The Gut Brain Connection:
How Your Gut Holds the Key to Better Brain Health

BY DR. EMERAN MAYER

a slew of research over the last few decades is showing that there is a definitive connection between your gut and your brain and the probiotic bacteria in your intestines affects your mood, neurotransmitters and more. artwork: bruce riley

The intense information exchange and connection between your brain, your gut, and its microbiota takes place twenty-four hours a day, regardless if you sleep or are awake, from the day you are born to the day you die. All of that communication isn’t just coordinating your basic digestive functions—it also impacts our human experience, including how we feel, how we make decisions, how we socialize, and how much we eat. And if we listen carefully, this conversation can also guide us toward optimal health.

We are living in unprecedented times. What we eat and drink has changed dramatically, and we are exposed to more chemicals and drugs than any people who ever lived. We are beginning to learn how these changes, along with chronic life stress, can affect not only the gut microbes, but also their complex dialogue and connection with the gut and the brain. These conversations play an important, well-established role in common syndromes of the gastrointestinal tract, in particular IBS, as well as in some forms of obesity. And we are beginning to recognize how disturbances in the gut microbial world can influence our brain. Recent studies have implicated altered brain-gut-microbiota interactions in brain disorders such as depression, anxiety, autism, Parkinson’s, and even Alzheimer’s disease. But even those of us who don’t suffer from these diseases can improve our health by learning more about this vital conversation.

What Is a Healthy Gut Microbiome?

To keep our gut microbiomes healthy, we first need to know what constitutes a healthy gut microbiome.

Since your gut microbiome is an ecosystem, it’s helpful to think of it as an ecologist would. Think of the human body as a landscape, with different parts of the body as distinct zones, each of which provides its own distinct habitat for microorganisms. These range from the vagina, home to just a few species, to the mouth, which houses a diverse array of microbes. Even within the digestive system, there are distinct zones, including low-diversity habitats in the stomach and small intestine, and high-diversity habitats in our large intestine, which has more microbes than any other location in the body, and the largest diversity of microbes as well. As you will see this gut microbiome is intimately connected to our brain.

Many factors determine the landscape of your gut microbiome, analogous to the factors that have shaped natural landscapes. One important factor is your genetic makeup and the way these genes are modified through the influence of early life experiences, good and bad. The activity of your immune system is also important, as are your eating habits, lifestyle, and environment and the nature of your unique gut reactions, which reflect your habits of mind.

A limited number of longitudinal studies have been completed on the composition of the gut microbiota, and they seem to show that dietary changes, immune function, and the use of medications, in particular antibiotics, can trigger shifts from one state to another and affect the guts connection to your brain, among other things. These shifts can be temporary, rapidly switching back to the healthy default state, or persistent, resulting in chronic disease. So depending on your gut microbial landscape, you may be more prone to develop prolonged digestive discomfort following a gut infection or show unhealthy spikes in blood sugar following a dessert. This microbial landscape may determine who will benefit more from switching to a healthy diet or from taking probiotics, and who will be more sensitive to the effects of a course of antibiotics.

Diversity

One of the generally agreed-upon criteria for a healthy gut microbiome and gut brain connection has been its diversity and the abundance of microbial species present in it. As in the natural ecosystems around us, high diversity of the microbiome means resilience and low diversity means vulnerability to perturbations. Fewer microbial species means a diminished ability to withstand perturbations such as infections (by pathogenic bacteria, viruses, or the pathobionts living in our gut), poor diet, or medications.

There are some noticeable exceptions to this rule, including the microbiota living in the gut of a newborn and in the vagina, which have low microbial diversity when they’re healthy, and for good reasons. The newborn’s microbiome needs flexibility in order to create a pattern of communities of gut microbes during the early programming period, which is unique for each individual. The vaginal microbiome needs flexibility in order to adjust its function to the unique demands of reproduction and delivery. Nature has developed clever alternative strategies to ensure the stability of these unique habitats and protect them from infections and disease. Both habitats are dominated by lactobacilli and bifidobacteria. These bacteria can produce many antimicrobial substances, and they have the unique ability to produce enough lactic acid to create an acidic milieu that is hostile to most other microorganisms and pathogens.

