Case summaries and exploratory analyses

Case 1

Case 1 involved a 29-year-old female with a past medical history of chronic rhinosinusitis. She was on multiple anti-inflammatory and allergy medications in addition to T4 and T3 therapy. She sought to adopt sustainable dietary, exercise, and stress management practices from participating in the study. She enrolled with a very high symptom burden (MSQ = 126) with the worst symptoms related to chronic rhinosinusitis, dermatological, musculoskeletal, and gastrointestinal systems. Her complaints specifically consisted of acne, dry skin, hair loss, joint and muscle aches, belching, bloating, and alterations in bowel habits, including constipation and diarrhea. She additionally complained of excessive weight, food cravings, compulsive eating, as well as cognitive and mood concerns with poor concentration, poor memory, anxiety, and depressed mood. Her initial FFQ revealed dietary patterns consisting of gluten-free refined products, refined potatoes, a variety of fruits, vegetables, processed and unprocessed meats, and dairy substitute products. She endorsed a predilection and craving for carbohydrate-rich foods.

Initial laboratory findings were skewed and invalid, as the participant was actively sick with an acute on chronic sinus infection. She was taking antibiotic medications at the time of the laboratory evaluation, however, there was some concern that the participant was possibly overmedicated with a suppressed TSH and elevated T4 and T3. The use of urinary organic acid testing revealed an increased need for vitamin B supplementation, most noticeably folate, as suggested by elevated formiminoglutamic acid (FIGLU) [23]. The participant also had a significantly elevated plasma copper. Stool testing revealed decreased short-chain fatty acids (SCFAs), most noticeably butyrate. SCFAs consist primarily of acetate, butyrate, and propionate, which are physiologically active byproducts produced via the fermentation of soluble dietary fibers and resistant starches by commensal bacteria throughout the colon [24]. Their concentrations vary along the length of the gastrointestinal tract with the highest levels in the cecum and proximal colon [24]. Butyrate acts as a fuel source for colonic enterocytes, with immune modulating properties through histone deacetylase inhibition, allowing for the suppression of macrophages and dendritic cells [24]. Additionally, SCFAs have an overall pH-lowering effect on the colon, allowing for the growth of beneficial bacteria, specifically Lactobacillus and Bifidobacterium [24].

At week six of the program, the participant was counseled to increase the consumption of folate-rich foods, such as organ meats and leafy greens, and experiment with eliminating foods high in fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAPs) for gastrointestinal symptom relief [25]. She was encouraged to explore whether fermented foods exacerbated her allergy symptoms. She was instructed to consider lowering her thyroid medication dose given the concerning elevations found at study onset and to monitor for potential signs and symptoms of hyperthyroidism.

Following the program, the participant’s MSQ decreased from 126 to 43, with residual symptoms primarily related to her continued sinus and allergy complaints. She reported the exacerbation of allergy symptoms with fermented foods, a 12-pound weight loss, and the start of corticosteroid treatment just prior to final laboratory testing given another sinus infection. She later notified the medical team of further imaging revealing an anatomic abnormality of her maxillosinus structure and pursuit of corrective surgery.

A review of her second FFQ documenting the 10-week program showed strict adherence to the AIP diet with the elimination of refined carbohydrates, white potatoes, processed meats, eggs, nuts, grains, and dairy, as well as increased consumption of unprocessed meat, vegetables, and fruit, and the new inclusion of coconut, plantains, cassava flour, and maple syrup as the only sweetener. The participant’s exit survey revealed improvements in sleep, the beginning of an exercise program, and improvements in body composition. Laboratory testing revealed continued suppressed TSH with elevated total and free T4. The participant notified the team that she had previously decreased her thyroid medication, Synthroid, from 112 mcg to 100 mcg at week six followed by a further decrease to 88 mcg just prior to her final interview at week 10. She reported still experiencing signs concerning for hyperthyroidism and was planning to pursue an additional decrease in medication in conjunction with further treatment for chronic sinusitis.

Review of repeat nutritional testing showed stable, but continued, elevation in her FIGLU as well as plasma copper. Repeat stool testing showed continued low SCFAs.

Case 2

Case 2 involved a 41-year-old female with a history of depression, the use of selective serotonin reuptake inhibitor (SSRI) medication, and T4/T3 therapy. Her goals were to lose weight, improve food cravings, improve energy, and adopt a healthier lifestyle as a result of the study program. She entered the program with an MSQ of 98. Her worst symptoms affected the head, ears, eyes, nose, throat (HEENT), dermatological, musculoskeletal, neuropsychological, and genitourinary (GU) systems. More specifically, she complained of excessive mucus production in her pharynx, throat irritation, dry skin, hair loss, hyperhidrosis, joint aches and stiffness, anxiety, mood swings, irritability, excessive weight gain, food cravings, and compulsive and binge eating behaviors. Her initial FFQ revealed a diet consisting of refined grain products, refined potatoes, a variety of fruits, vegetables, regular processed and unprocessed meats, dairy, and eggs. She reported cravings for carbohydrate-rich foods and the regular consumption of sugar-sweetened soda beverages.

