How Leaky Gut Can Lead to Depression, Anxiety, and Migraine Headaches

In Part 6 of her Leaky Gut series, Dr. Doni explains how leaky gut affects more than just your digestion. It can also affect the Gut-Brain Axis, which can lead to neurological symptoms including depression, anxiety, and migraines.

Part 6 of Dr. Doni’s Series on Leaky Gut

In the first three parts of this series we have taken a broad look at Leaky Gut: what it is, how to test for it and how to treat it. Here are the links if you would like to catch up:

Then, in parts 4 and 5, we explored the top 10 underlying causes of Irritable Bowel Syndrome (known as IBS), how they relate to Leaky Gut, how to test for them, and possible treatment options:

Today, I am going to explain how the brain and the gut are closely interconnected and how this can have a major influence on both leaky gut and IBS.

The Gut-Brain Axis

Leaky Gut, Gut-Brain Axis, vagal nerve, depression, anxiety, migraine, migraines, headache, headaches, intestinal permeability, digestive system, nervous system, inflammation, Brain-Gut Axis, hormones, cytokines, neurotransmittersThe simple fact is that the gut and the brain communicate so closely with one another that, not only does our brain have an effect on the health of our gut but our gut also influences our brain. This is known as the Gut-Brain Axis and there is a plethora of new research exploring how this communication works and the influence it has on our health and wellbeing.

The two-way nature of this communication mechanism means that, while it is usually called the “Gut-Brain Axis,” and sometimes the “Brain-Gut Axis,” perhaps it should really be named the “Brain-Gut-Brain Axis” (for the purposes of this article, I will use the more familiar term “Gut-Brain Axis”).

In fact, because communication signals travel from your gut to your brain and back again, when things go wrong, it becomes something of vicious cycle where problems in your gut trigger neurological symptoms in your brain that, in turn, aggravate your gut.

I’m going to explain in more detail how this happens, but first let’s consider how many people may be affected by this vicious cycle without realizing it is the cause of their health issues. Let’s focus on migraines, anxiety, and depression—each of which could stem from an issue in the Gut-Brain Axis. They are very common conditions, as you can see here:

However, most of them will treat these symptoms in isolation, often using prescription and/or over the counter drugs without understanding that a headache or mood change is related to their digestion. Estimates suggest that as many as 80% of people in the US suffer from leaky gut, and we can assume that a some proportion of those people who suffer from migraines, anxiety, or depression could relieve their symptoms by treating their digestive systems.

How Does Leaky Gut Affect The Gut-Brain Axis?

An understanding that the brain and gut respond to each other is not new—it has been researched and documented since the late 1880s. That we say we have ‘butterflies in our stomach’ when we are nervous or excited brings attention to the fact that what is happening in your mind (fear, anger, love) is actually not just “in your head” but also in the gut. In fact, the gut has been named our “second brain.” And, as I have already alluded to, communications also go the other way as well—from your gut to your brain.

There are three kinds of messengers that are sent through your body: hormones, cytokines, and neurotransmitters.1, 2 When you are stressed or unwell and the bacteria in your gut get thrown out of balance, your hormones jump right in and disrupt communications not only within your digestive system but also communications between your gut and your brain. Cytokines are minuscule signaling molecules that can be triggered by food sensitivities that develop due to leaky gut and/or imbalances of bacteria in the intestines.3 Once triggered, they can travel from your belly to your brain in no time, spreading a message of inflammation along the way. In fact, research is now confirming that the same cytokines from your gut can pass through the blood brain barrier (BBB) to affect your mood and cause headaches—a situation referred to as “Leaky Brain.” 4

The Vagal Nerve: From Brain to Stomach and Back Again

The third set of messengers is neurotransmitters. These are the messengers that communicate throughout the nervous system, including the nervous system in the digestive tract.  The main communication mechanism in the Gut-Brain Axis is the vagal nerve; an important part of the autonomic nervous system—the system that takes care of “behind the scenes” functions such as your heart beat and bowel movements. The vagal nerve carries messages sent by this auto-pilot system from your brain to your gut, as well as from your gut to your brain. Cytokines and hormones from the gut also transfer their message via the vagal nerve to the brain. I want you to remember the name of this important nerve because it is one of the key components of the Gut-Brain Axis and it holds the power for you to influence it (I will explain how a bit later).

Taking Action: Two Simple Steps

Now that you know your mind has a direct effect on your digestion (and vice versa), it can open up a whole world of new approaches to digestive distress that you might not have previously considered. Simple stress remedies can support the release of anti-stress messages and address anxiety, depression, and headaches as well as digestive problems. My 99-cent ebook, Stress Remedies, includes practical tips that you can integrate into your day-to-day routine—or you can download a one-page graphic here to print and hang on your wall that will remind you of what they are.

