Butterflies in your stomach. A gut-wrenching feeling. Your stomach suddenly drops… You’d better go with your gut.

I don’t know about you, but all of these phrases packed together gives me a general sense of unease, and for good reason. For most people, these sayings have become synonymous with the kind of scary, traumatic, or anxiety-provoking situations that simply make your stomach churn (pun intended).

On the other hand, for the positive psychology folks, we could also be talking about a remarkably exhilarating experience — falling in love, skydiving, riding a rollercoaster. There are endless scenarios that have elicited this reaction in our lives. But what do they all have in common?

All of these are intensely emotional experiences that seem to be best described by what’s happening in our stomachs at the time. Now, consider this for a moment — our most intense emotional experiences involve the gut SO much that we immediately tune into what it is telling us and then act accordingly.

Perhaps this seems highly intuitive. We know this to be true colloquially, culturally, but the truth is that researchers are just beginning to explore and discover all of the amazing ways the gut is connected to the brain and how it affects many other physiological processes. So far, they have found some pretty remarkable connections between what is going on in an organism’s gut (i.e., microbiome — more on that in a minute) and the quality of their mood.

Once you dive deep into the science of gastrointestinal (GI) functioning, you will also find that gut health (or lack thereof) seems to be strongly related to physiological brain health as well. In other words, it looks like an unhealthy gut may be a major factor contributing to neurological and emotional dysregulation.

Even though this field of study is still in its relative infancy, there is still a lot of science, information, and theory out there that is really important for us to know. Why, you ask? As clinicians, it’s our job to take a biopsychosocial (and cultural) approach to understanding our patients’ issues and concerns.

It’s also our responsibility to stay informed about emerging science and research so we can provide the best education and services for our patients. If you are thinking, “but I have no idea about any of this stuff!” don’t feel bad. The gut-brain connection is complex, but lucky for you I am here to break down the basics!

The Microbiome: What Is It?

According to NIH’s Human Microbiome Project (HMP), the term “microbiome” refers to “the collective genomes of the microbes (composed of bacteria, bacteriophage, fungi, protozoa, and viruses) that live inside and on the human body.” You can read a more in depth summary here, but for our purposes you can just focus on the idea that the bacteria are the heavy lifters we are talking about.

While we are generally trained to think of bacteria as harmful, the truth is that most of them don’t actually cause illness. In fact, research is showing that in many cases, a greater number of bacterial species is indicative of a healthier gut; having lower diversity (fewer species) of gut microbes has been linked to obesity and inflammatory GI conditions (think Crohn’s, IBS, etc.).

In general, science is pointing to the guideline that balance (or ratios) and diversity (or variety) of bacterial strains are two of the most important factors in how the gut regulates our physiological health.

Based on the early studies mapping genetic traits of human microbiomes (that is, the genetic traits of the microbes, not the humans) the HMP estimates that there are around 8 million unique microbial genes. EIGHT MILLION! That number is way more than the variation in human genes. If you are wondering, the ability of microbial genes to dictate human health factors is now suspected to outweigh that of our own human genetic code. Pretty powerful stuff.

The Gut-Brain Connection: Basic Physiology

Despite societal awareness that our gut and brain do, in fact, share a strong emotional connection, the physiological means by which they are related seems to be much more obscure.

People are often surprised to learn that the gut and brain actually share a direct connection via the nervous system. Actually, the entire gastrointestinal tract IS part of our autonomic nervous system — it’s ensheathed in layers of neurons that collectively make up what we call the enteric nervous system. How much more connected to the brain can you get?! Well, hold that thought because it continues.

The enteric nervous system allows the gut and brain to have bidirectional communication; the “first and second brain” have a lovely give and take relationship, which includes afferent signals (from body to the brain) and efferent signals (from the brain to the body).

Do you remember when kids used to tie two empty cans together with string and talk through them? That’s how close the communication is. You may be familiar with the vagus nerve, which is known to reduce pain, stress, and inflammation when it is stimulated. It is one of the primary pathways for sending “rest and digest” messages to the GI system and also for relaying physical sensations and experiences up to the brain for interpretation.

While there is a lot more to know about the physiological connection between the gut and brain, it gets complicated pretty quickly. Take home message: the gut’s connection to the brain is so important that it has its own nervous system and a direct connection to the brain in order to relay messages quickly and effectively.

Fight, Flight, and Inflammation

If you’re still with me, well done. We are inching closer to the more clinical aspects of why the role of the gut is so important. So, to recap: We know that the gut houses lots of bacteria that are heavy lifters when it comes to influencing other physiological functions. We know that the gut and brain are close friends with great communication skills.

But what happens when the fight or flight “switch” is flipped?

