Skip to main content

The “connection”

The gut is often referred to as the “second” brain because it contains the same tissue and can produce many of the same chemical messengers as the brain that sits in the cranium. If you have ever experienced “butterflies in your stomach” when you are nervous or excited, then you have experienced the “Gut-Brain Connection”. Other clinical examples in Functional Medicine include:

PANDAS: a disorder in which Obsessive Compulsive Disorder develops after a Staph infection of the GI tract

Autism and other spectrum disorders: Patients always have symptoms of gastrointestinal dysfunction and food sensitivities.

Irritable Bowel Syndrome: Patients usually have a psychiatric diagnosis as well and IBS tends to flare in times of stress. Even in conventional medicine IBS is often treated with anti-depressants.

Functional Medicine now describes the gut as an extension of the brain and the spinal column of the Central Nervous System. This understanding of the gut as part of the brain provides a new opportunity to access the Central Nervous System through the Gut-Brain connection. Hence, there are now mountains of research on treating mood disorders through the GI tract with techniques that focus on balancing the microbiome with nutrition, anti-microbials and probiotics.

What’s the Microbiome?

As it turns out, human beings are actually more bacteria than they are human. Amazingly, there are 100-1000 times more bacterial cells lining our sinuses, lungs, skin and intestinal tract than there are human cells in the body. We are only just beginning to understand the implications of such an obviously large influence on our bodies and now minds. This collection of cells is influenced by several factors:

  • What we eat
  • How much stress we have
  • How many antibiotics we take
  • Whether we were born by cesarean section or through the vaginal canal
  • Whether or not we were breastfed
  • How many pesticides are on our food
  • How “sterile” our environment is

As we learn more and more about the influence of the microbiome on human health, functional medicine is starting to understand that most disease and inflammation in the human body is caused by imbalance in the gut flora. In the United States and other industrialized countries, our microbiome is constantly under attack. We make poor food choices, are under quite a bit of stress, take antibiotics frequently, have frequent cesarean sections, use a lot of pesticides on our produce and sterilize everything. Hence, we have a lot of disease and inflammation. We also have a lot of depression, anxiety and other mood disorders. Understanding how to appropriately balance the microbiome through making better lifestyle choices gives us a simple path to resolving many of our inflammatory symptoms including mood disorders.

How does stress affect the gut? And how does an imbalanced gut cause stress in the brain?

Interestingly, when we experience emotional stress in life, this stress is physically represented by the types of neurotransmitters and hormones that we produce. Adrenaline and cortisol are the biochemical representatives of stress in the tissues of the human body and both have profound effects on the health and integrity of the GI tract. The function of these chemicals is to put the body into “crisis” mode in response to a stressor. When the body is in crisis mode, it diverts blood flow away from the GI tract in order to supply the arms and legs with blood for running away from a dangerous situation. Repeatedly diverting blood from the GI tract causes the gut wall to break down, resulting in the “leaky gut” phenomenon. Stress chemicals also suppress the immune system so that it cannot weed out the “unfriendly” or “pathogenic” bacteria. Long-term stress causes break down of the physical tissues of the GI tract and leads to an imbalanced microbiome. From here, we see digestive disorders, poor absorption of nutrients, food allergies and systemic inflammation start to develop.

Once the integrity of the gut wall breaks down and we develop a poorly-balanced microbiome, the effects on the conscious “brain” and mental health are multi-fold. As 95% of the serotonin in the human body is produced in the GI tract, a “happy” gut is one that produces plenty of serotonin to share with the brain. “Friendly” bacteria themselves produce B Vitamins, amino acids, short-chain fatty acids and other molecules that human beings need to produce adequate serotonin and dopamine, our “happy” neurotransmitters.

This scenario completely changes when the GI tract tissue is damaged by stress and the microbial population favors “unfriendly” types of bacteria. In this unhappy situation, the gut is less likely to produce enough serotonin and the “unfriendly” bacteria produce chemicals that are over-stimulating to the brain, contributing to the pathology of anxiety and depression.

It is much easier and less risky to interrupt a dysfunctional gut-brain connection at the level of the gut than the level of the brain. Psychiatric medicine can, at best, take a guess at what’s going on in a depressed person’s Central Nervous System and prescribe a drug that may or may not be of benefit. This type of medicine is useful when a mood disorder renders a person non-functional, when the person is a danger to themselves or others, or when the person is not cognitively capable of caring for himself or herself appropriately. Cognitive Behavioral Therapy, a talk therapy technique that “reframes” the thought patterns of the person with depression to create a “sunnier” reality, is quite useful. This type of talk therapy benefits the biochemical side of depression by functionally reducing the amounts of cortisol and adrenaline a person produces in response to day-to-day situations. Reduction of these gut-damaging chemicals is quite beneficial for our gut-brain connection.  

How do I know what my gut microbiome looks like?

We know our microbiome is in need of balancing through observation of our own bodies.

With a well-balanced microbiome, a human being will:

Have at least one (possibly 2-3) well-formed, appropriately-colored, easily-passed bowel movement per day

Have little-to-no gas, bloating, reflux, heartburn or noise coming from the abdominal area

Have no pain or cramping in the abdominal area

Have little-to-no symptoms of systemic inflammation such as allergies, asthma, muscle pain, auto-immune disease, fibromyalgia, metabolic disorders, obesity, etc…

Buffer stress well without becoming overwhelmed

If any of the above is not true, likely the microbiome has become unbalanced along the way and is in need of fixing.