Initial laboratory findings revealed an elevated TSH at 4.75 μIU/mL and hs-CRP of 6.97 mg/L. Initial organic acid nutritional testing showed elevated suberic and adipic acids as well as an increased need for multiple B vitamins, most noticeably riboflavin as suggested by elevated glutaric acid [26]. Red blood cell (RBC) analysis for polyunsaturated fatty acid (PUFA) composition revealed elevations in omega-6 fatty acids and the low end of normal omega-3 fatty acids, resulting in a disturbed omega-3:omega-6 ratio. Stool testing revealed no pathogenic organisms, however, there was evidence of lipid malabsorption as measured by fecal phospholipids and cholesterol.

At week six of the program, the participant was counseled to increase the consumption of fish rich in omega-3 fatty acids, folate-rich foods, as well as glycine-rich foods such as bone broth. She was encouraged to explore the use of AIP-complaint digestive bitters to assist in the digestion and absorption of nutrients [27].

Following the program, the participant’s MSQ decreased from 98 to 12 with no further severe symptoms. She reported a 15-pound weight loss, improvements in energy, the cessation of soda consumption, and the beginning of a formal exercise regimen.

A review of her second FFQ documenting the 10-week program showed strict adherence to the AIP diet with the elimination of refined carbohydrates, potatoes, eggs, legumes, coffee, nuts, seeds, grains, and dairy, as well as increases in the consumption of unprocessed meat, vegetables, fruit, avocado, and sweet potatoes.

Laboratory testing revealed a decrease in her TSH to 2.34 μIU/mL, with otherwise stable hormone levels and unchanged thyroid antibodies. Her hs-CRP decreased from 6.97 to 5.02 mg/L, however, it was noted to be a significant outlier (despite the decrease) when compared to the group average and was not included in the post-hoc secondary data analysis.

A review of repeat nutritional testing showed the improvement and normalization of previously elevated suberic and adipic acids and the presence of ketone bodies. The participant was noted with a deficiency in folate as suggested by a markedly elevated FIGLU [23]. The participant saw a decrease in overall omega-6 RBC volume and improved omega-3:omega-6 RBC ratio. Repeat stool testing showed resolved lipid malabsorption and normalized secretory IgA.

Case 3

Case 3 involved a 34-year-old female with no significant past medical history. She began the study, taking only T3 replacement therapy at approximately 5 mcg four to six times daily. She sought to improve her dietary patterns, removing foods she was sensitive to, improve sleep, as well as begin a formal stress management program with yoga and meditation. She entered the program with a high MSQ score of 83, with the worst symptoms affecting the HEENT, dermatological, gastrointestinal, and neuropsychological systems. More specifically, she complained of dark circles under her eyes, sinus congestion, sneezing, acne, constipation, bloating, fatigue, lethargy, poor concentration, decreased memory, indecisiveness, depressed mood, excessive weight gain, food cravings, and behaviors of compulsive and binge eating. Her initial FFQ revealed a diet consisting of occasional gluten-free products and a variety of fruits, vegetables, potatoes, unprocessed meats, eggs, and infrequent dairy except for ice cream.

Initial laboratory findings revealed a TSH of 3.55 μIU/mL with low free T4 (fT4 = 0.31 ng/dL). Initial thyroid peroxidase (TPO) antibodies were 135 IU/mL and anti-thyroglobulin antibodies (TGA) were 2.0 IU/mL. Given these findings, the participant was counseled to begin either T4 only or combination T4/T3 therapy based on her weight. Initial organic acid nutritional testing showed an increased need for vitamin B6 as suggested by elevated xanthurenic acid [28]. RBC analysis for PUFA composition revealed elevations in omega-6 fatty acids, specifically linoleic acid and gamma-linolenic acid, and low normal omega-3 fatty acids, specifically DPA and DHA. This caused a disturbed omega-3:omega-6 ratio. Stool testing was with microscopic, and culture analysis revealed rare Blastocystis hominis and an overgrowth of Klebsiella oxytoca.

At week six of the program, the participant was counseled to continue increasing the consumption of omega-3 fatty fish, organ meats, and foods rich in vitamin B6. Additionally, she was encouraged to explore the inclusion of fermented foods.

Following the program, the participant’s MSQ decreased from 83 to 10 with no further severe symptoms. She reported an overall 10-pound weight loss with increased energy. She stated she was overall much happier with the resolution of brain fog as well as gastrointestinal complaints, including bloating, belching, and gas. She also reported improvements in her skin and acne.

