A Case Study in Autoimmune Disease – Part 3 – Implementing Support

(Before reading this post, be sure to check out A Case Study in Autoimmune Disease – Part 2 – Evaluation, where Dr. Ian gives an overview of Molly’s initial test results.)

Neuro Rehab

We began a course of brain-based therapy in the office called “neurologic rehabilitation.” Basically, we took the findings from her exam and began to customize brain-based exercises she could repeat at home after being taught in office which targeted the weaknesses that were creating symptoms and vicious cycles. In particular, we targeted her parietal lobe and vagus nerve/brain stem. She noted that within weeks of starting the therapy, she was digesting better and seemed less preoccupied with her body image. This was critical because when doing deep dietary intervention, there is always the possibility of doing more harm than good. Even though she was not perfect on keeping up with the home-based exercises, it appears what we did in office significantly helped her.


Molly was an avid runner and because of a chronic knee and hip issue, she was prevented from her favorite pastime, jogging. This was her outlet for stress. We began breaking up scar tissue with our shockwave device, doing gentle chiropractic adjustments, and using muscle activation techniques to get her flexibility up and pain relieved. We got her back on the trail after about 6 weeks and slowly increased her miles so she could get the benefits of exercise. I think Molly may have been most excited about this, but the reality was as her fatigue went away, she immediately wanted to become more active. Cortisol management through exercise may be one of the most effective ways of helping my clients so this was very satisfying to watch her improve and get back on the trail.

Repeat BW

 Previous8 Week Follow Up16 Week Follow Up
Homocysteine12.5 >9.79.6
TSH1.2 (normal!)Not repeatedNot tested
Vitamin D3195 (Too high, dose adjusted down)Not tested
Ferritin1516 (Started iron supplementation and gave dietary recommendations)47
Eosinophils57 (Determined she was reacting to a few specific foods in her diet)3
EBV15.415.619.1 (Not unusual to see a mild increase before it drops)
Candida Abs IgA +Normal  

Repeat DUTCH

As you can see, her hormone reserve (DHEA-S) has come up (from 37 to 81) and she is showing a strong ovulation response! Her husband is happy the testosterone came up from 3.8 to 6.3 (she is too!) and her estrogens have started to recover. Overall, she noted an improved menstrual cycle with fewer cramps and less irritability.

Lessons and Takeaways

Molly was a complicated case, but she is a quintessential example of how the functional medicine model works. She was suffering from a disorganized immune system brought on by stress from hormones, gut, dietary imbalances and an inability to manage her stress load. Even though it sounds complicated, the reality is, we changed her diet with guidance from our nutritionist, customized supplementation based on her labs, used some basic in-office therapies like PeMF, worked through her structural problems and gave her the confidence through repeat labs and the resolution of her symptoms that she was back on track in life!   She came to us frustrated, upset and let down by her western medical providers. I knew because of her motivation and initial blood work and exam findings we could change her life. But don’t take it from me; below is her testimonial on her results to date.

Molly’s Review

“I can’t recommend Dr. Ian and the rest of the staff at [Dr. Autoimmune] enough–they have truly changed my life. I came in earlier this year for help with Hashimoto’s thyroiditis. I had recently discovered the autoimmune origins of my hypothyroidism and decided to see whether there was any truth to the idea that nutrition and lifestyle changes could actually have a noticeable effect on how I felt. After following through on an elimination diet (and eliminating gluten for good), taking the supplements Dr. Ian and Natalie suggested, and doing neurofeedback, I can honestly say I’ve never felt this good–ever. I thought feeling low energy and motivation was just a part of my personality, but after almost five months of working with the team here, I can see that’s not the case. I have a level of energy that amazes me most days, which has affected my work life and relationships for the better, plus my generalized anxiety has quieted down. I can’t shut up to my friends and family about how much better feel, and the team at Dr. Autoimmune is to thank for that. From Joy and Danielle at the front desk, to Natalie the nutritionist, to Dr. Ian, I felt seen, cared for, and consistently prioritized during my  whole treatment. The best investment I’ve ever made!”

A Case Study in Autoimmune Disease – Part 2 – Testing

(Before reading this post, be sure to check out A Case Study in Autoimmune Disease – Part 1 – Evaluation, where Dr. Ian gives an overview of Molly’s case and what she presented with initially.)

Molly’s blood work findings:

Homocysteine 12.5 TSH 1.2 (normal!) Vitamin D 31 Ferritin 15 WBC 4.4 Eosinophils 5 EBV positive for reactivation Candida Abs IgA +  


Having an elevated homocysteine level above a 7.0 increased the chance that Molly was suffering from an inability to methylate, which is one of the most important detoxification reactions the body undergoes. It also may indicate a B vitamin deficiency that must be corrected because methylation requires specific forms of B vitamins.