Someone with low-diversity, relatively unstable gut microbial communities may never show any signs of overt disease. However, when the microbiota of such high-risk individuals are perturbed, diseases are more likely to develop and disturb the gut brain connection. A growing scientific literature demonstrates that diseases such as obesity, inflammatory bowel disease, and other autoimmune disorders are associated with reduced gut microbial diversity, often as a consequence of repeated exposure to antibiotics. Other diseases may join this list in the future.

How does gut microbial diversity protect against disease? Diversity is closely linked to two critical properties of healthy ecosystems—stability and resilience.

Stability and Resilience

Although you may carry different microbial species than your coworker or cousin, you tend to carry the same key set of species for long periods. This stability is critical for your health and well-being. It ensures that friendly gut microbes can return quickly to an equilibrium state following a stress-related perturbation, which allows them to keep up their beneficial activities over time. This makes a microbiome resilient and strengthens the gut brain connection.

Conversely, some people’s gut microbiota are especially sensitive to perturbation. Mrs. Stone, who developed protracted symptoms of a gastroenteritis during her vacation in Mexico, clearly started out with a gut microbiome that was less resilient and stable than that of her fellow vacationers. Was her microbial landscape altered by the chronic stress she was under at the time of her vacation? Or did she start out with a less stable microbial landscape from the first years of her life, when a series of early adverse life events permanently changed it?

The emerging ecological view of gut microbial health contrasts with claims promoted by the food supplement industry and by the media that a healthy microbiome is composed of defined populations of specific species of microbes. In fact, only 10 percent of gut microbial species are shared between individuals. In other words, you and a friend might both have a healthy microbiome, but you might have vastly different communities of gut microbes. Put another way, there are several stable healthy states of the gut microbiota and hence the gut brain connection.

All this means that no quick analysis of your gut bacterial species—for example, your ratio of Prevotella to Bacteroides, or Firmicutes to Bacteroidetes—can assess the integrity of your gut-brain axis and your health status. It also means that it’s really not possible to provide a one-size-fits-all recommendation about which probiotics to take or which dietary intervention will provide specific benefits or strengthen the gut brain connection unequivocally in every case.

Vastly different communities of gut microbes, however, can produce very similar patterns of metabolites. This suggests that future tests will assess gut microbiome health, and hence gut brain connection health, not simply by looking for specific microbial populations, but by looking at which genes are expressed and which metabolic pathways are active.

How Your Gut Health Affects Your Brain Health and Beyond

The brain-gut-microbiome axis and connection is most vulnerable to health-harming perturbations during three periods: from pregnancy through infancy (the perinatal period), adulthood, and old age. And scientists now agree that the first few years in life, starting during development in the womb, matter most for our long-term health and well-being.

Our gut-microbiota-brain connection and interactions are shaped early in life, from before birth to age eighteen, through our interactions with the world—our psychosocial influences, diet, and chemicals in our food (including antibiotics, food additives, artificial sweeteners, and more). Early life—from before birth to age three—is a particularly crucial period for the shaping of the gut microbial architecture. Both the microbiome and brain circuits are still developing, and changes during this time tend to persist for life. Furthermore, gut sensations and associated emotional feelings are being filed into the database in your brain, shaping for life your background emotions, temperament, and ability to make beneficial gut decisions.

Throughout adult life, both what we eat and how we feel exert a profound influence on the chemical conversations our gut microbes have with other key players in our intestine, including immune cells, hormone- and serotonin-containing cells, sensory nerve endings, and more. This “gut-based caucus” sends signals back to the brain, influencing our desire to eat, our stress sensitivity, how we feel, and how we make our gut decisions. Meanwhile, our emotions, and their associated gut reactions, exert a profound influence on the complex dialogue in our gut, and this exerts a large influence on what type of messages the gut connection sends back to the brain.

The consequences of altering the gut-microbiota-brain dialogue and connection may not manifest until later in life, when the diversity and resilience of the gut microbiota both decrease. This makes it likely to make us more vulnerable to developing degenerative brain disorders such as Alzheimer’s or Parkinson’s disease. To prevent these devastating disorders, we need to pay attention to how we treat our gut-brain-microbiota axis and connection much earlier in life, long before the damage of the brain manifests as serious symptoms.