  1. Take Control of the Gut-Brain Axis: Stimulate Your Vagal Nerve

Remember I said that the vagal nerve is the key to controlling the Gut-Brain Axis? Well here’s a simple exercise you can do to stimulate your vagal nerve when you have a headache or feel anxious or depressed.

  • Step 1: Take deep breaths—inhale as deeply as you can while counting to 5 and then exhale as slowly as you can through your mouth with your lips pursed. Repeat for 5-10 minutes.
  • Step 2: Take a mouthful of liquid—you could use warm water or even your own saliva—and hold it in your mouth (while breathing through your nose) for as long as you can or up to 3 minutes.
  • Step 3: Dip your forehead (as well as your eyes and top part of your cheeks if possible) in a bowl of cold of water (50 degrees F) for 3 minutes.
  1. Take Control of Your Diet to Reduce Inflammation

The main goal here is to reduce inflammation by choosing foods that are least likely to cause inflammation and cytokines to be released. The way to do that is by avoiding food allergens, including those triggered by IgG and IgA antibodies, most commonly dairy proteins (casein and whey), gluten, eggs, and soy protein.

Another approach is to reduce your “sugar” intake, especially refined sugars and high fructose corn syrup (HCFS) both of which are found mainly in processed foods. Research shows that sugars, and especially fructose can send a message from your gut to your brain that affects your mood. 5 Learn more about how to reduce your sugar intake and why in this recent podcast I recorded with my colleague, Dr. Trevor Cates.

Working with a Practitioner

Patients often come to me having struggled with migraines, anxiety, and/or depression for many years, if not a lifetime. They really want to get better but don’t know where to begin. When they start working with me, I start by looking at all the information that we have from their past experiences and from tests that may have already been performed.

Next, we consider further tests to help us gather additional information about exactly which “stress messages” are perpetuating the vicious Gut-Brain-Gut cycle so we can address them very specifically. These tests might include a food sensitivity panel, a salivary cortisol panel, a urinary neurotransmitter panel, a stool analysis, or blood work to identify nutrient deficiencies or hormone imbalances.

Once we have all the information we need, I help my patients create a step-by-step strategic plan to address each of the issues in a manner that allows their body to heal. Throughout this process we keep an eye on how their body responds to treatment and adjust the plan accordingly.

To help structure this process, I have designed a 6-month program specifically for healing Leaky Gut. It allows us to discover exactly what you should eat and what you should avoid, and which herbs and supplements you need to take to help improve your digestion. To find out more, click here.

What to Expect

Healing Leaky Gut and the Gut-Brain Axis takes time and persistence, but it is possible. It can take time to put all the steps in place, to identify all the contributing factors and to make lifestyle and diet changes. While this process can be overwhelming and frustrating, I encourage you to not lose hope, because as I’ve learned from my patients, it is possible to feel better little by little. Each person and situation is unique, so it’s hard to say definitively how long it will take before you see improvement—it could be anywhere between a few weeks and a few months.

In the next post of this series, I’m going to explore the connection between weight gain and Leaky Gut. To be sure you don’t miss it, you can receive it direct to your inbox by subscribing using the box in the right margin. Or, if you prefer you can sign up for my newsletter here.

I look forward to your comments and questions below. What have you discovered about the Brain-Gut-Brain Vicious Cycle and how it affects your health? What has helped?

–Dr. Doni
4th August 2015



  1. Emeran A. Mayer. Gut feelings: the emerging biology of gut–brain communication. Nat Rev Neurosci. Nat Rev Neurosci. 2011 July 13; 12(8): 10.1038/nrn3071.
  2. Gershon MD. The Second Brain. Harper Collins; New York: 1998.
  3. Emeran A. Mayer, Tor Savidge, and Robert J. Shulman. Brain Gut Microbiome Interactions and Functional Bowel Disorders. Gastroenterology. 2014 May; 146(6): 1500–1512.
  4. Saskia van Hemert, Anne C. Breedveld, Jörgen M. P. Rovers, Jan P. W. Vermeiden, Ben J. M. Witteman, Marcel G. Smits, Nicole M. de Roos. Migraine Associated with Gastrointestinal Disorders: Review of the Literature and Clinical Implications. Front Neurol. 2014; 5: 241.
  5. Melissa Ochoa, Jean-Paul Lallès, Charles-Henri Malbert, and David Val-Laillet. Dietary sugars: their detection by the gut–brain axis and their peripheral and central effects in health and diseases. Eur J Nutr. 2015; 54: 1–24.

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