A review of her second FFQ documenting the 10-week program revealed strict adherence to the AIP diet with the elimination of refined carbohydrates, potatoes, eggs, legumes, nuts, seeds, grains, and dairy, as well as increases in the consumption of unprocessed meat, vegetables, fruit, and avocado, and the new regular inclusion of coconut products, plantains, homemade liver pate, and bone broth.

Laboratory testing revealed an increase in TSH to 7.35 μIU/mL, however, during the final exit interview, the participant noted decreasing her use of T3 replacement to only 5 mcg one to two times daily, in addition to not starting any T4 replacement. An examination of her hormone levels showed an increase of free T4 from 0.31 to 0.77 ng/dL and total T4 from 2.0 to 5.0 μg/dL. T3 levels had maintained with the normal range. As the participant was not taking any replacement T4 and had decreased total T3 replacement use, the authors speculated that her thyroid began producing increased amounts of T4 due to decreased exogenous suppression and improvements in endogenous synthesis. The authors additionally speculate that the dietary intervention, in conjunction with decreased exogenous suppression, contributed to the participant’s increased T4 levels. As the participant decreased her use of thyroid replacement medications significantly during the intervention, her thyroid function laboratory data could not be included in the final data analysis. It should be noted, however, that the participant’s TGA normalized to <0.9 IU/mL and TPO antibodies decreased from 135 to 107 IU/mL.

A review of repeat nutritional testing revealed significant improvements in her RBC PUFA, analysis with increases in RBC eicosapentaenoic acid (EPA), docosapentaenoic acid (DPA), and docosahexaenoic acid (DHA) and decreases and normalization of RBC linoleic acid and gamma-linolenic acid. Repeat stool testing showed no overgrowth of pathogenic organisms with no noticeable lipid malabsorption. There was still overgrowth of additional Klebsiella species but no microscopic visualization of Blastocystis hominis.

At the end of the study during the exit interview, given her significant improvements, the participant informed the study team of her decision to continue her use of Liothyronine 5 mcg one to two times daily and repeat thyroid testing in three months.

Case 4

Case 4 involved a 38-year-old female with no additional, significant past medical history who began the study taking 100 mcg of Synthroid. She wanted to improve her diet, sleep, weight, and energy and begin a formal exercise practice. She entered the program with a moderate symptom burden (MSQ = 55) with the worst symptoms affecting her dermatological, gastrointestinal, musculoskeletal, and neuropsychological systems. More specifically, she complained of acne, hair loss, dry skin, constipation, belching, bloating, joint pain, stiffness, muscle aches, fatigue, tiredness, lethargy, poor concentration, insomnia, increased weight, food cravings, compulsive eating, and binge eating. Her initial FFQ revealed a diet consisting of infrequent gluten-containing products, a variety of fruits, vegetables, regular unprocessed and processed meats, eggs, dairy, potatoes, one to three alcoholic beverages weekly, corn-based products, water, kefir beans, and legumes. Prior to enrollment, she had been taking multiple supplements containing various vitamins and minerals, a probiotic, occasional fish oil, evening primrose oil, and collagen peptides.

Initial laboratory findings revealed a TSH of 2.85 μIU/mL, TPO antibodies of 180 IU/mL, TGA of 603.5 IU/mL, and a slightly elevated hs-CRP at 2.64 mg/L. Initial organic acid nutritional testing showed balanced nutritional markers likely related to her previous and ongoing supplementation. RBC analysis for PUFA composition revealed a high normal omega-6 fatty acid profile, resulting in a disturbed omega-3:omega-6 ratio. Stool testing showed low normal SCFAs and an overgrowth of Klebsiella pneumonie and Candida albicans. There was no evidence of lipid malabsorption.

At week six of the program, the participant was counseled to increase consumption of omega-3 fatty fish and animal protein. She was encouraged to consider including fermented foods and removing foods high in FODMAP to improve her constellation of gastrointestinal symptoms, including belching, bloating, and irregular stools [25].

Following the program, the participant’s MSQ decreased from 55 to 28 with the only continued frequent symptom of hair loss. She reported a 15-pound weight loss with increased energy, improved sleep, decreased food cravings, improved compulsive eating or overeating, and improved cognitive functioning.

A review of her second FFQ documenting the 10-week program suggested strict adherence to the AIP diet with the elimination of refined carbohydrates, potatoes, eggs, legumes, nuts, seeds, grains, and dairy as well as increases in the consumption of unprocessed meat, vegetables, fruit, and the inclusion of coconut products, gelatin, collagen, sauerkraut, and kombucha.

Laboratory testing revealed a decrease in her TSH to 2.06 μIU/mL with an increase of free T4 from 1.4 to 1.59 ng/dL and total T4 from 8.3 to 9.8 μg/dL. T3 levels maintained within the normal range. Her hs-CRP was still elevated at 2.90 mg/L with TGA and TPO antibodies also remaining elevated and clinically unchanged.

