Autoimmune disease is diagnosed when the immune system becomes overactive and starts attacking parts of your own body as though it were an invader. There are currently 80 identified autoimmune conditions, and they can run the spectrum from mild to dire. While an autoimmune diagnosis is plenty to deal with on its own, it is a little-known fact that, statistically, more people are diagnosed with mental health conditions among people who have an autoimmune disease, than occurs in the general population.
While it can feel like a bit like a “chicken-or-egg” conundrum as far as which came first, the autoimmune disease or mental illness, what we do know is that there are links between autoimmune conditions and a higher incidence of mental illness diagnoses.
But there is good news: healing the gut with food and natural remedies can help alleviate debilitating physical and mental health issues that stem from autoimmune health issues.
How is autoimmune disease typically handled by mainstream medicine?
In conventional medicine, pharmaceuticals are the only treatment option for patients diagnosed with autoimmune disorders. For many individuals, this treatment keeps their disease in remission and in many cases, allows them to remain mobile and lessen their pain.
However, there are other natural options that address autoimmune issues that most conventional doctors aren’t taught in medical school.
Food is a huge part of our lives and what we consume on a day-to-day basis drives how we feel. When I was first diagnosed with an autoimmune disease, I knew food would be an important part of my protocol.
I just didn’t know how.
My personal experience
Flashback to my early twenties: I had been given my first medication to alleviate my depression symptoms. There was no dialogue about food or nutrition at that appointment. My instructions were simple: “Take this pill.” The only time a doctor even approached the nutrition topic was to say, “You need to lose weight.”
Thankfully, shortly after that encounter, the light bulb went on. I realized that maybe I was feeling lousy because I was eating lousy food. Then, with the help of a fantastic holistic doctor, we discovered multiple food allergies and started eliminating the toxic foods. It didn´t take long to see an improvement in how I felt.
However, my story doesn’t stop there.
Ten years later, physical pain led me to my new autoimmune diagnosis. I told the rheumatologist I was starting the autoimmune-paleo protocol and listed the foods I was eliminating in hopes of reducing pain-causing inflammation. The gist of his response was that food does not matter; pills are what I need, and at the highest dose possible.
To my credit, I didn’t roll my eyes. But at that point in my life, I had only taken two college science classes and still instinctively knew that what I ate made a difference in how I felt.
And now, after years of study, I finally understand the scientific basis of why food and natural remedies are effective and how they work: through the gut-brain axis.

What is the gut-brain axis?
To naturally address autoimmune conditions, my counsel is to explore two main questions:
- Is the food you´re eating aggravating your condition through the gut-brain axis?
- Could adding in probiotic foods substantially reduce your symptoms?
The gut-brain axis is a hot topic in natural health. With just a few minutes of browsing web pages about nutrition and health, you will likely see the term.
So what the heck is the gut-brain axis? And why may it be crucially important to people who are dealing with autoimmune issues?
The gut-brain axis is the bidirectional mode of communication between the brain and the gut microbiome that resides in the stomach and intestines. For decades, science researchers thought all information initiated solely from the brain and then passed directly to the body.
While our brain does communicate with our gut, the reverse is also true—our gut microbiota sends messages that are received by the brain.
It turns out that the phrases “gut feeling” and “gut instinct” were spot on and decades ahead of the scientific explanation of their accuracy. Our microbiome is sending us messages, and we are finally piecing the codes together to interpret the messages.
The messages sent from our microbiome travel to our brains via the vagus nerve. It is one of the main connections from the digestive system back to the brain, informing it how our immune system, digestive tract and other essential body functions are working.
What is the microbiome?
The microbiome is the totality of the microbes that live in our bodies, including protozoans, bacteria, and fungi. There are over 100 trillion microbes in our bodies, and most of them live in the stomach and intestinal areas. Thankfully, most of them are good guys that help digest food, and create vitamins like Vitamins B and K. In addition, they fight off harmful pathogens.
Behind the scenes, the microbiome also works to keep our immune system functioning. In fact, 50%-70% of our immune system resides in our gut.
We have known for some time that when someone has an imbalanced microbiome, they are more likely to deal with a multitude of health issues:
- frequent colds
- high blood pressure
- cancer
- obesity
- irritable bowel syndrome
- Type 1 diabetes
- various forms of arthritis
- celiac disease
- other autoimmune diseases
- mental health issues
I would like to bring special focus to the effect a maladapted microbiome can have on one’s mental health.

What is the link between autoimmune disease and mental illness?
So what does the microbiome have to do with autoimmunity and mental health?
Contrary to the original model that all neurotransmitters are made in the brain, many of the neurotransmitters that control emotions are created via the microbiome. Ninety percent of the neurotransmitter serotonin, which regulates our sense of well-being and lowers anxiety, comes from the digestive tract.
However, for individuals contending with autoimmune disease, it is likely the messages between the gut and the brain are being hijacked or misinterpreted due to the body being under attack from the immune system. Knowing how crucial communication between the gut and brain is to our immune system and our mental health, it is important for people dealing with autoimmune issues to learn how to balance our internal systems and untangle the mixed messages in our bodies.
Over the next three posts, I will dive deeper into how we can use food, probiotics, supplements, and herbs to strengthen the good bacteria in the microbiome in hopes of calming down both the physical and mental autoimmune symptoms to bring peace back to our lives.