Improving Your Health by Targeting the Gut Microbiome

As we rapidly untangle the complex chemical conversations and connections between microbes, the gut, and the nervous system, we’re also extracting valuable information about how to apply this knowledge to improve people’s health.

How can we do this?

1. Practice Natural and Organic Farming of Your Gut Microbiome

Consider your gut microbiome as a farm and your microbiota as your own personal farm animals, then decide what to feed them to optimize their diversity, stability, and health, and optimize production of beneficial signaling molecules that affect our brains. Would you feed them food items that you knew were loaded with potentially harmful chemicals or enriched with unhealthy additives? This will be the first step in taking control of what you eat. It will increase your awareness next time you go to the market, are tempted to buy fast food for lunch, or debate whether you should order a dessert.

Note: Later on in this article we’ll get into the specifics of what to eat and not eat to keep gut brain connection and gut microbiome healthy. Keep reading.

2. Cut Down on Animal Fat in Your Diet

All the animal fat in the typical North American diet, regardless if it is visible or hidden in many processed foods, is bad for your health. It plays a major role in increasing your waistline, and recent data has shown that processed meat, which has a particularly high fat content, enhances your risk of developing several types of malignancies, including cancers of the breast, colon, and prostate. High animal fat intake is also bad for your brain health. There is growing evidence that dietary fat–induced changes in gut microbial signaling to the brain via the gut’s immune system can change our nervous system both functionally and structurally. Since our brain-gut axis and connection has not evolved to cope with a daily avalanche of fat and corn syrup, and a high-fat diet sets up a vicious cycle of dysregulated eating behavior that harms your brain health, become aware of these unhealthy consequences.

3. Maximize Your Gut Microbial Diversity

If you want to maximize your gut microbial diversity, increase its resilience, and reduce your vulnerability to chronic diseases of the brain, follow the old advice of nutritionists, cardiologists, and public health officials: in addition to eating moderate quantities of meats low in fat, mainly from fish and poultry, increase your intake of food items that contain multiple prebiotics in the form of different plant fibers, a combination of food items that we know today leads to greater gut microbial diversity.

Indigenous people living in the Amazonian rain forest know hundreds of dietary and medicinal plants, and eat a large variety of wild animal products. Over hundreds of thousands of years, our gut sensory mechanisms have evolved to recognize and encode a large number of such nutritional and medicinal plant signals. There are an impressive number of gut sensors that respond to a wide variety of herbs and phytochemicals, from wasabi to hot peppers, from mint to sweet and bitter tastes, to name just a few. We know that signals from these herbs and foods are transmitted to the brain and the enteric nervous system and that they have an important effect both on our digestion and on the way we feel. Nature would not have come up with these mechanisms over millions of years of evolution unless they provided a health benefit.

Learn to listen to your gut brain connection, which in this context means to remember that your gut has evolved an elaborate system to handle a huge variety of naturally grown vegetables, fruits, and other plant-derived foods, as well as smaller amounts of animal protein, but that it struggles to handle all the fat, sugar, and additives that the food industry adds to processed foods. Unless you have been diagnosed with potentially serious medical disorders, such as a specific food allergy (such as seafood and peanut allergies) or celiac disease, try to avoid extreme diets that limit the natural variety of foods, in particular plant-based food items. Develop your own personalized diet within the general constraints of the “ground rules” of high-diversity foods, mainly from plant sources.

Avoid mass-produced and processed foods and maximize organically grown food. Follow the advice that Michael Pollan gives in his recent book, Food Rules. Buy only things in the market that look like food. If they don’t, they most likely will contain food additives that could harm your brain, including artificial sweeteners, emulsifiers, fructose corn syrup, and vital gluten, to name just a few. For the same reasons, watch out for the hidden dangers in food you buy in the supermarket. Read labels to find out the components and additives in a food item; try to find out where it comes from. If you do this regularly, you will often be surprised that your fish or poultry comes from a country without rules for how these animals are raised and what they are fed, and how many calories are in a bag of so-called reduced-fat chips.

