Leaky Gut & Dysbiosis: What’s Damaging Your Gut—and How to Heal It From the Root

Why Gut Health Is Everything

Bloating, brain fog, random rashes—and still no answers? The root cause may be deeper than you think. It may be your gut.

Your gut isn’t just a digestive organ—it’s the epicenter of your entire health. Housing nearly 70% of your immune system, over 30 neurotransmitters, and trillions of microbes, your gut acts as the gatekeeper between wellness and disease. But what happens when that gate becomes compromised?

Dysbiosis and leaky gut—two distinct yet deeply interconnected conditions that lie at the root of everything from autoimmune flares to anxiety, fatigue, hormonal imbalance, and skin disorders.

In this blog, you’ll learn:

• The difference between dysbiosis and leaky gut
• How medications, food, and stress damage your gut
• Functional medicine protocols for restoring balance
• Powerful herbal and nutritional strategies (including Pau d’Arco, Sangre de Grado, and Chilcuague)
• The role of the lymphatic system and colon in gut repair
• And why gut issues, if left unchecked, can manifest as disease across every body system

Real-Life Example:

A 36-year-old woman came to me with eczema, fatigue, and bloating—yet all of her labs came back “normal.” She felt dismissed and defeated. But after addressing her dysbiosis and leaky gut through functional protocols, her skin cleared, energy returned, and she finally felt like herself again.

Dysbiosis vs. Leaky Gut: What’s the Difference?

Dysbiosis: Microbial Imbalance

Dysbiosis refers to an imbalance in your gut microbiome—the trillions of bacteria, fungi, viruses, and protozoa that inhabit your intestines. While some are protective, others can become harmful when overgrown or left unchecked.

Three Types of Dysbiosis:

1. Loss of beneficial bacteria (e.g., Lactobacillus, Bifidobacterium)
2. Overgrowth of opportunistic pathogens (e.g., Candida, Clostridium, Proteus)
3. Lack of microbial diversity (a root cause of inflammatory and immune disorders)

Symptoms of dysbiosis include:

• Bloating and gas
• Irregular bowel movements
• Skin issues (eczema, acne)
• Anxiety or depression
• Hormonal imbalance
• Food sensitivities
• Frequent colds or infections

Leaky Gut (Intestinal Permeability)

Leaky gut occurs when the tight junctions between cells in your intestinal lining become “loose,” allowing undigested food particles, toxins, and bacteria to leak into the bloodstream. This activates the immune system and sparks systemic inflammation.

Leaky gut is linked to:

• Autoimmune diseases (Hashimoto’s, lupus, rheumatoid arthritis)
• Chronic fatigue
• Brain fog
• Migraines
• Histamine intolerance
• Fibromyalgia

Dysbiosis often causes or worsens leaky gut.

Root Causes: What Damages the Gut?

1. Medications

• Antibiotics: Kill both harmful and beneficial bacteria, disrupting balance
• NSAIDs: Erode the gut lining, increase permeability
• Proton pump inhibitors (PPIs): Reduce stomach acid, leading to poor digestion and overgrowth of harmful bacteria
• Antidepressants and birth control: Alter gut microbiota and reduce diversity

A study published in Nature (2018) found that non-antibiotic drugs affect gut bacteria as significantly as antibiotics.

2. Diet & Processed Foods

• Refined sugar and processed carbs feed harmful bacteria and yeast (e.g., Candida)
• Artificial additives, preservatives, and emulsifiers weaken the gut barrier
• Gluten and dairy can trigger immune responses in sensitive individuals

3. Stress

The gut and brain are deeply connected via the gut-brain axis. Chronic stress:

• Increases gut permeability
• Reduces healthy bacterial diversity
• Impairs digestive enzyme production

Functional Medicine Protocol: The 5R Framework for Gut Healing

This foundational protocol is used by functional medicine practitioners worldwide to restore gut integrity and microbiome health.

