Understanding the Conversation Between Your Brain, Gut, and Microbiome

Dr. Dr. Vivian Zhang PT, DPT, MS
Have you ever had a gut feeling or butterflies in your stomach? Such experiences demonstrate the connection between your belly and your brain. The communication between your brain, your gut, and the microorganisms living in your gut is referred to as the brain-gut-microbiome axis. Understanding the communication pathways between the brain, gut, and microbiome is essential to optimization of health and well-being. In this blog, we will examine the components of the brain-gut-microbiome axis, explain the potential mechanisms behind how this communications system works, and discuss the implications these interactions have on your health.

What Makes Up The Brain-Gut-Microbiome Axis?

To simplify things, let us first break down the brain-gut-microbiome axis into its individual parts to familiarize ourselves with the participants in this complex three-way conversation.

The Nervous System

The nervous system is a network of nerves that serve as information highways in the body. The nervous system can be subdivided into the central and peripheral nervous system. The central nervous system consists of your brain and spinal cord, while your peripheral nervous system is composed of everything else. The brain is an organ of nervous tissue protected by the skull that is involved with functions such as movement, thinking, speech, emotions, breathing, and the release of hormones. The spinal cord housed in the vertebral column acts as an extension of the brain by carrying messages to and from the brain to the rest of the body. The peripheral nervous system branches off of the spinal cord and can be broken down into the autonomic nervous system and the somatic nervous system. When it comes to the brain-gut- microbiome connection we are more interested in the autonomic nervous system which oversees regulating physiological processes that keep us alive without us having to think about it, such as breathing and digestion. The autonomic nervous system is further split into the parasympathetic and sympathetic nervous systems. The parasympathetic nervous system prepares the body to “rest and digest” and the sympathetic nervous system prepares the body to “fight or flight”. These two systems help aid in survival and although we no longer find ourselves running away from bears regularly, we all continue to experience other forms of daily stressors. The nervous system as a whole is involved in collecting and sending out information that the body uses to function.

The Gut

The gastrointestinal tract aka the “gut”, is a system that goes beyond just your stomach. It represents the entire digestive tract, a long tube that runs from your mouth down to your anus through which food passes. This is analogous to a channel where water runs to create a river. Food that enters this pathway is first broken down mechanically and chemically in the mouth and stomach, before traveling to the small intestine where nutrients are absorbed, and finally ending its voyage in the large intestine where the remaining waste is eliminated. However, your gut is capable of more than just digestion, it also acts as a sensory organ that passes and receives information to and from the brain to assist in keeping us alive and healthy.

The Gut Microbiome

If our gut is the river, then our gut microbiome represents the many fish that live in it. A microbiome is a community of microorganisms, also known as microbes. These fascinating creatures have inhabited earth longer than us humans and first evolved around 3.5 billion years ago. They are found in pretty much all things – the air we breathe, the food we eat, and in our bodies. We are home to trillions of microorganisms in and on us. The main places microbes live in and on humans are in the skin, airways, urogenital tract, eyes, and gut. Of these locations, most microbes are housed in our gut. The gut microbiome consists of a variety of organisms including, bacteria, fungi, protozoa, viruses, archaea, bacteria, and bacteriophages. The gut microbiome varies from person to person and is influenced by a variety of factors like where you live, what you eat, and your lifestyle. The job of the gut microbiome is to help protect us from disease, break down and absorb nutrients in food, and support cognitive function.

Not all microbes are created equal. Going back to our river analogy, we need a balance of both predators and prey to have a healthy ecosystem. Similarly, a healthy gut microbiome consists of a balance of both good and bad bacteria. So, what causes an imbalance in our gut microbiome? Well, if you’ve ever contracted a stomach bug or had a urinary tract infection you may be familiar with your doctor prescribing a round of antibiotics to treat the infection. These antibiotics work by killing off bacteria so that you can feel better. However, these medications are not able to differentiate good bacteria from bad bacteria and as a result, end up killing off all bacteria regardless of how healthy they are for you. If you do not replenish the good bacteria it can result in an imbalance of too many bad bacteria and lead to health problems.