Molly was struggling with hormonal symptoms including low libido, severe cramping during menstruation and mood fluctuations. In addition to these challenges, her Epstein-Barr virus that most likely triggered her thyroid condition had become reactivated and was most likely wreaking havoc on her hormonal system. Throw in the inability to detoxify and you can begin to understand why she was having such a hard time.

Her ferritin (stored iron) was borderline low and certainly was part of her chronic fatigue. Most likely this was from the state of her gut, not from a lack of iron in her diet as she ate red meat. Keep in mind her TSH was spot on perfect and she still suffered from classic thyroid symptoms like fatigue, brain fog, constipation, cold intolerance and anxiety. Even though her TSH was normal, her vitamin D was not optimal. Vitamin D hormone regulates the immune system and is one of the primary protectors against viral infections.

It was obvious that Molly had been fighting infections for quite some time (candida + Epstein-Barr at the minimum) because her white blood cell (WBC) count was borderline low at 4.4. On top of this, her eosinophils were elevated which indicated either an environmental or food trigger (it can take up to 72 hours for symptoms to surface from food sensitivities).

Lastly, Molly’s Candida antibody was high. This indicated a severe immune reaction more than likely from overgrown fungus. Candida is found in every one of us but when Candida is overgrown from overconsumption of refined, processed sugars, it creates inflammatory havoc with the endocrine and immune system. Molly had symptoms of hypoglycemia and fatigue after meals, but after we lowered the candida in her body, her blood sugar swings were a thing of the past.

We also ordered specialty lab tests including:
1. Urinary hormone test
2. DNA based stool test
3. Wheat sensitivity test

1. The “DUTCH” test -Dried, Urinary Test Comprehensive Hormones:

Molly’s hormone levels were not in a great place. Her progesterone was fine, so she was ovulating, but her estrogen was in the tank. Estrogen is a critical component of a normal cycle and her levels were basically menopausal, yet she was only 35 years old. Molly’s DHEA-s level was also low. DHEA-s is a precursor hormone critical to estrogen production.

When someone experiences high levels of inflammation like leaky gut, infections, or food sensitivities, their hormonal balance is disrupted. This illustrates perfectly how the body is interconnected. If Molly had gone to a primary care or endocrinologist, they more than likely would never have connected her gut problems to a hormonal imbalance. Molly’s cortisol level was normal. In her condition, I would have expected an abnormal cortisol level, but except for her waking cortisol, her pattern was relatively fine. What is important was that her cortisone was low. Physiologically, this is important because it is an indication of chronic inflammation. So, her adrenal function was becoming taxed by inflammation and this was causing adrenal symptoms of fatigue, low motivation and chronic hip and knee problems.

2. The GI Map test:

This test is an amazing way to see what is replicating in the gut (good guys and bad guys), inflammation markers and digestive enzyme activity. Molly was in trouble because she was dealing with an overgrowth of virus and her firmicutes level was high, indicating bacterial overgrowth in her small intestine, A.K.A, SIBO (small intestine bacteria overgrowth). These infections were driving inflammation, hormonal disruption and the poor overall health her thyroid and body was in.

We immediately customized her supplementation to address both infections and to give her gut the support it needed to “weed & feed.” Molly began anti-microbials, gut healing compounds and prebiotics that were gentle yet effective in healing her gut. We also tailored her diet so she had everything she needed to keep her momentum once the supplements stopped. This was the most important aspect of her case and spending the three months of strict adherence to the diet changed her life!

3. Wheat Sensitivity Test

What you see above is Molly’s positive antibodies to wheat and markers indicating leaky gut. She also had active antibodies to LPS (lipopolysaccharides), which are basically bacterial poo. So, she had leaky gut (intestinal permeability), was highly reactive to wheat (and one exposure could be causing months of inflammation) and was mounting an immune reaction against gram negative bacteria (indicating small intestinal bacterial overgrowth). That was all from just one test!

This confirmed her gut was in big trouble and we needed to start her on a 5R program: Remove, Repair, Replace, Re-inoculate and Rebalance. Molly required a customized 3 month plan using dietary interventions (think a step above Paleo) and customized supplementation (led by our fabulous staff nutritionist). The amazing part is, within 30 days she was already feeling so much better!

The news about Molly’s condition only gets better, as you’ll read about in part 3 when we detail the in-office therapies she took advantage of.