Nutrition techniques that benefit mental health via promotion of a healthy microbiome

There are multiple strategies we can use to ensure that we maintain a healthy gut wall and microbiome. If you have already developed a dysfunctional gut-brain connection, you can use some of these strategies to rebuild a healthy relationship. Often, with persistence, a pro-active attitude and patience, nutrition can go a long way to making peace between the gut and the brain.

You are what your “bugs” eat

Functional Medicine is so highly focused on nutrition because it is the largest deciding factor for the health of the microbiome. What we choose to put into our mouths has such a profound impact on our health because each time we eat we either feed the good guys or the bad guys. When we consistently choose whole foods that are contain fiber, protein and beneficial fat sources, we are building a microbiome that will promote positive mood and an anti-inflammatory state of health. When we consistently make poor food choices, eating a diet high in refined carbohydrates and sugars and low in fiber,

we are setting ourselves up for inflammation in both mind and body. This aspect of nutrition is particularly important in the early stages of life, when the microbiome is first being established. If we think of the foods that American children usually eat (high sugar, high carb, no vegetables, etc…) we can start to see the influences on asthma, allergies, ADD, hyperactivity, poor immune function leading to recurring colds and obesity leading to Type 2 Diabetes and other metabolic diseases.

The good news is that we can turn this all around. We can make better choices by educating ourselves and making positive changes in our home environments. Start by getting rid of any product in your house that:

  • Is not a color found in nature
  • Has more than five ingredients in the ingredients list
  • Has sugar as one of the first three ingredients
  • Contains high-fructose corn syrup

Make sure that each meal you (and your family) eats contains:

  • A source of protein: eggs, meat, fish, poultry, beans
  • A source of roughage: vegetables (especially leafy green ones) fruits, whole grains
  • A source of beneficial fat: nuts, seeds, nutbutters/seedbutters, avocado, coconut, olives, beneficial oils like olive and coconut, whole-milk dairy (if no allergy)

These are the basic rules that will go a long way toward establishing a healthy microbiome. For bonus points, incorporate some of the strategies below.

Culinary Herbs:

Herbs that have a pleasant smell to them are often used for cooking. The aromatic quality of these herbs is the essential oil of the plant and represents the plant’s own immune system. In other words, the essential oil (or smell) of the plant is the strategy the plant uses for fighting off microbial infections. Hence, we can use the essential oils of culinary herbs to fight off “unfriendly” microbes. These herbs include:


And the list goes on and on and likely includes your favorite spice. The essential oils of garlic and oregano are often used in Functional Medicine in concentrated quantities in place of antibiotics for balancing the microbiome. Use caution with the garlic bulb if you have a digestive disorder as the fibers contained within the bulb are highly-fermentable and will feed “unfriendly” flora. You can bypass this hazard by extracting your garlic bulb into olive oil so that you just get the taste/smell of the essential oil. Cook with dried or fresh versions of these to make your meals more interesting and keep the “unfriendly” flora away.

Probiotic “cultured” foods:

Are probiotics for everybody? Not necessarily. Probiotic formulations have to customized to the individual and different preparations need to be used depending on the person and health issue. However, most people can tolerate probiotic foods, which provide a smaller dose of therapeutically beneficial organisms that can colonize the GI tract. A daily serving of probiotic foods can, in a healthy gut, protect the tissue from infection and provide a good influence on the immune system. In fact, most other cultures in the world include daily servings of fermented foods for this reason. Little known fact: the condiment ketchup started out as fermented tomatoes that were served as a “digestive” along with a meal. Now look what’s happened to it!

Yogurt/Kefir: made from cow’s or goats milk that is fermented by beneficial cultures. Pasteurized yogurts kill off the beneficial flora in the pasteurization process and then add it back in. For the real stuff, choose raw, whole-milk and add honey or maple syrup as a sweetener. Keep in mind that yogurts that contain high amounts of sugar do not offer any health benefit as the sugars negate the benefits of the beneficial cultures.

Sauerkraut/Kimchee/Pickled vegetables: made from fermented cabbage usually, but can include other pickled vegetables and spices. Best served as a “digestive” aid alongside savory dishes.

Kombucha tea: an effervescent drink made from a mushroom culture, often flavored with a little juice. You can buy this as a commercial preparation or make your own at home.

Tempeh/miso: made from fermented soybeans or soy bean paste. Only for those without soy allergies.

Prebiotic foods: these are foods that contain fibers to nourish probiotics. They include asparagus, broccoli, artichoke, Jerusalem artichoke, oat fiber and other fibrous foods. Caution with active digestive issues, as these foods will feed both the good guys and the bad guys. Once you have balanced the gut flora, you can use these foods to maintain this balance.

Other strategies to support a healthy microbiome:

  • Switch to natural cleaning agents that use essential oils instead of chemical anti-microbials
  • Educate yourself about the “Dirty Dozen” and “Clean Fifteen”, these are the produce items that are the most and least (respectively) contaminated with pesticides
  • Use anti-microbial herbs instead of antibiotics for infections that are treatable naturally
  • Let the kids and the dogs share toys
  • Don’t be scared of dirt!!! Its good for you…and your microbiome.

To summarize:
The mind and the gut can either work in harmony to produce well-balanced mental and physical health, or they can work against each other and produce mental and physical inflammation or disease.

The easiest and most effective way to work with a dysfunctional gut-brain connection is through balancing the microbiome

We are what our microbiome eats, so make it count!

Order healthcare's best supplements

Visit my store to order top-quality supplements and wellness products – delivered to your door.

Visit my store

Sign Up for Our Newsletter

Integrative Concierge Care for the Treatment of Chronic Disease

Find out more about becoming a patient at NENH

New Patient appointments are now available for 2025