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Essentials: How to Build, Maintain & Repair Gut Health | Dr. Justin Sonnenburg

Dec 11, 2025 39m 27s 17 insights
In this Huberman Lab Essentials episode, my guest is Dr. Justin Sonnenburg, PhD, a professor of microbiology and immunology at Stanford University. We discuss how microbes in our gut impact our mental and physical health and how diet and the environment affect the gut microbiome. We explain how lifestyle factors such as antibiotics and Western-style diets (high fat, low fiber and rich in processed foods) can damage gut diversity and whether prebiotics or probiotics are useful tools. Throughout the episode, we highlight evidence-based dietary and lifestyle strategies for improving gut health. Episode show notes: https://go.hubermanlab.com/VXfckJf
Actionable Insights

1. Prioritize Fermented Foods Intake

Consume a high amount of naturally fermented foods daily (e.g., yogurt, kefir, sauerkraut, kimchi) to increase gut microbiota diversity and decrease inflammatory markers, potentially reducing the propensity for inflammatory diseases.

2. Avoid Processed Foods Categorically

Strictly avoid heavily processed foods because their components (artificial sweeteners, weird fats, refined nutrients, emulsifiers) are detrimental to the gut microbiome, leading to metabolic syndrome and inflammation.

3. Increase Diverse Plant Fiber Intake

Aim to double or more your daily intake of plant-based complex fibers from whole grains, legumes, vegetables, and nuts (over 40 grams/day) to nourish your gut microbiota, which produces beneficial compounds for colon health and immune regulation.

4. Choose Unsweetened Fermented Options

Opt for unsweetened fermented foods, such as plain yogurts, as added sugars commonly found in commercial products can negate the health benefits and are detrimental to the microbiome.

5. Avoid Artificial Sweeteners

Actively avoid artificial sweeteners like sucralose, aspartame, and saccharin, as they can have a massive negative impact on the gut microbiome and contribute to metabolic syndrome.

6. Make Your Own Fermented Foods

Consider making your own fermented foods like sauerkraut or kombucha, as it is a cost-effective way to ensure a consistent supply of high-quality, live-microbe-rich options, provided proper preparation protocols are followed.

7. Reprogram a Dysbiotic Microbiome Deliberately

To change an unhealthy microbiome, focus on establishing a new stable state by combining access to the right microbes with a proper nourishing diet, as the microbiome is resilient and tends to revert to its original state.

8. Exercise Caution with Cleanses/Fasting

If undergoing a cleanse that flushes out the gut microbiota, be prepared to deliberately reconstitute a beneficial microbial community afterward, as leaving it to chance can lead to an undesirable microbial state.

9. Promote Safe Environmental Microbe Exposure

Allow children safe exposure to environmental microbes (e.g., from dirt during outdoor activities) to help educate their immune system and maintain proper balance, while still practicing appropriate hygiene in high-risk situations.

10. Vet Probiotic Supplements Carefully

Be wary of the unregulated probiotic supplement market; seek products with independent validation and consider finding well-designed studies that support a specific probiotic for your particular health needs.

11. Prioritize Whole Plants Over Purified Prebiotics

Choose a broad variety of whole plants for your fiber intake instead of relying on purified prebiotic supplements, as diverse plant fibers foster broader microbiota diversity and slower fermentation, which is generally more beneficial.

12. Consider Red Light Therapy

Utilize red light and infrared light therapy devices (e.g., Juve) for 5-10 minutes, 3-4 times per week, to potentially improve mitochondrial function, skin health, reduce pain/inflammation, and enhance metabolism and blood sugar regulation.

13. Utilize Comprehensive Blood Testing

Engage in comprehensive blood testing (e.g., Function Health) to gain insights into over 100 biomarkers related to heart, hormone, immune, and nutrient health, allowing for informed health interventions.

14. Avoid Long-Term Low Fiber Diet

Recognize that a low-fiber, high-fat diet, particularly when sustained over multiple generations, can lead to a progressive and potentially irreversible loss of gut microbiome diversity.

15. Explore Non-Caloric Plant Sweeteners

When seeking sweeteners, consider non-caloric plant-based options, as they may require smaller amounts and could be better processed by the body compared to synthetic artificial sweeteners, though more research is needed.

16. Be Mindful of Emulsifiers

Understand that emulsifiers in processed foods can disrupt the gut’s protective mucus layer, potentially leading to inflammation and metabolic issues.

17. Incorporate AG1 Daily

Consider taking AG1 daily, as Andrew Huberman does, for comprehensive foundational nutritional support, including probiotics, prebiotics, and adaptogens, to support gut health, digestion, immune function, mood, and mental focus.