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Gut Microbiome and Health

Aug 26, 2025

Overview

Dr. Josh Axe discusses the critical role of the gut microbiome in overall health, outlining causes of gut dysfunction and providing actionable strategies for healing through diet, lifestyle, and supplements. The episode highlights the link between gut health and various chronic conditions and offers a three-phase plan for gut restoration.

Importance of Gut Microbiome

  • Gut health impacts autoimmune diseases, longevity, immune regulation, metabolism, mental health, and more.
  • The gut contains 70% of the immune system and houses trillions of microbes (bacteria, yeast, viruses, fungi).
  • Imbalances in gut bacteria contribute to inflammation, chronic illness, and symptom flare-ups beyond digestive issues.

Common Causes of Gut Issues

  • Chronic stress, poor diet (sugar, refined grains, processed foods, seed oils, gluten, dairy), and environmental toxins.
  • Overuse of medications (antibiotics, NSAIDs, birth control pills) disrupts the microbiome and gut lining.
  • Poor water quality (chlorine, fluoride, heavy metals, microplastics) and excessive sanitation practices.
  • Glyphosate exposure, mold toxicity, and artificial food additives negatively affect gut health.

Signs and Symptoms of Poor Gut Health

  • Digestive: bloating, gas, diarrhea, constipation, food sensitivities, nutrient deficiencies.
  • Non-digestive: brain fog, chronic pain, skin issues, frequent infections, mood disorders, autoimmune conditions, fatigue, headaches, sugar cravings.

Three Phases of Gut Healing

Phase 1: Remove & Detox

  • Eliminate inflammatory foods and problematic substances: processed foods, sugars, gluten, seed oils, conventional dairy, alcohol, caffeine, non-organic/raw/cold foods.
  • Drink clean, filtered water.
  • Limit or replace gut-damaging medications where possible.
  • Engage in moderate exercise, walking, and use of infrared sauna or heating pads.
  • Consider a high-quality, soil-based probiotic (e.g., Bacillus subtilis) to target harmful microbes.

Phase 2: Repair

  • Emphasize easy-to-digest, warming, cooked foods: bone broth, soups, stews, cooked vegetables, baked fruits, and healthy fats.
  • Include herbal teas (ginger, licorice root, chamomile, peppermint) and, where tolerated, fermented foods.
  • Supplement with zinc, L-glutamine, humic/fulvic acid, and aloe vera (if not contraindicated).
  • Prioritize stress reduction, adequate sleep (8–9 hours/night), self-care, and time in nature.

Phase 3: Rebuild

  • Continue a healing diet; gradually expand food diversity as tolerated.
  • Use targeted probiotics (soil-based organisms, lactobacillus, bifidobacterium), prebiotics (applesauce, cooked fruits, steamed vegetables), and consider beneficial postbiotics.
  • Explore advanced therapies: photobiomodulation, acupuncture, peptide therapies (BPC-157, TB-500, KPV).
  • Listen to individual responses and tailor diet/strategies accordingly.

Testing and Personalization

  • Use GI Map stool test or blood tests (zonulin, I-FABP) to identify microbiome imbalances and leaky gut.
  • Adjust protocols based on individual food tolerances and specific gut issues (e.g., SIBO, histamine intolerance).

Recommendations / Advice

  • Focus first on gut and neuroendocrine health when addressing chronic conditions.
  • Avoid unnecessary antibiotic use, especially in viral infections.
  • Prioritize natural healing approaches and minimize reliance on conventional medications when possible.
  • Invest in high-quality supplements; avoid low-efficacy, cheap options.
  • Seek professional guidance from functional medicine practitioners for persistent or complex cases.

Questions / Follow-Ups

  • Consider personalized gut testing for accurate diagnosis and tailored treatment.
  • Assess individual reaction to specific foods and supplements; adjust healing phases as needed.