Hashimoto’s disease is a common autoimmune condition affecting 5 out of every 100 people in the United States, with women ten times more likely to develop the condition than men. Hashimoto’s disease affects the thyroid gland and is the most common cause of hypothyroidism in developed countries. Diagnosis most often occurs between the ages of 30-50.

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CC: Fatigue, Weight Gain, Thinning Hair, Brain Fog, Depression, Hashimoto’s Diagnosis

Haley* was a 38-year-old female who had been struggling with symptoms for the last 3-4 years after the birth of her second child. Two years prior to our consultation, she had been diagnosed with Hashimoto’s disease and was prescribed levothyroxine to manage her symptoms. Haley had not really seen any significant improvement and continued to struggle with fatigue, thinning hair, symptoms of depression, and brain fog. Her thyroid antibody levels had not been checked after her initial diagnosis, and she was told she’d “have to take the levothyroxine for life and she’d always have antibodies, so it wasn’t worth checking them anymore.” Haley had also struggled with weight gain, having gained a total of 35 pounds over the past 4 years despite exercising regularly and watching her diet.  

Haley did not have a history of thyroid issues prior to her second pregnancy, though she did have a lifelong history of on-again and off-again digestive issues, including bloating, constipation, and gas. She had her first child at age 32 and her second at age 34, and while her first pregnancy went smoothly, she did not feel great during her second, and it was after the second was born that she felt her health really started deteriorating. She lost some hair postpartum, but she felt it continue to thin and fall out over the past 4 years.  She had tried several hair-growth supplements and shampoos, none of which worked. Haley admitted her thinning hair was making her self-conscious and was contributing to depression symptoms, which had begun post-partum with her second child. Haley felt like it was just difficult to get excited about anything, and she just felt too tired to socialize or do any of the hobbies that used to make her happy or excited.

Haley’s fatigue was initially attributed to being a mom with two young kids at home, though it had continued to worsen over the past few years. Haley reported it was hard to get the energy to do basic tasks each day, and she didn’t sleep well even though she went to bed exhausted. Her brain fog and trouble remembering things had also worsened, and it made it challenging for her to keep up in her role at a social media management company. Haley was turning to a lot of caffeine to try to focus and get through her work days now. She didn’t really have the energy to exercise, though she tried to at least walk daily.

During a review of systems, Haley brought up that she had tried all sorts of diets over the last 3-4 years - low carb, low fat, Whole 30, and other restrictive diets - and none seemed to make a difference in her symptoms or weight. She was taking levothyroxine, vitamin D, and a multivitamin supplement at the time of our initial consultation together. When it came to stress, Haley felt she had a “regular” amount of stress that comes with having two kids and a full-time job, but she didn’t really think there was anything she could do to manage it better. Last, Haley had a regular menstrual cycle that typically lasted 28-29 days, though she felt her symptoms were amplified the week leading up to her period.

Lab Work Results

The following specialty labs were run:

Comprehensive Stool Test

A comprehensive stool test (the GI-MAP by Diagnostic Solutions) showed the following results: 

• Pancreatic elastase was low
• Elevated candida spp., opportunistic bacteria species
• Borderline high H. pylori
• Low commensal bacterial spp.
• Low sIgA
• Elevated anti-gliadin 

Genomic Testing

The following SNPs were identified using the DNA Health panel from DNA Life:

• COMT (slow enzyme activity)
• MTHFR (decreased methylation)
• GSTM1 deletion (poor glutathione production)
• MnSOD/SOD2 (higher oxidative stress risk)
• HLADQ2.5 (gluten intolerance)

Additional Lab Results

Lab Analysis 

Haley's lab work points to a few different problems that are contributing to her symptoms.

Dysbiosis, Malabsorption, and Other Gut Findings

Haley’s stool test showed low pancreatic elastase, indicating low digestive enzyme function and likely malabsorption. This can lead to not absorbing nutrients optimally from her diet and may cause bloating and digestive issues such as constipation, things that Haley had dealt with on and off for most of her life. Haley’s GI Map tests also showed borderline high H. Pylori: this scenario can indicate hypochlorhydria, as elevated levels of H. pylori can neutralize stomach acid. Hypochlorhydria may lead to poor nutrient absorption, digestive insufficiency, and even immune deficiency, which is backed up by Haley’s low secretory IgA levels. 

Her results also showed elevated candida spp. and opportunistic spp., with low commensal bacteria, indicating dysbiosis was present. A dysbiotic microbiome has been associated with Hashimoto’s disease, as well as autoimmunity in general. Last, Haley’s gut testing results also showed elevated anti-gliadin IgA antibodies, indicating Haley is also having an immune response to the gluten protein. Some studies have shown a gluten-free diet to be beneficial for Hashimoto’s patients, but it is primarily recommended if there is evidence of a reaction to gluten, such as in Haley’s case.  