A review of repeat nutritional testing revealed continued stability in vitamin and mineral markers with mild improvements in her RBC PUFA analysis, increased omega-3 RBC volume, and decreased omega-6 RBC volume. The participant also had elevated ketones related to weight loss and a low carbohydrate dietary pattern. Repeat stool testing revealed no growth of either K. pneumonie or C. albicans.

Case 5

Case 5 involved a 26-year-old female with no significant past medical history, who enrolled in the study on 75 mcg of Synthroid. Her primary goal for participating in the program was to conceive a child. She had reported to the medical team prior to the study that she had been having significant difficulty in becoming pregnant. Her baseline MSQ was low (MSQ = 37) and was the lowest symptom score of any member of the study. Initial thyroid testing revealed a normal TSH and thyroid hormone levels with elevations in both TPO antibodies and TGA. Her hs-CRP was within normal limits at 0.65 mg/dL. Initial organic acid nutritional testing revealed no specific vitamin or mineral needs. Stool testing was notable for lipid malabsorption and low SCFAs.

The participant notified the study team during week eight that she had become pregnant. In conjunction with the study parameters and at the wishes of the participant, she discontinued participation in the study.

Case 6

Case 6 involved a 44-year-old female with no significant past medical history and began the study on 88 mcg of Tirosint. She sought to “feel like herself again,” wanting to improve her mood and energy. She entered the program with a moderate MSQ (MSQ = 56), with the worst symptoms affecting the gastrointestinal, musculoskeletal, and neuropsychological systems. Specifically, these complaints consisted of constipation, belching, bloating, joint pain, stiffness, muscle aches, fatigue, tiredness, lethargy, poor concentration, comprehension, and memory, anxiety, irritability, mood swings, and headaches. Her initial FFQ revealed a diet consisting of gluten-free grains, a variety of fruits, vegetables, regular unprocessed meats, eggs, minimal dairy consumption, potatoes, vegetarian-based soy products, and the regular consumption of lentils, beans, and legumes. She endorsed taking multiple supplements containing various vitamins and minerals, fish oil, curcumin, and a flavonoid complex.

Initial laboratory findings revealed normal thyroid function, however, there appeared to be low normal T3 levels and elevated reverse T3, indicating poor T4 to T3 conversion. Her hs-CRP was normal at 0.72 mg/L and TPO antibodies were elevated at 135 IU/mL. TGA was <0.9 IU/mL. Initial organic acid nutritional testing suggested deficiencies in riboflavin, as suggested by elevated glutaric acid, and vitamin B6, as suggested by elevated xanthurenate, respectively [26,28]. RBC analysis revealed a balanced PUFA composition with a high normal omega-3 RBC volume. The participant’s toxin profile revealed a markedly elevated whole blood mercury at 8.91 mcg/L. During the interview, the participant revealed consuming significant amounts of seafood and had several amalgam fillings with a history of recent dental work. Stool testing revealed low SCFAs and an overgrowth of Klebsiella oxytoca and Citrobacter freundii. There was no evidence of lipid malabsorption; however, there was no measurable fecal secretory IgA.

At week six of the program, the participant was counseled to consume animal protein and organ meats and increase her intake of vitamin B6-rich foods as well as fermented foods. Following the program, the participant’s MSQ decreased from 56 to 33 with an improvement in energy, headaches, joint pains, and cognition. She continued to report similar gastrointestinal symptoms of constipation, bloating, and belching in the setting of an overall excellent rating for her health.

A review of her second FFQ documenting the 10-week program showed strict adherence to the AIP diet with the elimination of refined carbohydrates, potatoes, eggs, legumes, nuts, seeds, grains, and dairy, as well as increases in the consumption of unprocessed meat, vegetables, and fruit, and the new regular inclusion of bone broth and collagen.

Laboratory testing revealed nearly identical values for thyroid function, thyroid antibodies, and hs-CRP, with no clinically significant changes. There was a decrease in white blood cell (WBC) count from 6.9 x103/µL to 5.9 x 103/µL as well as a decrease in neutrophil percentage from 69% to 59% and increase in lymphocyte percentage from 21% to 32%.

A review of repeat nutritional testing suggested a resolution of the riboflavin and vitamin B6 deficiency as suggested by normalized glutaric acid and xanthurenate [26,28]. Whole blood mercury decreased from an elevation above 8 mcg/L to within normal limits at 2.56 mcg/L. Repeat stool testing showed no growth of either K. oxytoca or C. freundii, an increase in total SCFAs, and a normal level of secretory IgA.

