How I overcame autoimmunity, Lyme & hormonal imbalance

Hi there!  Thanks for stopping by! I'm Chelsea, your hostess over here at The Autoimmune Nutritionist. I am a Registered Nutritionist and Autoimmune Protocol Certified Coach who has overcome Hormonal imbalance, GERD, Hashimoto's thyroiditis, Guttate Psoriasis and Lyme disease. My passion is to empower others on their health journey to thrive and live amazing lives!

I thought it would be a good idea to kick things off here by telling you about myself, my health issues, and the journey that inspired me to become a nutritionist, specialize in hormonal health and autoimmunity, and create this site. You can read the About page for a simplified version, but the even shorter version goes like this: my health deteriorated over many years, I hit rock bottom and have come out the other side with balanced hormones and reversed autoimmunity! Here's the full story:

Lets go back…

My mid 20's were colored with frequent illness, many episodes of severe vertigo, ocular migraines, chronic insomnia,  hormonal problems, extremely low blood pressure, and GERD (reflux disease).  After suddenly developing a rash all over my body that did not go away, I was diagnosed with my first autoimmune disease, Guttate Psoriasis and was treated with powerful steroid creams and light therapy.  

At the same time, I was very lucky, and despite these challenges, I managed to maintain a happy life with a successful career in the fitness industry, a hobby of triathlon training and racing, an excellent social network, exciting travels, and met my future husband! In fact, for most people looking in, I was a vision of health and wellbeing!

In my late 20's, I was diagnosed with my second autoimmune disease, Hashimoto's thyroiditis. After finally finding out what was going on, my relief quickly turned to despair. As is the case for most people diagnosed with autoimmunity, I was informed by my Doctor that there was nothing that could be done to stop the progression of my disease. I was told that throughout my life, my body would continue the slow destruction of its own thyroid and that my condition would be managed only by increasing the dose of synthetic thyroid hormone I had been prescribed.

This did not seem right to me! I was not prepared to give up and let my body deteriorate! I knew I had no choice but to dig deep and find the root cause of my autoimmunity and hormone imbalance. My desire to live well with autoimmunity led me to continue my education in holistic health.

I enrolled as a part-time holistic nutrition student, continued to work full time as a fitness Director and trainer, and maintained my hobby of endurance sports training and racing, pushing it harder than before and becoming increasingly competitive. I think part of my fascination with pushing my body to the limits was because I didn't feel well. I believed the more 'fit' I got, and the more I 'accomplished,' the healthier I would become. 

Hitting Rock Bottom

In 2015 and 2016, my symptoms were increasing in intensity and frequency, but I was determined to maintain my active lifestyle and push through no matter what. Even though my health was deteriorating, I booked a trip to India for a Yoga teacher training course and left in February of 2016 for six weeks. I also decided to adopt a Vegan diet (more on the significance of this later).

Overall my experience in India was amazing, but when I returned, things took a downward spiral. All of my symptoms that would come and go over the past nine years came on strong and took over my life. My occasional dizzy spells turned into dizziness ALL THE TIME. I could not think clearly. My weight steadily dropped despite making no dietary changes. My thyroid was visibly swollen and painful. I couldn't get warm. I slept only a couple of hours a night. It felt like I was muddling through life just hanging on by a thread.

Then the intense neurological pain started, and the situation became grim. It felt like I was getting cut in my fingers, hands, feet, and ribs, like a knife was slicing into me over and over again. I also had a constant ice pick headache, which feels exactly as it sounds; like an icepick was stabbing me in the top of my head… all the time!

An MRI revealed abnormal lesions in my brain, which resulted in a referral to the MS clinic in Toronto. The neurologists there concluded that the lesions were not in line with MS, and my neurological symptoms were too aggressive to fit the bill.

At the same time, I was tested for Lyme disease through Igenix labs in California, where I got a positive result for chronic Lyme disease. My emotions went from relief that I was dealing with a "treatable" condition to the realization that getting treatment was going to be tough. Financial stress after learning the cost of getting treated in the US, combined with my symptoms and struggle to stay afloat with my job, led to depression. Adding to this was a strong feeling of guilt that I was ruining my husband's life who had become my caregiver. I felt like a burden and went to a very dark place. It is very tough for me to talk about these strong emotions, but I feel it is important not to leave them out as I know that many others with chronic illness suffer from them.

I became unable to keep up with the demands of my life, leading to the eventual stepping down from my career and racing. 