1. Remove

• Eliminate inflammatory foods (gluten, dairy, sugar, alcohol)
• Identify food sensitivities with an elimination diet or IgG food sensitivity test
• Remove pathogens (yeast, parasites, bacteria) using:
• Herbal antimicrobials: berberine, oregano oil, Pau d’Arco, garlic
• Prescription agents (when necessary and guided by a practitioner)

2. Replace

• Digestive enzymes—

  Help break down food improve nutrient absorption reduce bloating and support overall digestion

  I recommend this high-quality Digestive Enzyme to improve better absorption
• Betaine HCl (if stomach acid is low)
• Ox bile (for those without a gallbladder or with fat malabsorption)
• Reintroduce key nutrients like zinc, magnesium, and B vitamins

3. Reinoculate

• Probiotics (choose strain-specific, high-quality formulas)
• Prebiotics: inulin, FOS, acacia fiber (unless SIBO is present)

4. Repair

• L-glutamine:

  helps heal the gut lining supports immunity reduces sugar cravings and aids in tissue repair especially after stress or digestive inflammation

  I recommend this high-quality L-glutamine for digestive inflammation and support.

• Zinc carnosine
• Slippery elm, marshmallow root, licorice (DGL)
• Sangre de Grado: Powerful Amazonian resin shown to help with gut ulcers and inflammation

5. Rebalance

• Sleep: 7–9 hours supports microbiome restoration
• Stress reduction: meditation, breathwork, adaptogens (ashwagandha, rhodiola)
• Movement: regular exercise supports gut motility and microbial diversity

How Lack of Exercise Impacts Gut Health

Physical activity is not only essential for cardiovascular health and weight balance—it plays a powerful role in supporting a healthy gut microbiome. Regular movement promotes beneficial bacteria, enhances microbial diversity, and strengthens the integrity of the gut lining.

On the other hand, a sedentary lifestyle can disrupt this balance, contributing to dysbiosis and leaky gut. Here's how:

• Reduced Microbial Diversity: Inactivity lowers the presence of beneficial bacteria like Faecalibacterium prausnitzii and Roseburia, both of which help regulate inflammation and maintain gut balance.
• Increased Gut Permeability: Lack of movement weakens the tight junctions in the intestinal wall, allowing toxins and pathogens to leak into the bloodstream—fueling inflammation.
• Altered Metabolism: Physical inactivity disrupts the gut’s production of short-chain fatty acids (SCFAs) like butyrate, which are essential for colon health and energy regulation.

Clinical Insight: A 2023 study published in Nature found that aerobic exercise—even without dietary changes—can positively shift gut microbiota composition and increase the abundance of health-promoting bacteria.

Takeaway: You don’t need intense workouts to benefit. Just 30 minutes of daily movement—like walking, cycling, or yoga—can significantly enhance gut health, reduce inflammation, and build microbial resilience. Exercise is one of the simplest yet most powerful ways to heal from the inside out.

Functional Medicine Protocol: Supplements & Herbs That Heal the Gut

1. For Dysbiosis (Microbial Imbalance)

Supplements:

• Berberine: Broad-spectrum antimicrobial; targets bacteria, parasites, and yeast Are you in search of a reliable berberine?  This one is third-party tested and highly absorbent.
• Caprylic Acid: Helps control Candida and yeast overgrowth
• Saccharomyces boulardii: A beneficial yeast that helps crowd out pathogens
• Oregano Oil (enteric-coated): Antibacterial, antiviral, and antifungal
• Probiotics: Multi-strain formulas with Lactobacillus and Bifidobacterium
• Prebiotics: Inulin, FOS, acacia fiber (avoid if SIBO present)

Herbs:

• Pau d’Arco: Antifungal and antimicrobial; inhibits Candida and harmful bacteria
• Neem: Antibacterial and antiparasitic
• Black Walnut & Wormwood: Effective for parasites and fungal overgrowth
• Heliopsis longipes (Chilcuague): Antibacterial and digestive stimulant

N-Acetylcysteine (NAC) and Gut Healing

NAC (N-Acetylcysteine) is a powerful antioxidant and mucolytic agent that plays a key role in gut restoration—especially when dealing with chronic infections, dysbiosis, or detox overload.