Case 7

Case 7 involved a 33-year-old female with a past medical history of dyshidrotic eczema, elevated thyroid antibodies, including TPO and TGA. She was noted to be euthyroid without the utilization of thyroid hormone replacement medication prior to enrollment. She wanted to improve stress, improve symptoms in thyroid autoimmunity while continuing without the use of any thyroid replacement medication, improve eczema, and find a sustainable dietary template that met her needs. She entered the program with a very severe symptom burden (MSQ = 114) with the worst symptoms affecting the HEENT, dermatological, gastrointestinal, musculoskeletal, and neuropsychological systems. More specifically, she complained of watery eyes, circles under her eyes, hay fever, sinus problems, nasal congestion, frequent throat clearing, acne, dry skin, rashes, hair loss, constipation, belching, bloating, fatigue, tiredness, lethargy, poor concentration, confusion, poor memory, anxiety, excessive weight, food cravings, and compulsive binge eating. Her initial FFQ revealed a diet following a gluten-free and dairy-free template with a variety of fruits, vegetables, unprocessed and processed meats, eggs, and limitations on starches and potatoes. She was also taking numerous supplements prior to the study but had recently stabilized on magnesium and fish oil.

Initial laboratory findings revealed a TSH of 1.06 μIU/mL, TPO antibodies of 273 IU/mL, TGA of 4.8 IU/mL, and a normal hs-CRP at 0.43 mg/L. Initial organic acid nutritional testing showed numerous imbalances, including elevated adipic and suberic acids. The participant had significantly elevated levels of the ketone body beta-hydroxybutyrate (BHB) likely related to her low carbohydrate consumption. Riboflavin was deficient, as suggested by elevated glutaric acid [26]. She was otherwise balanced in her additional vitamin and mineral markers. The participant’s toxic element screen revealed elevated blood mercury at 4.74 mcg/L. Stool testing revealed additional imbalances, including marked lipid malabsorption, low SCFAs, and an overgrowth of Klebsiella pneumonie and Citrobacter freundii. Microscopic evaluation also revealed evidence of trophozoites of Dientamoeba fragilis. Fecal calprotectin and fecal secretory IgA were within normal limits.

At week six of the program, the participant was counseled to continue with increased consumption of omega-3 fatty fish, animal protein, and organ meats. She was counseled to take AIP-compliant digestive bitters to support improved lipid and nutrient absorption [27]. She was counseled on the removal of high FODMAP-containing foods given her gastrointestinal symptoms, including belching, bloating, and constipation [25].

Following the program, the participant’s MSQ decreased from 114 to 56 with continued eczema and rashes, despite improvement in acne. Constipation remained despite improvements in bloating and belching. She reported increased energy, decreased lethargy and apathy, minimal compulsive eating or overeating and improved cognitive functioning. In continuing discussions with the participant and at the suggestion of the study doctor, she reported secondary evaluations for constipation revealing dyssynergic constipation and pelvic floor muscular weakness.

A review of her second FFQ documenting the 10-week program showed strict adherence to the AIP diet with the only challenges occurring early in the first few weeks during a 10-day vacation. Laboratory testing revealed stability in her TSH at 1.13 μIU/mL with an increase of free T4 from 1.11 to 1.19 ng/dL and free T3 from 2.2 to 2.5 pg/mL. Her hs-CRP remained low at 0.38 mg/L, TGA relatively unchanged at 4.8 IU/mL, and there was a significant decrease in TPO antibodies from 273 to 190 IU/mL.

A review of repeat nutritional testing revealed continued stability in vitamin and mineral markers with the normalization of elevated glutaric acid [26], as well as the normalization of previously elevated suberic and adipic acids. The participant no longer had elevated ketone bodies, likely related to the inclusion of additional carbohydrates and certain starches during the program. The previously elevated whole blood mercury had fallen from 4.74 to 1.79 mcg/L.

Repeat stool testing showed the resolution of previously noted severe lipid malabsorption. There was no microscopic evidence of D. fragilis. She was noted to still have low total SCFAs and overgrowth of previously noted Citrobacter species. Fecal calprotectin and fecal secretory IgA remained normal. Upon completion of the study, the participant continued without the utilization of thyroid hormone replacement.

Case 8

Case 8 involved a 33-year-old female with a past medical history of attention deficit hyperactivity disorder (ADHD) and depression who was recently diagnosed with subclinical hypothyroidism and autoimmune thyroiditis via elevated TPO antibodies and TGA. She began the study program without the utilization of thyroid replacement medication. She wanted to improve stress, delay or stop the progression of any thyroid autoimmunity, continue without the use of any thyroid replacement medication, address poor sleep and low energy, and improve diet. She entered the program with a very severe symptom burden (MSQ = 108) with the worst symptoms affecting dermatological, gastrointestinal, musculoskeletal, and neuropsychological systems. More specifically, she complained of dry skin, flushing, hyperhidrosis, nausea, abdominal pain, bloating, joint pain, muscle aches, stiffness, fatigue, tiredness, lethargy, poor concentration, confusion, poor memory, mood swings, irritability, anxiety, excessive weight gain, food cravings, compulsive and binge eating. Her initial FFQ revealed the intake of chicken, beef, and, occasionally, fish, restrictions on fruit intake - only berries, a variety of vegetables, grains, potatoes, and some candy and chocolate. She used a daily B complex as well as magnesium in addition to the prescribed medications Vyvanse, Fluvox and low dose naltrexone (LDN).