Modern food producers have abandoned any consideration of the complexity of the microbial world and the importance of the gut brain connection and natural diversity of life, choosing instead to maximize output and profitability. Industrial farming of beef, poultry, fish, and other seafood defies ecological principles, creating patches of devastated ecological landscapes sustainable only through the use of antibiotics and other chemicals. Furthermore, the waste produced by these livestock and fish farms, and the antibiotic-resistant microorganisms that escape them, harms surrounding habitats as well. Ultimately, products coming from such surrounding compromised ecosystems—be it the water, soil, or air—will find their way to you, and will be a risk for your health.

Reducing the microbial diversity in the soil, on plants, and in the GI tract of farm animals may ultimately harm our own gut microbiome and its connection to our brain and our nervous system. Keep in mind that pesticides used to grow GMO foods may not directly harm our human bodies, but they are likely to affect the function and health of our gut microbes and their interactions with and connection to the brain. The same holds true for residues of low-dose antibiotics that remain in many mass-produced meat and seafood products.

4. Eat Fermented Foods and Probiotics

While the science is still evolving, it’s still prudent to maximize your regular intake of fermented food products and all types of probiotics to maintain a strong gut brain connection and gut microbial diversity, especially during times of stress, antibiotic intake, and old age. All fermented foods contain probiotics—live microorganisms with potential health benefits, and a few commercially available probiotics contained in fermented milk products, drinks, or in pill form have been evaluated for their health benefits. Unfortunately, there are also hundreds of such products in all shapes and forms, whose producers make vague claims of health benefits. Yet for many of them, we don’t even know if enough live organisms reach your small and large intestine to exert their claimed beneficial effects. But people have been eating naturally fermented, unpasteurized foods for thousands of years, and you might want to include some of them in your regular diet. Such products include kimchi, sauerkraut, kombucha, and miso, to name just a few. Various fermented milk products, including kefir, different types of yogurts, and hundreds of different cheeses, provide probiotics as well. I recommend selecting low-fat and low-sugar products that are free of emulsifiers, artificial coloring, and artificial sweeteners.

If you consume fermented dairy products, such as probiotic-enriched yogurts, you are also feeding your own microbes an important source of prebiotics (such as the milk oligosaccharides we discussed in the previous chapter), and if you’re eating fermented vegetables, you’re feeding your gut microbes another form of prebiotics, such as dietary fiber from complex plant carbohydrates. Probiotic bacteria you eat as an adult do not become a permanent part of your gut microbiota, but regular intake of probiotics may help to maintain gut microbial diversity during times of trouble, and it can normalize the pattern of metabolites produced by your gut microbes.

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5. Be Mindful of Prenatal Nutrition and Stress

If you’re a woman of reproductive age, it is equally important to remember that your diet will influence your child as well—from pregnancy, through childbirth and the period of breastfeeding, until the child is three years old, when his or her gut microbes are fully established. The maternal gut microbiome produces metabolites that can influence fetal brain development, and diet-induced inflammation of the gut-microbiome-brain axis may harm a fetus’s developing brain. In fact, full-blown inflammation during pregnancy is a major risk factor for brain diseases such as autism and schizophrenia, and low-grade inflammation from a mother’s high-fat diet may be sufficient to adversely affect the fetal brain development in more subtle ways. On the other hand, stress during pregnancy or maternal stress when the child grows up has well-documented negative effects on the development of the brain and the gut microbiota, often resulting in child behavioral problems due to a disturbed gut brain connection.

6. Eat Smaller Portions

This limits the calories you consume, keeping the amount in line with your body’s metabolic needs, and simultaneously reduces your fat intake. When eating packaged foods, be aware of the recommended serving size on the label. The calorie count on your potato chip bag may seem reasonable, but it refers to eating just a few chips. Eating the whole bag may serve up far more calories and fat than what you want to eat that day.

7. Fast to Starve Your Gut Microbes

Periodic fasting has been an integral part of many cultures, religions, and healing traditions for thousands of years, and prolonged fasting may have positive impact on brain functions and well-being. A popular explanation for the benefits of fasting is based on the idea that it cleanses the gut and the body by getting rid of harmful and toxic substances. Even though people have believed this throughout history, there is little scientific evidence for this hypothesis. But based on what we now know about brain-gut-microbiota connection and interactions, fasting may have a profound effect on the composition and function of your gut microbiome and possibly on your brain.

