Dr. Justin Sonnenburg: How to Build, Maintain & Repair Gut Health | Huberman Lab Podcast #62

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My guest this episode is Dr. Justin Sonnenburg, Professor of Microbiology & Immunology at Stanford University. Dr. Sonnenburg’s research focuses on how microbes in our gut impact our mental and physical health and how diet and your environment shape your gut microbiome. We discuss the architecture of the gut microbiome and microbiota variability in different regions of the gastrointestinal (GI) tract and how these can change in response to diet, environment or genetics. We explore the early establishment of your microbiome and how your mode of delivery into the world (C-section or not) shapes your gut. We also discuss lifestyle factors that can alter your microbiome and the integral role the gut microbiome plays in communicating to other organs, including your brain. Dr. Sonnenburg details his recent clinical study, which found that diets rich in fermented foods (but not fiber) increase microbiota diversity and reduce signals of inflammation. Additionally, we examine how foods typical in Western Diets (e.g., high fat, low fiber, processed foods) can negatively impact the gut microbiome. Throughout the episode, we discuss actionable tools from peer-reviewed clinical findings that anyone can implement, regardless of budget, in order to optimize their gut microbiome and health.

#HubermanLab #Microbiome #GutHealth

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Dr. Justin Sonnenburg Links:
Center for Microbiome Studies:
Dr. Sonnenburg’s Lab:
Dr. Sonnenburg’s Published Work:

Article Links:
“Gut-microbiota-targeted diets modulate human immune status”:

Book Links:
“The Good Gut: Taking Control of Your Weight, Your Mood, and Your Long-Term Health”:
“The 4-Hour Chef: The Simple Path to Cooking Like a Pro, Learning Anything and Living the Good Life”:

Other Links:
NIH Human Microbiome Project:

00:00:00 Dr. Justin Sonnenburg, Gut Microbiome
00:02:55 The Brain Body Contract
00:04:16 AG1 (Athletic Greens), ROKA, Helix Sleep
00:08:30 What is the Gut Microbiome?
00:12:49 Gastrointestinal (GI) Tract & Microbiota Variability
00:16:00 Breast Feeding, C-Sections & Pets
00:21:56 The Human Microbiome Project at Stanford
00:26:30 Traditional vs. Industrialized Populations
00:28:58 Resilience of the Microbiome
00:35:10 Regional Differences Along Your GI Tract
00:42:04 Fasting, Cleanses & Gut Health
00:51:19 Dietary Differences
01:01:24 Simple vs. Complex Carbohydrates, Processed Foods
01:07:03 Artificial & Plant-based Sweeteners
01:12:44 Cleanses: Useful? Harmful?
01:14:50 Your Microbiome & Your Immune System
01:20:17 Dietary Fiber & Fermented Foods
01:32:13 High-Fiber vs. High-Fermented Diet; Inflammation
01:41:33 Ripple Effects of a Healthy Diet
01:45:00 Does a High-Fiber Diet Make Inflammation Worse?
01:47:22 Over Sterilized Environments
01:50:15 The Gut Microbiome’s Effect on Physiology
01:56:45 Gut-Brain Connection
01:59:30 Probiotics: Benefits & Risks
02:04:20 Prebiotics: Essential?
02:07:00 Tools for Enhancing Your Gut Microbiota
02:11:12 Dr. Sonnenburg’s Research, Zero-Cost Support, YouTube, Spotify, Apple Reviews, Sponsors, Patreon, Thorne, Instagram, Twitter, Neural Network Newsletter

Please note that The Huberman Lab Podcast is distinct from Dr. Huberman’s teaching and research roles at Stanford University School of Medicine. The information provided in this show is not medical advice, nor should it be taken or applied as a replacement for medical advice. The Huberman Lab Podcast, its employees, guests and affiliates assume no liability for the application of the information discussed.

Title Card Photo Credit: Mike Blabac –
Audio Engineering: Joel Hatstat at High Jump Media


Disclaimer: This content including advice provides generic information only. It is in no way a substitute for a qualified medical opinion. Always consult a specialist or your own doctor for more information.

andrew huberman,huberman lab podcast,huberman podcast,dr. andrew huberman,neuroscience,huberman lab,gut health,microbiome,microbiota,Justin Sonnenburg,artificial sweeteners,plant based diet,intermittent fasting,high fiber diet

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  1. I'm pleased to announce that I'll be hosting two live events in May 2022.
    These are part of a series called, "The Brain Body Contract: An Operating Manual for Human Performance."
    Tuesday, May 17th: Seattle, WA
    Wednesday, May 18th: Portland, OR
    Learn more at
    Pre-sale tickets go on sale on Tuesday, March 8th at 10 AM PT (use code: huberman)

  2. Finally! Someone who can explain to me in clear language why some people choose a plant-based diet and some people choose meat or both. It seems to me like the high fiber and plant-based diet keeps us light and energetic in pursuit of "the hunt" and the meat and carbs leave us full and satisfied to relax and celebrate with others. This would explain the satisfaction of going to a steakhouse with your family or friends for dinner rather than grabbing a "quick" salad for lunch and why simple snacks like nuts and berries and fermented foods or fasting benefits many of us in the morning for energy and clarity