Initial laboratory findings revealed a TSH of 13.45 μIU/mL, TPO antibodies of 185 IU/mL, and TGA of 1.8 IU/mL. Her hs-CRP was elevated at 2.59 mg/L and all total and free thyroid hormone levels were within normal limits. Initial organic acid nutritional testing showed a likely folate deficiency, as suggested by a markedly elevated FIGLU [25-26]. Plasma copper was high normal at 151.5 mcg/dL. RBC volume of omega-3 fatty acids, including EPA, DPA, and DHA, were within normal limits. Her toxic element screen revealed elevated whole blood mercury at 4.82 mcg/L, and stool testing revealed an overgrowth of Klebsiella pneumonie. Fecal calprotectin and fecal secretory IgA were within normal limits.

At week six of the program, the participant was counseled to continue with the previous consumption of omega-3 fatty fish and increase the intake of various AIP-compliant foods, including animal protein and organ meats. Additionally, she was encouraged to explore the removal of high FODMAP-containing foods given her gastrointestinal symptoms, including abdominal pain and bloating [25].

Following the program, the participant’s MSQ decreased slightly from 114 to 85, with continued symptoms in the gastrointestinal, dermatological and musculoskeletal systems despite improvements in acne, bloating, belching, energy, joint pain, compulsive eating or overeating, and cognitive functioning.

A complete objective analysis of the participant’s health following the program could not be conducted, however, as she was lost to follow-up, unable to complete her final FFQ, stool, and organic acid testing. Review of food journals during the study revealed challenges with frequent travel to various social engagements and consumption of foods outside of the AIP template.

Final laboratory testing was also difficult to interpret, as the participant was acutely ill with an infection as evidenced by an elevated WBC count, platelets and hs-CRP. In terms of thyroid hormone fluctuations, the participant’s TSH had risen to 31.92 μIU/mL with slight increases in free and total hormones (T3 and T4). TGA had increased to 4.5 IU/mL, but TPO antibodies had decreased from 185 to 123 IU/mL. As of the final communication with the participant at the end of the study program, she has not started thyroid replacement medication.

Case 9

Case 9 involved a 36-year-old female with a past medical history of ruptured ovarian cysts, dysmenorrhea concerning for endometriosis who enrolled in the study on 45 mg of NP thyroid. She wanted to improve stress, joint pain, fatigue, bloating, IBS-like symptoms, minimize symptom exacerbation during menstrual cycles, and decrease hair loss. She entered the program with a very severe symptom burden (MSQ = 119) with the worst symptoms affecting the HEENT, dermatological, gastrointestinal, genitourinary, musculoskeletal, and neuropsychological systems. Specifically, symptoms included headaches, pruritic eyes, dark circles under her eyes, pruritic ears, otalgia, hay fever, sinus problems, excessive mucus, hair loss, constipation, belching, bloating, joint pain, stiffness, muscle aches, fatigue, tiredness, poor concentration, coordination and memory, anxiety, mood swings, irritability, frequent urination, and discharge. Her initial FFQ revealed a diet low in total animal products with the majority of animal protein coming from eggs and chicken. She consumed numerous fruits and vegetables, no dairy, minimal gluten consumption with the majority of grain-based foods being gluten-free or rice-based. She took magnesium and vitamin D as supplements and used histamine-2-receptor antagonists as needed for worsening allergic symptoms.

Initial laboratory findings revealed a TSH of 2.79 μIU/mL, TPO antibodies of 471 IU/mL, TGA of 3.4 IU/mL, and hs-CRP within normal limits at 0.76 mg/L. Initial organic acid nutritional testing revealed elevated adipic acid. RBC analysis of omega-3s was within normal limits due to the regular consumption of fatty fish. Plasma copper was low at 70.6 mcg/dL and RBC magnesium was also low despite supplementation at 27.8 mcg/g. Vitamin D was noted to be 83.4 ng/dL and the participant was instructed to discontinue the supplementation of 10,000 IU daily until re-testing in 12 weeks. Her toxic element screen revealed elevated whole blood mercury at 4.66 mcg/dL. Stool testing revealed low SCFAs and an overgrowth of Citrobacter species. Fecal calprotectin was normal and fecal secretory IgA was undetectable.

