6 Key Tools to Improve Your Gut Microbiome Health

Thank you for joining the Huberman Lab Podcast Neural Network—a once-a-month newsletter with science and science-related tools for everyday life. This newsletter aims to provide you with actionable information in a condensed form. It relates to a recent episode of the Huberman Lab Podcast, “How to Enhance Your Gut Microbiome for Brain & Overall Health.”

We all have trillions of microorganisms living inside our gut—not just our stomach but our intesti­nes and throat and mouth, and on our skin, in our eyes and nasal passages. Maybe that sounds bad or gross, but… it turns out these microbiota are essential for our immune, brain and hormone health—in part because they make chemicals that immediately impact how the rest of our body functions, including neurotransmitters like serotonin. The bottom line is: we need to nurture these living microbiota cargo to best support our mental and physical health. During Episode 62 of the Huberman Lab Podcast, I explored the impact of the gut on the nervous system (i.e., the gut-brain axis) and how the gut contributes to your feelings of hunger and satiety. In Episode 63, I interviewed Dr. Justin Sonnenburg, Professor of Microbiology & Immunology at Stanford University, and world expert on the microbiome to discuss how gut microbes affect mental and physical health and how we can all improve our gut health.

Microbiota diversity is a measurement of the number of different species of microbiota in our gut. Low diversity is considered a marker of dysbiosis (microbial imbalance) and has been associated with autoimmune diseases, obesity and cardiometabolic conditions. Below, I summarize 6 tools that can help increase microbial diversity and improve overall gut and thereby, body and brain health.

#1 Eat Fermented Foods

Dr. Sonnenburg discussed the findings of his recent human study, in collaboration with Dr. Chris Gardner of Stanford, in which they investigated whether diets high in plant-based fiber or fermented foods would influence the health of the gut microbiome. Their results show that fermented foods increased overall gut microbiota diversity, as well as reduced key markers of inflammation (aka ‘inflammatome’).

​In the study, participants ate six servings per day of fermented foods, however, higher total amounts of ingested fermented foods did not lead to further benefits. Instead, consistently incorporate fermented foods into your daily diet to achieve better outcomes for gut microbiome health and inflammation reduction.

Try incorporating low-sugar fermented foods into your diet, such as sauerkraut, plain yogurt, kimchi, kombucha, natto, kefir or even drinking brine. Find these products in the refrigerator section to ensure there are live active cultures. (Shelf-stable fermented foods are pasteurized, therefore, will not offer the same boost to the gut microbiome.) Also, there are cost-effective ways to make your own fermented foods, such as kombucha or sauerkraut, at home.

What About Fiber?

In this study, a high-fiber diet did not lead to an increase in microbiota diversity. However, high-fiber diets did increase the amount of carbohydrate active enzymes which help digest fiber and could further enhance the microbiome’s ability to degrade other complex carbohydrates. Additionally, some participants in the high-fiber group showed a reduction in markers of inflammation. Plant-based, high-fiber foods (i.e., vegetables, legumes, and whole grains) offer significant benefits for overall health and can help provide key nutrients for established microbiota.

#2: Prebiotics and Probiotics

​Prebiotics: fermentable dietary fiber or microbiota-accessible carbohydrates; supplements of food for established gut microbiota

​Probiotics: live bacteria or yeasts that can colonize in the gut microbiome

Synbiotics: mixtures of prebiotics and probiotics

Augmenting the gut microbiome with low levels of prebiotics and/or probiotics while still focusing on eating whole quality foods leads to improvement in gut microbiome health.

In cases of dysbiosis, such as after taking antibiotics, during high periods of stress, traveling or changing your diet, higher levels of prebiotics and/or probiotics can aid in recovery and replenish your gut microbiome. However, the excessive intake of probiotics has been linked to the induction of brain fog; therefore, if you experience these symptoms, you could try to reduce the level of supplements that you are ingesting.

Since prebiotics and probiotics are considered supplements, they are not FDA-regulated products. When choosing a supplement, look for an independently validated product. Finally, the gut microbiome is uniquely personalized. Therefore, supplementation will impact individuals differently.

#3: Sleep

Throughout many podcast episodes, I have emphasized the foundational role that sleep has in overall health. As the gut microbiome is highly attuned to the amount of stress you experience (through direct links to cells of the immune system), achieving the proper quality (deep) and duration (generally 6-9 hours) of sleep each night is essential to manage stress and, in turn, to ensure gut microbiome health. See our “Toolkit for Sleep” (NeuralNetwork Newsletter #3) and listen to Episode 2, “Master Your Sleep & Be More Alert When Awake,” for more tips on achieving better-quality sleep.

#4: Avoid Processed Foods

Foods additives are ubiquitous in processed foods. Emulsifiers, detergent-like additives, can disrupt the mucus layer of the GI tract. In animal models, emulsifiers reduce microbial diversity, induce low-grade inflammation, and cause an increase in body fat, higher blood sugar levels and insulin resistance – key markers of metabolic syndrome.

The typical Western Diet (i.e., high fat, low fiber, higher in processed foods) does not provide gut microbiota with many of the key essential nutrients. When you eat complex, plant-based fiber, the gut microbiota produces fermentation by-products, such as short-chain fatty acids (e.g., butyrate). These substances reduce inflammation, help maintain the gut’s mucosal barrier, regulate the immune system, and modulate metabolism along the GI tract. To enhance the health of your gut microbiome, prioritize a diet rich in whole foods, plant-based fiber, and fermented foods.

#5: Artificial Sweeteners

Clinical studies have yet to fully tease apart the impact (if any) that artificial sweeteners have on the gut microbiome. However, within animal models, there is evidence that artificial sweeteners can disrupt the gut microbiome. A recent study showed that neuropod cells in the gut can discriminate between natural and artificial sweeteners. Further, these cells send a unique pattern of signals to the brain, depending on whether the sugars they sense are nutritive (i.e., contain calories) or are non-caloric sweeteners.

An interesting finding from the Human Microbiome Project is the high degree of individualization of the gut microbiome. Potentially, try removing some artificial sweeteners from your diet to see if you notice an effect and also consider that artificial sweeteners might be capable of influencing your gut microbiome.

*Non-caloric plant based sweeteners like stevia are probably fine, but there have not been many studies of stevia in regards to the microbiome.

#6: Don’t Over-Sanitize Your Environment

Microbiota are present on any and all surfaces which have come into contact with the environment. Dr. Sonnenburg notes, “Exposure to microbes from the environment is likely an important part of educating our immune systems and keeping everything in the proper balance.” The gut microbiome is also populated from social interactions, including skin contact by shaking hands, hugging, kissing etc. and interactions with pets and dirt, and grass. Over-sanitization of our environments or excessive use of antibiotics can eliminate sources of good gut microbiota. While it is still important to eliminate the introduction of disease-causing pathogens and harmful environmental chemicals (e.g., pesticides), consider that many environmental microbes play an integral role in the establishment and maintenance of a healthy gut microbiome.

Stay Connected

New episodes of the Huberman Lab Podcast are out each Monday on YouTube, Apple Podcasts, Spotify and all major podcast platforms. Please subscribe to those channels. I post additional science and science-based tools on Instagram, Twitter and Facebook.

Thank you for your interest in science!

Best wishes,
Andrew