Thyroid Antibodies and Panel

In re-running a full thyroid panel for Haley, we found that she still had elevated TSH despite being on medication, as well as borderline high reverse T3 and low free T3. Haley wasn’t producing enough free T3 for her thyroid to function optimally, and she still had elevated anti-TPO antibodies, indicating inflammation and autoimmune activity in the thyroid gland. Altogether, these numbers can contribute to her ongoing fatigue, weight gain, and feelings of depression.  

Elevated Inflammation 

In addition to elevated thyroid antibodies, Haley had elevated hs-CRP, a sensitive marker of inflammation. She also had an elevated  omega-3 index, indicating inflammation is present. Low vitamin D has also been associated with chronic inflammation.

Hormone Imbalances

In addition to her thyroid hormone levels, Haley had a few other irregular hormone findings, including low progesterone, low DHEA, and borderline low testosterone. Thyroid function is important to help direct ovarian function, and it’s possible her ongoing thyroid issues are contributing to low sex hormone output. Low progesterone can put women in a relative estrogen dominance state, which may also explain why Haley felt her symptoms worsen around the week before her period. Low DHEA and low testosterone can also contribute to fatigue and feelings of depression. Last, Haley also has changes in her 24-hour cortisol rhythm, with low cortisol throughout the day but elevated cortisol at night, lending to her difficulty falling asleep even though she’s tired.  

Multiple Micronutrient Depletions

Haley had several vitamin and mineral depletions apparent on her micronutrients testing, including low zinc, magnesium, selenium, iron, vitamin D, vitamin B6, vitamin B12, CoQ10, and vitamin C. Selenium is a particularly important mineral for thyroid health, and six months of selenium supplementation have been shown to reduce antibody levels in Hashimoto’s patients. Zinc has been shown to be important for the conversion of T4 to T3, while vitamin C has been studied for its beneficial impact on normalizing thyroid hormone levels in patients taking levothyroxine.  

Genomic Findings

Haley’s genomic testing showed mutations with several genes important for detoxification and control of inflammation, including MTHFR, COMT, MnSOD, HLADQ2.5, and GSTM1. Specific MTHFR mutations, such as C677T polymorphism that Haley had, have been associated with a higher risk of hypothyroidism and inflammation. GSTM1 and MnSOD are related to glutathione and superoxide dismutase production, two antioxidants that are important for reducing oxidative stress and inflammation; mutations in these genes can lead to elevated oxidative stress in the body. Last, HLADQ2.5 is related to a higher risk of gluten reactions and celiac disease.  

Interventions

Haley’s endocrinologist agreed to co-manage her case as he was the provider prescribing levothyroxine. Her therapeutic plan recommendations are listed below.

Supplementation

• Started magnesium glycinate, 400mg at night
• Started vitamin D3, 4000 IU once/day (Apex Energetics Liqua-D)
• Started comprehensive digestive enzyme to help support food breakdown and nutrient absorption (Apex Energetics Enzymix-Pro)
• Started having digestive bitters prior to meals to help stimulate stomach acid and digestive enzyme production.
• Trace Minerals by Thorne (contains zinc, selenium, and other minerals) once/day
• Antioxidant reds powder 1 scoop per day to help reduce inflammation
• For 8 weeks, we followed the gut repair plan below:

• Gi-MicrobX, an antimicrobial blend to help eradicate opportunistic microbes in the gut
• Gastromend (Designs for Health) to support healing the gastric lining and overall stomach health as well as address H. pylori
• We followed this up with probiotic rotations, including S. Boulardii and Lactobacillus/Bifidobacterium spp. in addition to prebiotic and probiotic foods in the diet.
• To further address her borderline H. pylori levels and support stomach acid production, we added in the following:

• 1 oz cranberry juice after meals
• 1-2 cups green tea daily

• Started 3g fish oil daily to help reduce inflammation and improve thyroid signaling.  
• Started Imunnoglov

Nutritional Changes

Nutritionally, we emphasized an anti-inflammatory, whole food, nutrient-dense Paleo diet rich in fruits, vegetables, healthy fats, and protein.  