At week six of the program, the participant was counseled to continue with increased consumption of omega-3 fatty fish and animal protein, including organ meats. She was guided on foods highest in copper and magnesium. Additionally, she was encouraged to explore the removal of high FODMAP-containing foods, given her collection of gastrointestinal symptoms, including bloating, abdominal pain, and constipation [25]. She was additionally given education on monitoring allergic symptoms around the intake of fermented foods.

Following the program, the participant’s MSQ decreased dramatically from 119 to 32, with continued symptoms of painful menstruation and other fluctuations during ovulation. The participant reported complete elimination of joint pain, as well as anxiety, depressed mood, and impaired cognitive functioning. Multiple allergic symptoms, including sinus complaints and hay fever, resolved without the use of medication. She reported increased energy, decreased lethargy and tiredness, as well as resolved frequent urination and insomnia.

A review of her second FFQ documenting the 10-week program showed strict adherence to the AIP diet with regular consumption of bone broth, organ meats, coconut, and AIP-allowed starches. Laboratory testing revealed stability in her TSH at 3.06 μIU/mL with all total and free hormone remaining in the low normal ranges. Her hs-CRP remained low and decreased to 0.36 mg/L. TGA remained unchanged at 3.6 IU/mL as did TPO antibodies measured at 481 IU/mL.

Review of repeat nutritional testing showed improvement in multiple vitamin and mineral markers with normal levels of all B vitamins. Previously elevated adipic acid had normalized. Plasma copper had increased into the normal range, however, RBC magnesium still remained unchanged. The previously elevated whole blood mercury had fallen slightly from 4.74 to inside the normal range at 4.19 mcg/L.

Repeat stool testing showed the normalization of SCFAs. The previous overgrowth of Citrobacter species was resolved. There was now a detectable and normal level of fecal secretory IgA.

The participant continued following the dietary pattern and increased her thyroid replacement medication to 60 mg of NP thyroid while seeking further evaluation and support for ongoing menstrual complaints.

Case 10

Case 10 involved a 39-year-old female with a past medical history of mild transaminitis who began the program on 75 mcg of Levothyroxine and 5 mcg of Liothyronine. She wanted to improve stress, energy, bloating, IBS-like symptoms, sleep, and hair loss, and minimize/lower inflammation and lose weight. She entered the program with a moderate to severe symptom burden (MSQ = 89), with the worst symptoms affecting the HEENT, dermatological, gastrointestinal, musculoskeletal, and neuropsychological systems. Specific complaints consisted of headaches, dizziness, pruritic eyes, tinnitus, otalgia, excessive clearing of throat, sore throat, acne, dry skin, hair loss, diarrhea, constipation, belching, bloating, heartburn, abdominal pain, joint pain, stiffness, muscle aches, fatigue, tiredness, lethargy, anxiety, mood swings, irritability, and depressed mood. Her initial FFQ revealed the majority of animal protein coming from chicken and fish, numerous fruits and vegetables, minimal to no dairy, nut-based dairy substitutes, a mixture of whole grain and processed grain foods, rice, coffee, and coconut products. She took numerous vitamin and mineral supplements, including selenium, zinc, magnesium, biotin, iron with vitamin C, B12, and vitamin D.

Initial laboratory findings revealed a TSH of 2.09 μIU/mL, TPO antibodies above the reference range at >600 IU/mL, and TGA at 2.1 IU/mL. Her hs-CRP was elevated at 2.42 mg/L. Initial organic acid nutritional testing revealed elevated suberic acid. She has elevated FIGLU suggestive of folate deficiency [23] as well as elevated xanthurenate, suggesting B6 deficiency [28]. RBC analysis of omega-3s was within normal limits and related to the participant’s regular consumption of fatty fish. Her toxic element screen revealed elevated whole blood mercury at 7.58 mcg/L and elevated selenium at 427 mcg/L. Upon further questioning, the elevated selenium may have been caused by 400 mcg of selenium supplementation every day for over a year. She was asked to discontinue supplementation given the concern for toxicity. Her initial blood chemistry revealed an elevated ALT at 57 IU/L with normal AST at 32 IU/L. Initial stool testing revealed low SCFAs and an overgrowth of Citrobacter freundii and fungal Geotrichum species. Fecal calprotectin was normal.

At week six of the program, the participant was counseled to continue with increased consumption of omega-3 fatty fish as well as animal protein, focusing on red meat as well as organ meats. She was educated on foods highest in copper and magnesium and encouraged to decrease high FODMAP-containing foods given her gastrointestinal symptoms of bloating, abdominal pain, diarrhea, and constipation [25]. She was instructed on folate and vitamin B6-rich foods, including organ meats, beef, leafy greens, spinach, mushrooms, and beets, as well as the use of AIP-compliant bitters to improve digestion [27].

Following the program, the participant’s MSQ decreased dramatically from 89 to 6, with no frequent or severe symptoms. The participant reported complete elimination of joint pain, anxiety, depressed mood, irritability, and gastrointestinal symptoms. She reported markedly improved sleep, energy, skin, lethargy, feelings of soreness, and a 14-pound weight loss.