Key Benefits:

• Breaks down biofilms: NAC helps disrupt the protective layers (biofilms) that pathogens like Candida and harmful bacteria use to hide from antimicrobials.
• Boosts glutathione: As a precursor to glutathione, NAC supports detoxification during microbial die-off and inflammation control.
• Reduces oxidative stress: Calms the gut lining and helps lower systemic inflammation and intestinal permeability.

How to Use NAC in Gut Protocols:

• Dosage: 600–900 mg, 1–2 times daily (varies by phase and tolerance)
• Timing: Take away from food and minerals for better absorption
• Best combined with: Antimicrobials (e.g., berberine), binders (e.g., activated charcoal), and glutathione or vitamin C

Cautions:

• Use cautiously if you have ulcers or active gastritis
• Start slowly to monitor for Herxheimer (die-off) reactions like fatigue or brain fog

2. For Leaky Gut (Intestinal Permeability)

Supplements:

• L-Glutamine: Repairs and fuels intestinal cells
• Zinc Carnosine: Heals gut lining and protects mucosa
• Collagen Peptides: Supports tissue regeneration
• Quercetin: Anti-inflammatory and stabilizes mast cells —
  • Are you in search of a reliable quercetin supplement?  This one is third-party tested and highly absorbent.
• Vitamin D: Modulates immune response and tight junction integrity
• Omega-3 Fatty Acids: Reduce systemic inflammation— Are you in search of a reliable omega-3 supplement? This one is third-party tested and highly absorbent.

Herbs:

• Slippery Elm & Marshmallow Root: Coat and soothe the intestinal lining
• Licorice Root (DGL): Promotes mucus production and healing
• Sangre de Grado: Regenerates tissue, reduces inflammation
• Aloe Vera (inner part): Soothes GI tract and supports tissue repair

3. For Gut-Brain Axis Support

• Magnesium (glycinate or threonate): Calms nervous system and mind 
  • This one is third-party tested and highly absorbent.
• B-Complex Vitamins: Essential for neurotransmitter production
• L-Theanine: Calms the gut-brain
  • Are you in search of a reliable L-theanine supplement? This one is third-party tested and highly absorbent.
   
• Ashwagandha or Rhodiola: Adaptogens that regulate the HPA axis

What If You Can’t Use Ashwagandha?

If Ashwagandha isn’t a fit for you—due to thyroid sensitivity, overstimulation, or nightshade intolerance—there are several other adaptogens and herbs that support stress regulation, gut-brain function, and adrenal balance.

Top Functional Alternatives:

• Rhodiola rosea – Great for mental fatigue and burnout. Stimulates focus and improves stress resilience. Best used in the morning.
• Holy Basil (Tulsi) – A calming adaptogen that reduces anxiety, inflammation, and supports the immune system and digestion.
• Eleuthero (Siberian Ginseng) – Enhances endurance, supports adrenal recovery, and strengthens immunity without overstimulation.
• Schisandra chinensis – A liver-supportive adaptogen that boosts clarity, balances hormones, and protects against oxidative stress.
• Reishi Mushroom – Calms the HPA axis, improves sleep, modulates immunity, and supports gut microbial balance.
• Lemon Balm (Melissa officinalis) – Eases anxiety, calms the nervous system, and supports digestive harmony.
• Magnolia Bark (Honokiol) – Powerful for reducing nighttime anxiety and cortisol-related insomnia without dependency.