Slowly climbing back up

A huge turning point is when I became fortunate enough to get treated by an amazing functional medicine doctor in Canada, and after responding well to six months of antibiotic treatment for the Lyme, my neurological symptoms that developed when I hit rock bottom disappeared! I became well enough to return to a somewhat normal life, but there was still a lot of healing to be done. My autoimmunity and hormonal imbalances had worsened. And my gut needed even more healing due to the six months of intensive antibiotic treatment I had received for the Lyme.

Using resources from my nutrition school and the support of a fantastic Naturopath, I slowly started to make dietary and lifestyle changes. I transitioned to the AIP elimination diet (a very big deal considering I had been Vegan for years), worked extensively on my gut health, dramatically reduced my daily toxic load, and immersed myself in mindfulness practice.

It was at this time that I decided to shift the focus of my career. I felt drawn to understand the root causes of autoimmunity and chronic illness. I was motivated to find a way to live the life I wanted to live and felt compelled to empower others to do the same. After completing my studies to become a Registered Nutritionist, I went on to become an Autoimmune Protocol Certified Coach. Shortly after, 'The Autoimmune Nutritionist' was born with the mission to empower others to take control of their health and live amazing lives.

How I healed my hormones and autoimmunity

I am very fortunate that I am now living symptom-free, and as I write this, I am actually pregnant! Something I believed would not be possible due to my hormonal imbalance. I am still a work in progress! I will always be following a low inflammation diet, working on my gut health, using safe products, detoxing my body daily, and practicing mindfulness and meditation. This is fine with me as I have a higher quality of life than I did even in my teens and twenties! It was a long road to get here, but I can genuinely say I wouldn't change my journey if I had the choice.

In my case, what worked for me was a combination of conventional and holistic techniques. I decided to go the conventional route to rid my body of Lyme disease, which helped me get to a state of health where the deep healing could begin, and I could slowly heal my body naturally. I also continue to take prescription Thyroid medication to help my overall hormonal health as there was significant damage done to my thyroid before I was able to get my Hashimoto's under control.

The bottom line is, true healing requires a multi-faceted approach. Conventional medicine is sometimes helpful, and individualized health coaching is essential to identify underlying causes of hormonal imbalance and autoimmunity such as food intolerances, infections, gut imbalances, etc. However, the body will never fully heal if it is constantly being fed foods that it is intolerant to and exposed to unnecessary toxins and chemicals every single day.

I know a lot of you can relate to my health journey, and I am here to help you with yours. Here I am sharing some key components that helped me to become well!

Diet and The Gut health connection

Leaky Gut (also known as intestinal permeability) is a PREREQUISITE for autoimmunity to develop!
There are many other contributing factors to autoimmune disease developing, such as infection, toxic exposure, chronic stress, and environmental factors. These factors will vary from person to person and are not always within our control to change. They increase the risk but are not necessarily the tipping point to autoimmunity developing.

Although these factors contribute to the development of autoimmunity, they are not prerequisites for autoimmunity to develop (i.e., not everyone with exposure to heavy metals or chronic stress will develop autoimmunity)

There are only TWO known risk factors that are PREREQUISITES for autoimmunity to develop: 

1) Genetics
2) Leaky Gut (intestinal permeability)

This means that you could have every single autoimmune disease risk factor, but if you don't have the genetic predisposition AND the leaky gut, autoimmunity will not develop.

Another way to look at it: you could have every autoimmune risk factor listed above AND the genetic component, BUT if you don't have a leaky gut, you're good! Autoimmunity will not develop without the Leaky Gut.

When I first learned this vital information, I had many aha moments. I realized that my gut health issues went very far back. I've had 'stomach issues' since I was a kid. Being a child of the '80s and '90s, antibiotic prescriptions were readily given out (banana milkshake anyone!?). Being a 'vegetarian' for most of my teenaged life in the late ‘90s/’2000s, I can assure you my vegetarian diet was anything but high in vegetables! I basically lived off of soy-based products, dairy, refined carbs and microwaveable dinners. Throw in a constant attempt to keep calories and fat low (yes, this was the era of fat being 'bad') and a few bouts of disordered eating, and I can guarantee my gut was anything but balanced.

Working on my gut health was key to me becoming well. I find it very interesting that the timing of my hitting 'rock bottom' came shortly after switching to a vegan style of eating and improved rapidly after adopting a low inflammation AIP diet. For many with gut health issues, a low inflammation diet is key.