Recall that when your stomach is empty, it activates periodic high-amplitude contractions that slowly but forcefully sweep from the esophagus to the end of the colon. At the same time, the pancreas and the gallbladder secretion release a synchronized burst of digestive juices. The combined effect of this reflex, called the migrating motor complex, is analogous to a weekly neighborhood street sweeping. We don’t yet know what this street sweeping does to our gut microbes or whether it alters the metabolites they produce. There is good evidence that it removes microbes from the small intestine, where normally only a few reside, and sweeps them into the colon, where most gut microbes live. In people with an inactive migrating motor complex, microbes grow more abundantly in the interior of the small intestine, a condition called small intestinal bacterial overgrowth. This causes abdominal discomfort, bloating, and altered bowel habits. We don’t know whether fasting also reduces the abundance of microbes living in the large intestine, and if the microbes living in close proximity to the lining of the gut are affected as well, affecting the gut brain connection.

Fasting may also reset the many sensory mechanisms in the gut that are essential for gut-brain connection and communication. These include our main appetite control mechanisms, which sense satiety. Having no fat in the intestine for one or more days may enable vagal nerve endings to regain their sensitivity to appetite-reducing hormones such as cholecystokinin or leptin, and it may also return sensitivity settings in the hypothalamus to normal levels.

8. Don’t Eat When You Are Stressed, Angry, or Sad

To farm your gut microbes optimally, feeding is only half the story. We’ve seen that emotions can have a profound effect on the gut and the microbial environment in the form of gut reactions. A negative emotional state will throw the gut-microbiota-brain axis and connection out of balance in several ways. It makes your gut leakier, it activates your gut-based immune system, and it triggers endocrine cells in the gut wall to release signaling molecules such as the stress hormone norepinephrine and serotonin. It can also reduce important members of your gut microbial communities, in particular lactobacilli and bifidobacteria. These can profoundly change the behavior of gut microbes. These behavioral changes are likely to influence the structure of microbial communities, how the microbes break down food components, and which metabolites they send back to the brain.

For all these reasons, no matter how conscientious you are when selecting your food at the Whole Foods market, and no matter how much you believe in the health benefits of the latest fad diet, feelings of stress, anger, sadness, or anxiety always turn up at your dinner table. They can not only ruin the meal; if you eat when you’re feeling bad, it can also be bad for your gut and bad for your brain. Think about Frank, who became intolerant to food when worried about not being close enough to a restroom in an unfamiliar restaurant, or Bill, who couldn’t stop vomiting when he was stressed. If you are not mindful of the stress or other negative emotions in your body, it can lead you into seeking comfort food, even though such food is unhealthy.
For these reasons, scan your body and mind and tune in to your emotions before you sit down to eat something. If you are stressed, anxious, or angry, try to avoid adding food to the turmoil in your gut.

In addition, if you have always been an anxious person, or suffer from an anxiety disorder or depression, the influence of these negative mind states on the activities of your gut microbes when it comes to digesting the leftovers of your meal is even more pronounced, and it may be difficult to change the situation even if you are aware of it. In this case, it is prudent to seek the help of a physician or psychiatrist to treat such common conditions.

9. Enjoy Meals Together

Just as negative emotions are bad for your gut-microbe-brain axis and connection, happiness, joy, and a feeling of connectedness are probably good. If you eat when you’re happy, your brain sends signals to your gut that you can think of as special ingredients that spice up your meal and please your microbes. I suspect that happy microbes will in turn produce a different set of metabolites that benefit your brain. As noted by the authors of several scientific articles about the Mediterranean diet, some of the health benefits you get from eating a Mediterranean diet are likely to come from the close social interactions and lifestyle common in countries adhering to such a diet. The resulting sense of connectedness and well-being almost certainly affects the gut and influences how your gut microbiota respond to what you eat.

After scanning your body and becoming aware of how you feel, try to switch to a positive emotional state and experience the difference this shift has on your overall well-being. Various techniques have been proven effective at this, including cognitive behavioral therapy, hypnosis, and self-relaxation techniques, as well as mindfulness-based stress reduction. You may see benefits every time you eat a meal, or you may notice benefits that occur over time.

10. Become an Expert in Listening to Your Gut Feelings

Mindfulness-based stress reduction can also help you get in touch with your gut feelings and reduce the negative biasing influence of thoughts and memories on these feeling states. This sort of mindfulness helps relieve disorders of the gut-brain axis.

