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How to Support the Gut, Part 4: Our Second Brain

Posted by cleanteam


Hi everyone, Dr. Junger here. 

There is an incredibly intricate and tight connection between our gut and our brain that science is only beginning to understand.

Articles are continually being released about the “gut-brain-axis” and our “second brain”, otherwise know as the nervous system in our gut.

Today, I want to finish our 4-part exploration of the gut by focusing in the nervous system. I’ll walk you through what it does, what gives it problems, and what we can do to support it.

The Gut’s Nervous System  

We have a nervous system that runs all through our gut.

Tiny nerve filaments touch the intestinal wall cells, muscle cells, and immune cells that form the walls of the digestive tube, directing and coordinating their functions.

These nerves make up the enteric nervous system or the nervous system in our gut. “Enteric” means “relating to our intestines.” You may have come across this word on supplements like enteric-coated probiotics or aspirin. Here, the supplement is coated so it can pass through the acidity of the stomach to the intestines.

These nerve filaments, spread throughout the gut like a net, send and receive information to and from our gut neurons, which coordinate, modulate, and regulate all of them at the same time, continuously.

In other words, the neurons in your gut orchestrate peristalsis and digestion, and modulate immunity and the hormonal system. Without them, the gut would cease to work.


Our Second Brain

The gut’s nervous system is often referred to as our “second brain”. If you were to isolate these neurons and clump them all together, they would form a mass of neurons larger than the ones in your head.

In fact, the brain in your gut is way more active in the production of neurotransmitters than the brain in your head. Serotonin, the neurotransmitter responsible for the feeling of happiness and well-being, is primarily manufactured in the gut—90 percent of it, in fact.

On top of all this activity, the brain in the gut helps run your intuition, communicating with you through feelings. These feelings are generated electrically inside your body by the neurons in your gut. That’s why we call it a “gut feeling.” It’s a parallel, powerful sense of knowing.

Listening to your gut is one of the most important lessons you can learn, which makes repairing and taking better care of it one of the most important thing for you to do.

What does our second brain do?

Even under the most optimal circumstances the brain in the gut is super busy. It is constantly coordinating nearly every aspect of the gut’s functions.

Take, for instance, peristalsis, the contractions of the muscles within the intestinal tube. During peristalsis, the second brain sends signals to every muscle cell through nerve filaments, allowing food and waste products to move along the intestines.

At the same time, it’s coordinating signals to and from the gut’s immune system to the rest of the immune system throughout the body.

It also coordinates the responses from the hormonal system. The most common example is that it stimulates the adrenal glands to release cortisol when stress is experienced.

As you can see, our second brain is an incredibly complex and important part of our gut system. While it is impossible to describe all of the functions of the second brain, it is becoming clearer that our second brain is intimately connected to the health of our gut. When we are experiencing gut dysfunction, our second brain must go into overdrive to coordinate and do its best to take care of the continually increasing load of problems.

Let’s go a little deeper into some of these problems.

Gut Damage

Over the last few weeks, I have been sharing some of the causes of gut damage. These include chemicals in our food and water, nutrient deficiencies, food triggers, stress, alcohol, and medications.

And what damage’s one part of the gut system, let’s say the intestinal flora, has consequences for all the other parts.

So, once again, when there is dysbiosis and hyperpermeability or “leaky gut”, the second brain is affected.

Under the conditions of leaky gut, our second brain must diverts its attention to coordinate the responses of the immune system and compensates for many other imbalances that occur.

The second brain quickly becomes so busy coordinating these other “emergency” functions that the normal everyday functions also get affected.
Let’s look at two of these normal functions that are affected by gut dysfunction.


Peristalsis is one of the first to feel the pinch. Constipation is the most common symptom on the planet, even if most people suffering from it don’t know it.

As the second brain is occupied with other more pressing matters, the usual signals to move the bowels are reduced. One bowel movement a day is considered great by a lot of people, but it is really constipation’s mildest expression.

Neurotransmitter Production

Neurons communicate by manufacturing and releasing neurotransmitters. In order to manufacture them at the rate needed, nutrients have to be available. Some of the nutrients essential for neurotransmitter production are the first ones depleted when we are experiencing gut dysfunction.

These include B vitamins, magnesium, calcium, and potassium. Without these nutrients our second brain is unable to create the necessary neurotransmitters. This can result in mood swings, brain fog, anxiety, and more.


The Gut Feeling

The picture above describes how the health of our GI tract can influence our second brain and finally the brain on the top of our head. As you’ll see when the second brain is influenced negatively, we can start to feel real effects in our day to day lives.

If you start with the box labeled “Stress, Dietary or Environmental Triggers”, these are all the causes of gut dysfunction that we have been talking about for the last few weeks. Chemicals in our food and water, nutrient deficiencies, food triggers, stress, alcohol, and medications are the common ones many of us experience daily.

When too many of these causes occur, we move to the next box labeled,  “intestinal flora changes”. This is where the bacteria in the gut is modified, creating an environment where the intestinal wall becomes "leaky".

From here, you can follow the cascade of reactions that goes from leaky gut, to the immune system firing up, to alterations in neurotransmitter’s (second brain) and finally, the change to our mood and how we feel.

Once this cycle begins, changes in how we feel can become another stressor encouraging us to eat poorly and continuing the spiral.

What do we do about it?

All of the strategies and tools we have mentioned over the last few weeks will help to support our second brain. While I separate the various parts of the gut from each other so they are easier to talk about, all of the parts work together as a whole.

This means that most of the tools of gut repair will not only affect the intestinal flora, but also the intestinal wall, the immune system and the nervous system.

Let’s remind ourselves of a few of our gut repair tools.

1. Discover your trigger foods. One of the major causes gut damage is the constant presence of trigger foods. Discovering which foods are causing reactions is a major health win. You can learn how to do this here.

2. Take a multi-strain probiotic. The truth is we are still learning about which probiotics are the most useful and in what quantities. But we do know that probiotics support the intestinal flora. I recommend rotating your probiotics to include different strains and different amounts.

3. Get a shower and water filter. Keep chlorine and other chemicals from being absorbed and damaging your microflora by using a shower and drinking water filter. Use the water-filter buying guide from the Environmental Working Group to help you find a filter that’s a good fit for you.

4. Do the Clean Gut Cleanse. I come back to a gut repair program each week because it’s the best all around approach to supporting our gut health. It removes the items that are causing damage to our gut while utilizing many tools to repair it all at once. Many of these tools you can take from the program and build them into your life, increasing the ways you support your gut daily.

To your health,

Alejandro Junger, M.D.


Topics: Clean Life


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