  3. Great topic… But I couldn't listen to the whole thing… The guest speakers every other word was umm… Ummmm.. Ummm. Ummm… Goodness man

  4. Outstanding information.
    I train professional and amateur Bodybuilders and gut health has always been an issue for most who attempt to ramp up the food to grow. Sugar addiction also is an issue with my lifestyle change clients. Your Podcast is a wealth of information. I am trained in Biology (Purdue) and spent 5 years doing research with Analytical Chemist and Bodybuilding Godfather, John Parrillo. (John is the man who came up with the idea of fasted cardio, Fascia Stretching, Fruit making you fat and so much more. He is a Pioneer. John also proclaimed he would make a 300 pound Bodybuilder and Ronnie Coleman emerged. John worked with Ronnie on Nutrition and training early in his career. This is what shaped Ronnie's understanding if Bodybuilding. Just a little history for you.)But we trained and provided nutrition plans for scores of folks and then monitored them weekly with Bodystats and had some we were having bloodwork done to see how the food regimen was affecting the athletes internal working, as well as the obvious physical manifestations of progress or regress. We worked with a variety of people from Gastric Bypass clients who need to change their lifestyle to professional Bodybuilders preparing for events.
    You should have John Parrillo on your Podcast. He was way ahead of his time. John is 73.

  5. Thank you so much!! This help me a lot because i have gastroesophageal reflux since i was a child and things like maneage stress are very important. 🙏🙏🙏

  6. Dr. Justin plant based diet is gonna make you a diabetic, just like he is himself.

    Standard American diet is a plant based diet, people eat WHEAT,CORN and SUGAR(plant) plus PLANT OILS.
    Tons of CARBS in EVERY POSSIBLE form and size, the worst plant oils poisoned with too much vitamin E, and just a tiny little bit of MEAT.

    With all due respect… it is already a plant based diet with a lot of FIBER! LOL

  7. Fascinating! Thank you so much, Dr.Huberman, for this valuable information and for making it available to all!

  8. 15 grams of Fiber in American diet ?? Wtf I don’t believe you sorry! The American diet is loaded with Fiber don’t know we’re you get your research from please give some links to the studies thanks 😊 and the American diet IS SUPER plant based as it is don’t under stand the constant push for even more plant . One would think ist all the plants that make people sick not the meat !!! Please make a study on the carnivore diet and compare with vegan and the SAD

  9. It’s so frustrating trying to make decisions about what’s best when we live in a world where the experts don’t seem to agree on anything. One tells you to eat tons of plants and grains and another with an equally impressive background tells you plants and grains are toxic and contain anti nutrients. They all have studies to back their claims and tell you why the other studies are biased or meaningless.

  10. Thank you for this video, my life has been a living hell because I messed y stomach up, and I am so happy to have found this

  11. Thank you for this topic. I'm on lifetime antibiotics due to Endocarditis. 1000 mg of amoxicillin daily. My Infectious disease doc says it's necessary to keep what bacteria is still there at bay. I had an aortic valve replacement four years ago. While waiting for the surgery I had multiple small strokes from the bacteria flicking off of my valve.
    I now have issues that I believe is due to taking the antibiotics. Since I have no choice in that, would you have any recommendations for me on how I could help my gut? Thank you very much.

  12. What an great 2-part series on gut health and the interview with Dr. Sonnenburg was astounding! Thanks Andrew!!

  13. Some people don't have colons. How does the colon work? Seeeeems diverticulitis is becoming a big problem for many.

  14. Would love to hear a segment on Parkinson's. How the microbiome influences this syndrome and how to use the microbiome to influence dopamine (and other ways to preserve / boost dopaminergic neurons).

  15. Good day Dr Justin, I have 55cm of colon left, will that be sufficient for my microbiome to upkeep my health? It's 4 months post operation, had pre cancerous polip removed, got sepsis and a fistula. Fistula was almost dry in wound, Still not healed, just had a abcess burst from the Fistula over this weekend. I am really struggling with my health and trying hard

  16. That’s why that can’t figure out what microbiome is healthy because sugar carb based microbiome will always cause disease

  17. Now we're getting somewhere. I'd love to see huberman talk with dr ken berry about oils, gundry about lectins, and mercola.

  18. Andrew you say you are contradicting Chris Gardner by saying put "no processed food" as #1 dietary priority ahead of "eat mainly plants". To my understanding you are AGREEING with him. When he says "Eat food" he means Eat REAL food (non processed food). That is his number one rule.

  19. There has been plenty of information on detoxification of the human body, and flushing out the toxins the human was otherwise not able to release.
    Via grean coffee enema, sauna, aged enzyme detoxification protocols, and regular exercise.
    Changing the diet along with using pro-biotics to balance the gut.
    Keeping the internal organs clean, mainly the Liver, and small intestine
    are vital.

    Toxic humans have, and always will benefit from detoxification done the proper way.

    Much love to all.
    Stay drug free.

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