The Gut-Brain Connection: 6 Ways Your Gut Microbiome Impacts Mental Health

Functional nutrition expert Dr. Shari Youngblood explains how your gut microbiome affects brain health, mood, and mental well-being.

BY ISABEL NELSON

KEY TAKEAWAYS

• The gut-brain connection is a two-way communication system, meaning gut health plays a vital role in mental health and cognitive function.
• Many people lack essential nutrients and beneficial gut bacteria, especially from fermented foods, which support both digestive and brain health.
• Ultra-processed foods can disrupt the gut microbiome and are linked to poor brain function, mood disorders, and behavioral issues in both adults and children.

You can’t have a healthy brain without a healthy gut, according to Shari Youngblood, DCN, CNS, LDN, assistant professor and core faculty member in the Department of Integrative and Functional Nutrition at Saybrook University. “That would be like having a chlorinated and a non-chlorinated half of a swimming pool,” she says. The gut-brain connection is much stronger than you may realize. “You can think of your gut as your second brain” Dr. Youngblood says.

Dr. Youngblood spent more than 20 years living and working in the Mediterranean, experiencing the differences in approach to diet and food culture. She believes the American approach to food has harmful effects on the gut, and the brain often suffers collateral damage. “There are so many mental health conditions that, if we straighten out the gut, we can straighten out the mental health,” she says.

Here are six ways your gut microbiome may be influencing your brain.

1. How Ultra-Processed Foods Disrupt Gut and Brain Health

Eating ultra-processed foods can damage your gut microbiome and lead to mental health issues.

Dr. Youngblood’s most important advice to those seeking to improve brain function is to cut out ultra-processed foods. When it comes to diet having a negative effect on mental health, she says, “ultra-processed foods are the biggest culprits, especially those high in added sugars, seed oils, and synthetic additives.”

Dr. Youngblood says a poor diet can lead to behavioral problems in children: “If schools send kids to me for nutrition, nine times out of 10, if they have really bad behavior issues, it is because they are eating literally nothing but ultra-processed food.” A good breakfast, free of ultra-processed food, is crucial for young children to perform and feel their best. “If your gut’s inflamed, undernourished, or out of balance, it’s like trying to play a symphony with broken instruments,” says Dr. Youngblood.

2. The Best Foods for Brain Health and a Stronger Gut

Nutrient-dense whole foods improve brain health by restoring gut balance and reducing inflammation.

Foods that support mental health tend to be nutrient-dense, anti-inflammatory, and gut-friendly. Says Dr. Youngblood, “Fatty fish, like salmon, deliver omega-3s that help with mood regulation. Leafy greens provide folate and magnesium; both are crucial for stress resilience. Berries are like antioxidant armor for your neurons. Even something as simple as eggs can help; they’re rich in choline, which supports memory and focus.”

Pay attention to the quality of the food as much as you can, especially with regards to how the food was made, or how the animals involved were treated. For example, cows that feed on grass provide healthier meat and milk than those that eat grain, and pasture-raised chickens lay healthier eggs.

3. Fermented Foods That Support Your Microbiome and Mental Health

Fermented foods deliver natural probiotics that support mood, digestion, and cognitive performance.

Fermented foods feature in many cultures all over the world, and for good reason: They provide natural probiotics to support a healthy gut and thus a healthy brain. According to Dr. Youngblood, the No. 1 thing most people need more of is fermented foods. “We often sanitize our food to death, but these living foods—kefir, sauerkraut, miso, kimchi, kombucha—can reintroduce helpful gut microbes,” she says.

Even a forkful of sauerkraut a day can make a difference to your gut microbiome, but make sure those living foods are still living. “If you're looking for sauerkraut, don't get the stuff on the shelf,” Dr. Youngblood says. “That stuff has been sterilized and put in jars for shelf life. Refrigerated is the way to go.”

4. How To Tell If Your Gut Is Affecting Your Brain

Imbalances in the gut-brain axis can cause brain fog, poor sleep, and low mood.

Dr. Youngblood describes the gut-brain connection as being like a two-way information superhighway. “If there's anything going on in the gut, the brain knows about it," and vice versa.

If something is wrong in your gut, you might experience the usual symptoms that come with digestive discomfort: bloating, irregular bowel movements, or other symptoms of food sensitivities. However, your brain might also be trying to tell you something about your diet. “Foggy thinking, low mood, poor sleep, and even skin issues can all be signs,” Dr. Youngblood says. “If your brain feels like it's ‘running on empty’ or your mood is swinging wildly, your gut may be out of tune.”

5. Why Your Cravings Might Come From Your Gut Bacteria

An unhealthy gut microbiome can trigger sugar cravings and influence eating habits.

The gut is populated by massive amounts of bacteria. Some are beneficial, some moderately bad, and some very harmful. When the bad ones begin to overpopulate, Dr. Youngblood warns, they crowd out the good microbes you need for digestion, absorption, and waste management. They can also make you crave more of the sugary foods that allow them to continue colonizing your intestines.

Growing and maintaining a healthy gut microbiome is crucial for brain function, so it’s vital to feed the good bacteria, not the bad. “Start by feeding your microbes like you’d feed a garden: fiber-rich plants, fermented foods, and variety,” Dr. Youngblood says. “Even small changes, like adding a serving of beans or switching to sourdough, can shift the terrain.”

6. How Stress and Mental Health Affect Digestion

High stress levels disrupt digestion and blood sugar, making it harder for your gut and brain to function properly.

Your mental state can affect how you uptake the food you eat. Carbohydrates in your food can have a different effect on your glucose levels depending on your state of mind during consumption, Dr. Youngblood says. This is due to the two nervous systems in your body—the sympathetic and the parasympathetic—that are mutually exclusive. You might know one of those systems as “fight-or-flight,” but the other is known as “rest-and-digest,” meaning the body is prioritizing digestion and healing instead of reacting to a perceived threat.  Dr. Youngblood says that the stresses of everyday life can trigger your fight or flight response when you don’t need it. Only one system can be active at a time, so losing that “rest and digest” time affects gut health.

“We keep this low level of chronic stress because we have commutes, our kids are driving us crazy,” Dr. Youngblood says, “so we keep ourselves in a constant state of fight-or-flight, which means everything nonessential gets shut off.” Digestion is one of the processes that gets shut down in that mode, and blood sugar is one of the most affected areas, which in turn affects your brain. “That elevated state will also elevate your cortisol, and it will elevate your adrenaline and norepinephrine, and that affects how your body uptakes glucose, for example,” Dr. Youngblood says. Food consumed while the body’s cortisol levels are elevated is more likely to create in a spike in blood sugar than the same food consumed with lower cortisol levels.