As clinicians, we tend to think of fight or flight as a reaction that starts in the brain during a fearful situation and sends a reaction to the body, including a cascade of instructions and chemicals designed to get us moving. The pathway that performs this function, called the HPA axis (that is, hypothalamic-pituitary-adrenal axis) is helpful in a crunch, but as modern humans with a large cerebral cortex that perceives stress everywhere, the HPA axis can also get stuck in a negative feedback loop that causes chronic stress.

Since we are talking on a physiological level, whenever you hear “stress” I want you to think: cortisol. And whenever you hear “cortisol,” I want you to think: inflammation. From now on. Forever. Because this is the primary reason that stress and poor mental health can wreak havoc our physical health.

But wait a minute. For this inflammation-producing pathway to be a negative feedback loop, that means that there has to be a signal that is also returned back to the brain, right? This is where gut health comes in.

We can experience an external stressor that sends us into fight-or-flight-HPA axis-stress-cortisol-inflammation mode. But the same is also true for internal stressors as well.

To use a simple example, just think about being dehydrated or hangry (you know, hungry-angry). When our bodies are not in a state of homeostasis (everything being calm and balanced and healthy), it is stressful for our brains too. And if our microbiome is out of balance or unhealthy because the “right” bacteria aren’t in charge, you can bet that our brain suffers.

Food for Thought: Lightning Round

So how do we ensure that we maintain a healthy, balanced, and diverse microbiome with good bacteria leading the way? Keep these things in mind:



Consuming probiotics and prebiotics help to achieve and maintain the balance and diversity within our microbiome. Probiotics are strains of live bacteria (found in capsule form or in foods like yogurt, kimchi, kombucha), while prebiotics are essentially “food for the good bacteria” and include foods with insoluble fiber. Think plants: garlic, onion, flaxseed, asparagus, broccoli, leafy greens, etc.

The quality of food we eat dictates how well our gut-brain system can convert nutrients into neurotransmitters. Processed, refined, sugary, or inflammatory (dairy, gluten , or other allergy-producing) foods not only reduce our ability to manufacture the hormones and chemicals we need, but they also create an immune response that can cause inflammation and dysfunction in the brain. Are you feeding your brain rocket fuel or contaminated, cheap gas?

Eating a “traditional” diet (fruits, vegetables, fish, olive oil, nuts, seeds, etc.) is correlated with a 30-35% reduction in anxiety and depression as compared to a Western diet (processed foods, fast food, chips, soda, etc.).

Anxiety and depression are often treated with SSRIs, but 90-95% of serotonin is found in the gut! This is why GI side effects are common with SSRI medications and also why gut health is such an important factor in eliminating mood disorders.

What Studies are Showing

While microbiome research is still in its infancy relative to other disciplines, the existing findings are so compelling that it’s growing FAST. Many studies have shown that administration of probiotics can actually have a functional effect on people’s mental health symptoms.

One review analyzed ten different studies that administered probiotics to participants who had been diagnosed with anxiety, depression, and/or cognitive dysfunction. The authors found significant improvement of mental health symptoms in nearly all of the studies.

Another study found a significant reduction in ADHD diagnosis in kids who had been given a probiotic back when they were 0-6 months old.

The benefits of probiotics also seem to apply to cognitive impairment too; administration of a liquid probiotic to seniors with Alzheimer’s yielded improvements in their cognitive functioning (and other measures of health) after only 12 weeks.

While these are just a few examples that demonstrate the importance of a healthy gut in reducing mental health issues, there are many more. Follow some of the references linked to throughout this article to fall into a virtual rabbit hole of microbiome science!

How Do I Apply This With Patients?

After learning about the many ways in which gut health can impact brain functioning, many clinicians feel moved to use these ideas to help their patients improve…but they don’t know what they can do or where to start. If you find yourself in this category, I would first like to encourage you because you have already achieved one of the hardest steps: being able to integrate gut health into the conceptualization of your patients’ presenting problems.

The next thing to consider is what, if any, interventions you can perform while taking appropriate scope of practice and competence into consideration. As clinicians we are not M.D.s; we cannot give medical advice or recommend medications or supplements unless we have some kind of specialized training that makes us competent in that specific area.

What we CAN do — without any concern about whether we are practicing outside our scope — is to provide psychoeducation and resources. As we know, education is often the first step that has to happen before real change can take place and there is no special license or certification required for you to help your patient understand why eating more vegetables and less sugar will help improve their mental (and overall) health.

In addition to helping your patient understand their mental health from the inside out, you can also do a little bit of research yourself to increase your own competence in this area. I recommend Grain Brain and Brain Maker by Dr. David Perlmutter or The Mind Gut Connection by Dr. Emeran Mayer as great places to start.

Increasing your knowledge will also help you make great referrals as well — patients should be encouraged to follow up with their doctor and maybe a nutritionist, if they have the resources. Once they have a plan in place from another health professional, you can help them even more by working on treatment adherence and setting small, achievable goals to improve the health of their microbiomes…AND, of course, their brains.