Another key part of healing my gut involved balancing out my gut bacteria and reducing Candida overgrowth. I was able to confirm these suspected imbalances through comprehensive stool testing (the GI map, which is one of the tools I sometimes use with clients in my 1:1 health coaching practice).

Supplementation was an important part of healing my gut and the key supplements that helped me were: 

1. Digest Plus - Optimizing digestion was key and while switching to AIP diet helped this greatly, I needed extra help from digestive enzymes that included HCL to help rebuild my stomach acid levels
2. Ox Bile – I took Ichol Plus to help my body digest fats. I suspected I did not digest fats well (especially fatty meat) and my GI map test confirmed this.
3. Intesti-bal – I took this for the Candida overgrowth
4. Probiotics – I spent several months on these shelf-stable high dose probiotics HMF 50 to increase my good gut bacteria and crowd out the bad as well as a probiotic yeast Saccharomyces Boulardii to crowd out the Candida. For maintenance, I currently use HMF travel as they are an excellent shelf-stable, everyday probiotic and even contain some Saccharomyces Boulardii!
5. L-Glutamine - L-glutamine is an amino acid that studies have shown to be very helpful to repair leaky gut by supporting and repairing the mucosal lining in the gut

Reducing hormone-disrupting toxins

75% of the risk of autoimmunity developing comes from environmental triggers IE. Gut health, toxic exposure, infection, and chronic stress. This means that the majority of causes of Autoimmune disease are within our control and is empowering news for those living with chronic illness!

Reducing daily toxic exposure is key to reclaiming health and what we put on our skin and chemicals in our homes might be an even greater risk for toxin exposure than what we put in our mouths! We all do some form of cleaning every day, and the average woman uses 12 products on her skin daily, which can contain 168 different chemicals – most of them with little to no safety testing and many of them with proven harmful effects on autoimmunity, hormonal imbalance, infertility, and PCOS as well as cancer.

Swapping out the toxic products I was using daily in my everyday routine, as well as reducing toxins on my food was a huge part of my healing. I recently created the '4-step lifestyle detox' program to help others dramatically reduce toxins in their everyday life. You can receive this program for free by signing up for our newsletter here.


In my healing journey, the really deep and profound healing happened when I began learning mindfulness. Discovering mindfulness is the reason I consider my health challenges to be a blessing, as I am not certain I would have immersed myself in the teachings of mindfulness otherwise. I now live a more full and rich life than I did before my health crisis; this is largely due to my mindfulness practice.

Studies have proven that chronic stress is a large contributing factor for chronic health conditions. Adopting a mindfulness and meditation practice has been proven to reduce stress and improve chronic health conditions.

How we respond to most of the situations in your life directly relates to how much suffering we experience. Practicing mindfulness can be very helpful in teaching us how to relax with the present moment, whatever it may be. When we know how to let go, we suffer much less. Creator of the "Mindfulness Based Stress Reduction Program" (MBSR), John Kabat Zinn, sums this up nicely "you cannot control the waves, but you can learn to surf."

For many, taking care of the mind is their last priority. They will change their diet, learn how to source healthier foods, switch to safe products, and clean up toxins in their homes, but the idea of detoxing the mind can seem overwhelming, and too time-consuming. I really cannot emphasize enough how important this is, and in reality, most people have more spare moments in their day than they realize.

Mindfulness is described as 'awareness of the present moment.' Sounds pretty basic, right? On many levels, it is! But don't let the simplicity of mindfulness fool you.

Just like when you are learning any new skill, it is key to have a qualified teacher. Like any skill, mindfulness must be learned and practiced, eventually becoming a way of life. This is why it is called a 'mindfulness PRACTICE.' 

I started my mindfulness journey with an online, "Mindfulness Based Stress Reduction” course (MBSR). This course is an excellent foundation for learning the essentials of mindfulness and meditation. I took the course via “Soundstrue,” which is an amazing organization that offers mindfulness programs and books led by the world’s top teachers, including Eckhart Tolle, Tara Brach, Jack Cornfield, Jon Kabat-Zinn, and many others.  

“Mindfulness-Based Stress Reduction” is the most scientifically studied, tested & proven mindfulness training program. Evidence-based practices and principles are taught, leading to greater health, balance, and peace of mind. I cannot stress enough; the value of taking a foundational Mindfulness course like MBSR; it will change your life.

Hi, I’m Chelsea Lye, CNP!

I’m a Certified Nutritional Practitioner, AIP Coach and Yoga teacher showing you how to balance your hormones and reverse autoimmunity naturally.

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