How Do the Brain, Gut, and Microbiome Communicate?

Now that we have a better understanding of who the main conversationalists are, let’s take a deep dive into how they communicate. The dialogue between your brain, gut, and microbiome is neither a top-down nor bottom-up process, but an ever-evolving three-way conversation. Tridirectional signaling is made possible through various “communication portals” involving nervous tissue, hormones, immune cells, and intestinal microbiota. Keep in mind that the complex interactions between the gut, brain, and microbiome are not yet fully understood and is still an active area of research.

The Enteric Nervous System

The gut talks to the brain through its very own nervous system, also known as the enteric nervous system or the “second brain”. The enteric nervous system is made up of over 500 million nerves which is about 5x the amount that live in your spinal cord and works to maintain optimal digestive function. The enteric nervous system oversees the day-to-day operations of your gut so that you don’t have to consciously think about digesting your food. The gut receives information through the enteric nervous system about what is consumed to figure out how to best break it down. This means that your gut can sense the amount, type, and size of food in the stomach and as a result self-adjust the digestive tract’s contraction speed, strength, and pattern. Although the gut may not need the brain to perform everyday tasks, it continuously gives the brain feedback about what is going on, so the brain is ready to step in to respond when necessary. The enteric nervous system is essential for normal healthy digestion to occur.

The Vagus Nerve

The vagus nerve extends from the brainstem down to the gut. The vagus nerve acts as a highway for information to travel between the brain and all organs in the body, including the gut and its microbiome. Approximately 90% of the traffic flows from the gut to the brain, while 10% moves in the opposite direction. The vagus nerve is predominantly involved in parasympathetic nervous system activity but has sympathetic influences as well. The vagus nerve serves as a key pathway for communication about gut sensations and signals from your gut microbiota. When the vagus nerve is compromised it can have negative impacts on digestive health.

The Immune System

The gut houses a majority of your body’s immune cells which help to defend against potentially deadly microorganisms found in contaminated food and drink. Have you ever gotten food poisoning? Chances are your immune cells were hard at work helping you fight off the bacterial invaders you ingested. However, research now shows that the immune system can also be triggered by microbes that aren’t necessarily harmful as well. Whenever the immune system detects microbes, it responds by producing cell signaling cytokines. Cytokines can cross the gut lining, enter systemic circulation, and directly reach the brain, thus influencing its function.

Endocrine System

Your gut lining also contains endocrine cells that release hormones in response to the environment. These hormones interact with the brain and the rest of the body via the vagus nerve and systemic circulation. For example, the “hunger hormone” ghrelin is produced when our gut senses that our stomach is empty which signals to our brain that it is time to eat. Furthermore, scientists have discovered that the gut is the main place the body stores serotonin, an important hormone that helps us better digest food, sleep, and feel better. Research shows that 95% of your body’s serotonin is produced in the gut. Typically, when serotonin is released it activates sensory nerve endings in the vagus nerve and enteric nervous system, both of which as we know directly communicate with the brain.

The Gut Microbiome

The gut microbiome has evolved with humans for a very long time. In fact, microbes have lived in the guts of animals for hundreds of millions of years, because it was evolutionarily advantageous to do so.

Just like any good homeowner would invest to take care of their home, the gut microbiome had to develop ways to take care of its “home” aka our gut as well. By sensing and interacting with the body through various signaling pathways found within the gut, immune system, enteric nervous system, and brain, the gut microbiome was able to increase its chances for survival by optimizing its living conditions. Communication between the gut microbiome, gut, and brain has always been important and continues to have long-term effects on our health. Early gut-brain connection research focused on digestion, but new research suggests that the health of our gut microbiome is critical to preventing and treating illness and disease.

How Does the Brain-Gut-Microbiome Axis Impact Your Health?