• For Haley, we focused on having quality protein (such as grass-fed beef, poultry, fish), fat (such as avocado, olive oil, and flaxseed), and fiber with each meal to keep energy levels balanced while limiting sugar, refined carbohydrates, and fast food.  We initially followed an autoimmune (AIP) paleo protocol for 8 weeks to help reduce inflammation while healing her gut before transitioning to a traditional AIP diet. 
• We did eliminate gluten due to her test results and chose a Paleo approach for its studied benefits on autoimmune thyroid disease.  
• Additionally, we included functional fibers to help support the growth of beneficial gut bacteria, including sources of inulin, beta-glucan, and fructo-oligosaccharides. 
• We had Haley focus on hydration and increasing her water intake as well, and started to switch her to half-caf coffee before transitioning over to green tea to help cut down on her caffeine intake and coffee dependence.  
• We also focused on eating hygiene: chewing food well, slowing down and stepping away from work while eating, and taking a few slow breaths before starting a meal.

Lifestyle Recommendations 

• Haley continued walking consistently every day, and after one month, we had her start working with a trainer twice a week to incorporate weight training into her routine.  
• Additionally, we focused on bringing more “breaks” into Haley’s day, which involved short walks, getting outside, or doing something fun with her family that she enjoyed to break up her work schedule and get her up and moving.
• We had Haley incorporate stress reduction and nervous system regulation strategies, including breathwork, meditation, and yoga (depending on her schedule), to help address her high-stress levels and support the regulation of hormones.
• We focused on consistent sleep hygiene and had Haley create a “winding down” routine, power down technology after dark as much as possible, and incorporate guided meditation to help her sleep.

After two months, Haley had completed her gut rebalancing protocol, and we focused in more on increasing her movement and supporting her nutrition and lifestyle. We continued with probiotic rotations but took out her antimicrobial supplements listed above.  At this point, she had lost 5 pounds and was feeling more energy and a little more positive about the future. We added in the following things to better support her overall hormone health:

• Women’s Hormone Balance by Ancient Nutrition (containing chastetree, ashwagandha, schisandra, reishi, and black cohosh)
• DHEA by Apex Energetics, twice per week
• T3 Conversion Booster by Weston Childs to help support T4-T3 conversion
• Nutritionally, Haley was happy with how she felt on the Paleo-type diet and continued on this plan. She started adding some organ meat to ground beef once per week to help with micronutrient intake as well.  

Follow-Up Labs 6 Months Later

GI-MAP & Micronutrient Testing Follow-Up Results: 

Haley’s micronutrient re-test came with all results within normal limits, demonstrating that her plan was helping to restore her vitamin and mineral levels.  

Additionally, her GI-MAP results improved to normal ranges:

• Pancreatic elastase was normal (initially low)
• sIgA was within the normal range (initially low)
• Anti-gliadin antibody was within the normal range (initially high)
• No detectable candida spp., opportunistic bacteria levels had rebalanced
• Normal commensal bacterial spp. growth (initially low)

Follow-Up Interpretations and Continued Interventions

Over the course of six months, Haley implemented all recommendations with regular check-ins and guidance. As Haley’s energy and mood improved, she began exercising more and started to attend group yoga classes 1-2x per week in addition to walking and strength training. By month 3, Haley was sleeping more consistently and felt more in control of her stress during the day. By our sixth month together, Haley reported she didn’t really feel those depression feelings anymore and felt motivated to socialize and just enjoy her life more than she had in over a year. She had lost about 18 pounds overall and planned to continue to follow her nutritional plan and exercise.

All of Haley’s lab markers returned to normal ranges, with her omega-3 index rising to the intermediate risk range. She planned to continue her omega-3, antioxidant powder, magnesium, vitamin D, and women’s hormone balance supplement and was starting to wean off everything else to see how she felt once we saw her labs were back within normal range. Her endocrinologist felt she didn’t need the levothyroxine anymore, and she stopped taking that as well, with plans to follow up and re-check her thyroid panels in 12 weeks.

While Haley’s hair hadn’t quite grown back to what it had been pre-pregnancy, she felt like it had started to come back and was healthier, and she noted she had new growth in the temple regions where it had been thinning the most. She felt it was shinier and thicker overall than it had been in the prior few years.

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Summary

This case highlights the complex nature of autoimmune conditions such as Hashimoto’s disease. While Hashimoto’s is often treated with thyroid medication, this just addresses the symptoms of thyroid dysfunction and doesn’t investigate underlying causes that may lead to autoimmunity, such as gut dysbiosis or chronic stress and inflammation. Additionally, learning about genomics related to individual patient cases can help highlight areas that may need additional support beyond basic nutrition and exercise advice; those with gene mutations relevant to inflammation and detoxification are more likely to experience immune dysregulation and chronic inflammation that can lead to autoimmune conditions.