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Health Gut
3 Min Read
Last Updated: 12.06.23

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

Huberman interviews Dr. Justin Sonnenburg, Stanford professor, about the gut microbiome’s impact on health, diet, and environment. They discuss microbiota, gut establishment, and the role of fermented foods in increasing diversity and reducing inflammation. They also explore how Western diets negatively affect the gut and offer actionable tools for optimizing microbiome health.

Key Takeaways

High level takeaways from the episode.

Gut microbiome: trillions of microorganisms throughout the digestive tract

  • Also found in the nose, mouth, and skin
  • Most microbes are in the distal gut and colon

Microbiome supports hormonal health, brain health, and immune system function

  • Manufactures neurotransmitters that impact mood and brain function

Factors that support a healthy gut microbiome

  • Fermented foods
  • Fiber

Microbiome constantly modified by behavioral and nutritional interactions, as well as mood and internal reactions to the outside world

Different microbiota along the digestive tract

  • Oral microbiota in the mouth, adapted to oxygen exposure
  • Esophagus and stomach have less dense microbial communities
  • Small intestine is less studied due to difficulty in accessing
  • Colon has the densest and most studied microbial community

Microbiota assembly occurs during the first days, weeks, months, and years of life

Factors affecting microbiota development

  • C‑section vs. vaginal birth
  • Breastfed vs. formula fed
  • Presence of pets in the household
  • Exposure to antibiotics

Human Microbiome Project (2008–2009)

  • Documented vast number of genes in gut microbes
  • Found tremendous individuality in gut microbiomes
  • Traditional populations had different microbiomes than industrialized societies

Traditional populations’ microbiomes more representative of early human evolution

  • Industrialized microbiomes may be adapted to current lifestyles or deteriorated due to antibiotics and Western diets

Mice study on fiber and microbiome diversity:

  • Mice on low fiber, high fat diet lost microbiome diversity over generations
  • Returning to high fiber diet did not recover diversity in later generations
  • Fecal transplant from high fiber diet mice restored diversity


Limited high-​​quality science on the effects of cleanses and fasting on the microbiome

Extended fasting can lead to bacteria that specialize in eating mucus

  • This can cause inflammation if mucus is consumed in excess

Short-​​term fasting may have metabolic benefits, but long-​​term effects on gut microbiota are unknown

Cleanses and flushes can disrupt the gut microbiota, leaving rebuilding to chance

Complex carbohydrates (microbiota accessible carbohydrates) are beneficial for gut microbiota

  • These carbs are fermented by gut microbiota and are important for health

Most human ancestors were hunter-​​gatherers, consuming large amounts of plant material

  • Example: Hadza hunter-​​gatherers in Africa consume 100–150 grams of dietary fiber per day, compared to 15 grams in a typical American diet

Processed foods have negative impact on gut biology and microbiota

Artificial sweeteners can have a massive negative impact on the gut microbiome and lead to metabolic syndrome

Emulsifiers in processed foods can disrupt the mucus layer, leading to inflammation and metabolic syndrome

Plant-​​based sweeteners: less negative or more healthy due to evolutionary exposure and smaller amounts needed for sweetness

Potential for personalized microbiome treatments in the future for precision health

Study findings suggested a depleted gut microbiome may not respond well to high fiber diet

  • Industrialized world may have lost fiber-​​degrading microbes

Over-​​sanitization may have negative effects on gut microbiome

  • Exposure to environmental microbes may be important for immune system education
  • Balancing exposure to microbes and maintaining hygiene is crucial

Probiotics may help with certain conditions, but results vary greatly between individuals

  • It’s best to find a study that supports the specific probiotic for the desired effect

Consuming a variety of plants and diverse fiber is better for fostering gut microbiota diversity than purified fibers

  • Purified fibers can cause rapid fermentation in the gut, which may have negative effects on liver metabolism


Science-​​based tools and supplements that push the needle.

Avoid Heavily Processed Foods for Gut Health


Exposure to Microbiota Early in Life for Gut Health


Low Sugar Fermented Foods for Gut Health


Maintain Healthy Gut and Orifice Biome for Immune System


Probiotic Recommendations for Gut Health


Avoid Saccharine for Microbiome Health


Fasting – Gradual Return for Microbiome Health



We recommend using this distillation as a supplemental resource to the source material.

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

    Huberman Lab Podcast #62

    Huberman interviews Dr. Justin Sonnenburg, Stanford professor, on the gut microbiome’s impact, diet, and actionable health tools to optimize microbiome and overall health.

Full Notes

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