The next time your body is under stress, such as from a challenging day at work, an infection, poor sleep, or an unhealthy diet, pay attention to how your body physically reacts. For example, you might notice that when you eat sugar, your pain sensitivity increases or when you fight with your spouse, your digestion suffers. When we fail to take care of our brain, our gut health suffers and when we fail to take care of our gut, our brain health suffers. This is why we commonly see GI disorders such as IBS, leaky gut, and SIBO come hand in hand with anxiety and depression. Effective communication between your brain, gut, and microbiome is critical for optimal health. When problems occur in one system, it impacts the entire system.

How to Improve the Health of Your Brain, Gut, and Gut Microbiome

Conventional medicine views the body as made up of distinct systems. However, the brain-gut- microbiome axis shows how interconnected these systems truly are. Treatment of brain and gut disorders need to be holistic. We can’t separate the brain from the gut, and the gut from the brain. Some things you can do to support your brain-gut-microbiome axis include managing your stress, eating a healthy diet, and engaging in regular exercise.

Reduce Stress

Your body is made to help you survive, which is why you have an internal alarm system designed to keep you safe from harm. Some people’s alarm systems are hyperactive, meaning they can be triggered more easily. How sensitive your alarm system is in part due to genetics but can also be shaped by your experiences throughout life. Childhood trauma for instance, can result in heightened bodily reactions to stressors in adults. Sensitivity to stress differs from person to person, which is why not everyone who experiences stress develops GI issues. If you are someone who has experienced trauma or chronic stress in your life, you may benefit from working with a health professional to help calm down your internal alarm system to improve the health of your gut, brain, and body as a whole. Below are tools you can use to help manage your stress levels.

Stress Management Tools:

  • Meditation
  • Make a daily gratitude list
  • Yoga
  • Taichi
  • Psychotherapy
  • EFT
  • Journaling
  • Breathwork


Eat a Healthy Balanced Diet

It turns out the saying “you are what you eat” is true! The metabolites that your microbiota produces depend on the type of food you eat. When you eat a diet that is low in fiber and high in animal fat the lining of your gut becomes more permeable or “leaky” which allows microbes to cross over more frequently. This can potentially result in chronic activation of our immune system leading to local and systemic inflammation. A diet rich in fruits and vegetables is best to support optimal gut health. Try to incorporate more color, fiber, and prebiotic and probiotic-rich foods and less sugar, unhealthy fat, and processed foods into your diet. If you are not sure where to start, following a Mediterranean-style diet can be a good guideline.


Regular physical exercise is not only part of a healthy lifestyle but is also a part of a healthy brain care regime. As previously discussed, a healthy brain = a healthy gut. Below are the current weekly physical activity guidelines recommended by the U.S. Department of Health and Human Services, Office of Disease Prevention and Health Promotion.

  • A minimum of 150 minutes of moderate-intensity cardiorespiratory exercise, 75 minutes of vigorous-intensity, or an equivalent combination of moderate-intensity and vigorous-intensity exercise per
  • Strength training of moderate or greater intensity that involves all major muscle groups on 2 or more days per


The Relationship Between the Brain-Gut-Microbiome Axis and the Pelvic Floor

Treating the pelvic floor involves treating the whole body. The current research suggests associations between the gut microbiome and endometriosis, infertility, and chronic pelvic pain, all of which are diagnoses that pelvic floor physical therapists often encounter. Although there is still limited research on how dysfunction in the brain-gut-microbiome axis may result in pelvic symptoms, we can make educated guesses that changes in pain sensitivity, mental health, and the immune system could be involved. It is therefore important to take the health of the brain, gut, and microbiome into consideration when it comes to addressing pelvic floor symptoms. Improving someone’s diet for example might help to improve anxiety levels and therefore decrease pelvic floor muscle tension and pain.

Final Thoughts

If you only take one thing from this article, take this: treat your gut and brain well! A healthy diet, stress- reduction techniques, and exercise are all ways to improve gut, brain, and mental health. Research to fully understand the mechanisms behind this communication pathway and the impact on our health is still underway. Future studies will hopefully help to develop better treatments for conditions such as chronic pain, IBS, depression, anxiety, and neurological disorders.


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