Pro Tip: Rotate adaptogens based on time of day or symptom focus.
• Daytime: Rhodiola + Holy Basil
• Evening: Reishi + Lemon Balm

4. For Lymphatic Movement & Detox

• Red Root: Supports lymphatic drainage
• Cleavers: Gentle lymph tonic
• Milk Thistle: Liver detoxification support
• Dandelion Root: Stimulates bile and liver cleansing

5. For Colon Support and Gentle Cleansing

• Magnesium Citrate or Oxide: Promotes regular bowel movements
• Triphala: Ayurvedic formula for toning and detoxing the colon
• Psyllium Husk, Flaxseed, or Chia Seeds: Add fiber to bind toxins
• Cascara Sagrada or Senna (short-term use): Stimulate elimination

Functional Food Add-Ins

• Bone Broth: Rich in glutamine, glycine, and collagen
• Fermented Foods: Sauerkraut, kimchi, kefir (if tolerated)
• Bitter Greens: Arugula, dandelion, mustard greens (stimulate bile and digestion)

Why the Lymphatic System Matters

Your lymphatic system is the body’s waste removal system. When sluggish, toxins from the gut and elsewhere cannot be effectively cleared—leading to inflammation and immune dysregulation.

How to support lymphatic flow:

• Hydration: At least half your body weight in ounces daily
• Movement: Rebounding, brisk walking, yoga
• Dry brushing & lymphatic massage
• Herbs: Red root, cleavers, burdock root

Colon Support: Cleansing Through Food & Herbs

A healthy colon ensures effective elimination of toxins and prevents reabsorption of waste.

Nourish with:

• Fiber: chia, flaxseed, psyllium
• Bitters: dandelion greens, arugula
• Herbs: triphala, senna (short-term), cascara sagrada, aloe vera (inner leaf)

Caution: Overuse of laxative herbs can weaken bowel tone—use them strategically and cyclically.

Herbs That Heal the Gut

1. Pau d’Arco

• Anti-fungal, antibacterial, antiviral
• Inhibits Candida overgrowth and supports microbiome balance
• Clinical studies support its anti-inflammatory and antimicrobial actions on gut pathogens

2. Heliopsis longipes (Chilcuague / Aztec root)

• A powerful salivary stimulant and natural analgesic
• Traditionally used to:
  • Support digestion
  • Eliminate oral and gut bacteria
  • Reduce pain and inflammation
• Studies show anti-microbial and immunomodulating effects, which can benefit the GI tract

3. Sangre de Grado (Croton lechleri)

• Known as “Dragon’s Blood,” used for:
  • Gastrointestinal ulcers
  • Irritable bowel syndrome
  • Bacterial infections
• Contains proanthocyanidins, alkaloids, and taspine, which promote tissue regeneration and reduce inflammation

A study in Phytomedicine found Sangre de Grado reduced diarrhea and gut inflammation significantly in clinical models.

Testing for Gut Issues

To treat precisely, you must test accurately:

• GI-MAP or GI Effects stool test: evaluates pathogens, dysbiosis, inflammation, and digestion
• Zonulin: marker for intestinal permeability (leaky gut)
• SIBO breath test: for methane/hydrogen gas overgrowth
• IgG Food Sensitivity Panel
• Organic Acids Test (OAT): gives insight into yeast, mold, and nutrient levels

What Happens If You Don’t Fix Your Gut?

An unhealed gut can lead to:

• Autoimmune disease
• Chronic inflammation
• Hormone imbalance
• Mental health conditions like anxiety, depression, ADHD
• Skin conditions: eczema, psoriasis, acne
• Blood sugar issues and metabolic dysfunction

Conclusion: Your Gut Holds the Answers

If you’ve been chasing symptoms—digestive, emotional, hormonal—without real answers, your gut may be the missing piece. Whether you’re dealing with bloating and brain fog or deeper chronic conditions, healing the gut using a root-cause approach can change your entire health trajectory.

By using functional medicine protocols, targeted herbs, lifestyle shifts, and therapeutic testing, you can begin to repair your inner ecosystem and reclaim your energy, mood, and resilience—naturally.