectively digest nor be able to repair your gut lining (we're mostly water!).
Additional Tips for a Happy Gut:
Eat a diverse, whole-foods diet rich in fiber.
Stay hydrated to support digestion.
Manage stress through meditation, yoga, or deep breathing.
Reduce processed foods, artificial sweeteners, and excessive alcohol.
Regular Exercise – Supports gut motility and microbiome diversity.
Quality Sleep – Aim for 7-9 hours of rest each night to allow the gut to repair.
Mindful Eating – Chew food thoroughly and avoid distractions while eating.
✅ Check out gut-friendly superfoods and teas here*
6. IgG Antibodies and Gut Health
IgG antibodies play a key role in immune regulation within the gut. IgG antibodies may help neutralize harmful bacteria and maintain balance in your gut microbiome. These are often taken as a supplement from bovine sources. Colostrum also contains IgG and is often produced from bovine and occasionally human sources as a supplement.
IgG food sensitivities refer to IgG obviously, but regarding IgG produced by your body to fight off invaders, in this case food. your body may become sensitive to various foods, thus testing for IgG food sensitivities may be helpful and then eliminating the foods; this can help identify specific foods triggering inflammation and leaky gut symptoms.
How IgG Antibodies Support Gut Health:
Identify and reduce food-related inflammation
Strengthen gut immune function
Aid in the healing of leaky gut
Favorites: Microbiome Labs - MegaIgG.
7. Carminative Herbs and Mucilaginous Support
Carminative herbs help soothe the digestive tract and reduce bloating, while mucilaginous herbs form a protective coating over the gut lining, promoting healing.
Top Herbs for Gut Health:
Ginger – Stimulates digestion and reduces nausea.
Fennel – Relieves bloating and gas.
Chamomile – Soothes gut inflammation.
Aloe Vera, Slippery Elm, Licorice Root & Marshmallow Root – Provide mucilaginous support to coat and heal the gut lining.
Favorites: Thorne GI Relief.
8. Gut Cleansing
A crucial step in restoring gut health is cleansing the digestive system to remove unwanted pathogens and toxins. This process supports natural detoxification and helps 'reset' the gut microbiome.
How to Support Gut Cleansing:
Increase Fiber Intake – Fiber from whole foods like vegetables, flaxseeds, and chia seeds helps move waste through the digestive tract. Start low and slow to avoid worsening symptoms.
Stay Hydrated – Drinking plenty of water supports digestion and flushes out toxins. Approximately half your body weight in water, otherwise 60-90 ounces daily.
Use Antimicrobial Herbs – Herbs like oregano, berberine, and garlic can help eliminate harmful bacteria and yeast overgrowth.
Incorporate Fasting – Intermittent fasting allows the gut to rest and promotes autophagy, aiding in gut repair. We often recommend a minimum 16 hours fasted and 8 hour eating window each day as tolerated.
Favorites: Gaia Herbs Microbiome Cleanse.
9. Using Binders to Remove Toxins
Binders help remove toxins, heavy metals, and harmful substances from the gut, thus preventing them from being reabsorbed into the bloodstream. toxins can be ingested or develop from pathogens in the gut like bacterial overgrowths (releasing LPS, lipopolysaccharides), Candida (releasing Gliotoxin), molds on foods releasing toxins (Aspergillus, ochratoxin A). They play a vital role in gut detoxification and reducing inflammation.
Best Binders for Gut Health:
Activated Charcoal – Binds to toxins and helps remove them through digestion.
Bentonite Clay – Absorbs heavy metals and supports gut barrier function.
Chlorella – A natural algae that binds to toxins while providing nutrients for detoxification.
Diatomaceous Earth – Assists in parasite cleansing and toxin removal.
Favorites: Quicksilver Scientific - UltraBinder.
10. Gut Testing for Personalized Insights
Testing your gut health can provide valuable insights into imbalances, allowing for targeted interventions and more effective treatment strategies. Comprehensive testing can identify dysbiosis, infections, and food sensitivities.
Types of Gut Health Tests:
Comprehensive Stool Testing – Identifies bacteria, yeast, parasites, and markers of gut inflammation.
SIBO Breath Test – Detects small intestinal bacterial overgrowth (SIBO) through hydrogen, hydrogen sulfide and methane gas analysis.
Food Sensitivity Panels – IgG food testing helps determine food triggers that contribute to inflammation and gut dysfunction.
Zonulin/Occludin/Candida Testing – Measures intestinal permeability (leaky gut) to assess gut barrier integrity.
A comprehensive gut health approach involves cleansing the digestive system, using binders to remove toxins, and testing to identify underlying imbalances. It is important to follow identify the root issue at hand and target it. Often pathogens are present, mechanical issues within the gut, or others. Following the Five R approach often helps the majority of others, but does take time, 6-12 months. Different modalities may be needed depending on gut symptoms severity.
Steps to Improve Gut Health:
Gut Cleansing: Supporting natural detoxification through fiber, hydration, and antimicrobial herbs can help remove unwanted pathogens and reset the gut microbiome.
Using Binders: Activated charcoal, bentonite clay, and chlorella help bind and eliminate toxins, reducing inflammation and improving gut function.
Testing the Gut: Comprehensive stool testing, SIBO breath tests, and food sensitivity panels can reveal infections, dysbiosis, and inflammation markers, allowing for targeted interventions.
Conclusion
Your gut health is foundational to your overall well-being, and supporting it with the right supplements can make a world of difference. Whether you're looking to improve digestion, heal leaky gut, or enhance nutrient absorption, incorporating probiotics, digestive enzymes, L-glutamine, collagen, and prebiotics can set you on the path to better gut health.
Start optimizing your gut today! Explore the best gut health supplements and build your personalized gut-healing toolkit.
Brendan Tennefoss, DNP, AGPCNP, ACHPN, AFMC
Disclaimer
This information is for educational and informational purposes only and is not intended as medical advice. It is not a substitute for professional medical diagnosis, treatment, or advice. Always consult a qualified healthcare provider before making any changes to your diet, lifestyle, or supplement regimen.
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