Mindfulness meditation is typically described as “nonjudgmental attention to experiences in the present moment.” In order to become more mindful you will have to master three interrelated skills: learn to focus and sustain your attention in the present moment, improve your ability to regulate your emotions, and develop a greater self-awareness. Under normal circumstances, the majority of bodily signals reaching your brain are not consciously perceived. A key element of mindfulness meditation is learning to become more aware of these bodily sensations, including the sensations associated with deep abdominal breathing, and with the state of your digestive system. By becoming more aware of these gut feelings, those associated with good and bad gut reactions, you can better regulate your own emotions. According to brain-imaging studies, including those performed by my colleague Kirsten Tillisch, meditation affects key brain regions that help you pay attention and make value judgments about the world around you and about events going on in your body. It also leads to structural changes in several brain regions, including those involved with body awareness, memory, regulation of emotions, and anatomical connections between the right and left hemisphere.  All of this helps to maintain the health of your gut brain connection.

11. Keep Your Brain (and Your Gut Microbiota) Fit

Of course, there is unequivocal evidence for the health-promoting effects of regular exercise, and no recommendations to achieve optimal health could come without the inclusion of regular physical exercise. Aerobic exercise has well-documented beneficial effects on brain structure and function, ranging from a reduction in the age-related decline in thickness of the cerebral cortex, to improved cognitive function and reduced stress responsiveness. In view of the close interactions and connections between the brain, the gut, and its microbes, there is no question in my mind that these brain-related health benefits of regular exercise are reflected in a positive way in the health of the gut microbiome.

12. How and What to Feed Your Gut Microbes

+ Aim to maximize gut microbial diversity by maximizing regular intake of naturally fermented foods and probiotics.
+ Reduce the inflammatory potential of your gut microbiota by making better nutritional choices.
+ Cut down on animal fat in your diet.
+ Avoid, whenever possible, mass-produced, processed food and select organically grown food.
+ Eat smaller servings at meals.
+ Be mindful of prenatal nutrition.
+ Reduce stress and practice mindfulness.
+ Avoid eating when you are stressed, angry, or sad.
+ Enjoy the secret pleasures and social aspects of food.
+ Become an expert in listening to your gut feelings.

Even though we humans are fascinated by the exploration of the frontiers in space and in the vastness of the oceans, it seems that until recently, we completely ignored the complex universe within our own bodies. While much is still to be learned about the influence of this system on our health and well-being, the emerging science is already having a major influence on our mind and body.

The brain-gut-microbiome axis connects our brain health closely to what we eat, how we grow and process our food, what medications we take, how we come into this world, and how we interact with the microbes in our environment throughout life. Now that we are beginning to fully understand this marvelous complexity of universal connectedness, in which we as humans represent only a tiny fraction, I am convinced that we will view the world, ourselves, and our health with very different eyes.

This new awareness will shift our focus from treating diseases toward achieving optimal health. It will shift us away from spending billions on treating cancer with warlike, scorched-earth therapies, on treating obesity with crippling surgeries of the gastrointestinal tract, and on dealing with the fallouts from cognitive decline with expensive long-term support measures. It will shift us away from being passive recipients of an ever-increasing number of medications to taking responsibility for the optimal functioning of our brain-gut axis by becoming ecological systems engineers with the knowledge, power, and motivation to get our gut-microbiota-brain connection and interaction functioning at peak effectiveness, with the goal of optimal health.

This article on the gut brain connection is excerpted with permission from The Mind-Gut Connection: How the Hidden Conversation Within Our Bodies Impacts Our Mood, Our Choices, and Our Overall Health by Dr. Emeran Mayer.

About The Author

Dr. Emeran Mayer was born in a small town in Bavaria where his family ran a confectionary business since 1873. After deciding against taking over the family business, he finished medical school at the Ludwig Maximilian’s University in Munich and completed his residency training at the Vancouver General Hospital in Vancouver, Canada before moving to Los Angeles. There he worked under the late John H. Walsh to study the role of gut-brain interactions at the prestigious Center for Ulcer Research and Education and completed his specialty training in Gastroenterology at UCLA. Visit his website at EmeranMayer.com