A review of her second FFQ documenting the 10-week program revealed strict adherence to the AIP diet with regular consumption of bone broth, organ meats, coconut, and AIP starches. She reported multiple daily servings of cruciferous and leafy green vegetables and increased intake of animal protein.

Laboratory testing revealed a suppressed TSH at 0.535 μIU/mL and the participant reported concern for overmedication. Her hs-CRP decreased from 2.42 to 0.84 mg/L, TGA decreased slightly from 2.1 to 1.7 IU/mL, TPO antibodies remained above the lab reference range at >600 IU/mL, ALT normalized to 13 IU/L and AST decreased within the normal range to 16 IU/L.

Repeat nutritional testing revealed marked elevation in ketone bodies likely related to participant’s weight loss and dietary changes. FIGLU remained elevated, however, xanthurenate had normalized suggesting a resolved B6 deficiency [28]. Blood selenium remained elevated and previously elevated blood mercury fell from 7.58 to 6.29 mcg/L. Repeat stool testing revealed resolution of prior Geotrichum yeast overgrowth and continued overgrowth of C. freundii. The participant continued following the study following the dietary pattern and chose to decrease her thyroid replacement medication to 50 mcg of levothyroxine.

Case 11

Case 11 involved a 39-year-old female with no significant past medical, who began the program on 75 mcg of Levothyroxine. She wanted to decrease stress, improve energy, decrease pain and irritability, and lose weight. She entered the program with the highest symptom burden of any participant (MSQ = 132), with the worst symptoms affecting the HEENT, dermatological, cardiac, pulmonary, gastrointestinal, musculoskeletal, and neuropsychological systems. Specific complaints consisted of headaches, faintness, dizziness, watery eyes, blurred/tunnel vision, dark circles under her eyes, pruritic ears, ear drainage, stuffy nose, sinus problems, excessive mucus, sore throat, dry skin, hair loss, flushing, irregular heartbeat, chest congestion, diarrhea, bloating, abdominal pain, joint pain, stiffness, muscle aches, fatigue, tiredness, lethargy, restlessness, anxiety, poor concentration, poor memory, mood swings, irritability, depressed mood, and frequent urination. Her initial FFQ revealed the majority of protein coming from chicken and eggs, with infrequent fish, red meat, and pork. She consumed numerous fruits and vegetables, regular dairy consumption, minimal refined grains, with regular whole grain and potato consumption. She took a daily probiotic and multivitamin.

Initial laboratory findings revealed a high normal TSH of 4.08 μIU/mL. Initial TPO antibodies and TGA were both within normal ranges although the participant’s previous bloodwork from less than six months prior to the study showed elevated TPO antibodies. Her hs-CRP was normal at 0.98 mg/L. Initial organic acid nutritional testing was markedly abnormal with only vitamin C in the normal range. There were marked elevations in suberic and adipic acids. She had an elevated methylmalonic suggestive of vitamin B12 deficiency [29]. Glutaric acid was elevated, suggesting a riboflavin deficiency [26]. Xanthurenate was elevated, suggesting a B6 deficiency [28]. RBC analysis of omega-3 volumes was low, with elevations in omega-6 RBC volume resulting in a markedly disturbed omega-3:omega-6 ratio. Urinary amino acids suggested significant protein catabolism given elevations in multiple essential and non-essential amino acids. Her toxic element screen revealed an elevated whole blood lead at 3.41 mcg/dL. Stool testing revealed low SCFAs and an overgrowth of Morganella morganii. While fecal calprotectin was normal, there was no identifiable fecal secretory IgA.

At week six of the program, the participant was counseled to continue with consumption of omega-3 fatty fish as well as increase animal protein, focusing on red meat as well as organ meats. She was encouraged to try removing high FODMAP-containing foods, given her gastrointestinal symptoms of bloating and abdominal pain [25]. She was educated on riboflavin, vitamin B6, and vitamin B12-rich foods, and the use of AIP-compliant digestive bitters to aid digestion [27].

Following the program, the participant’s MSQ decreased dramatically from 132 to 8, with no frequent or severe symptoms. The participant reported complete elimination of joint pain and muscle aches, as well as anxiety, depressed mood, and irritability. Gastrointestinal symptoms completely resolved, she reported the disappearance of rash/hives, improved energy, decreased hunger, panic attacks, termination of headaches, and a six-pound weight loss, with minimal to no continued hair loss.

A review of her second FFQ documenting the 10-week program revealed strict adherence to the AIP diet with regular consumption of bone broth, organ meats, coconut, and AIP starches. She reported multiple daily servings of cruciferous and leafy green vegetables and increased intake of animal protein.

Laboratory testing revealed that her TSH had decreased from 4.08 to 2.15 μIU/mL, with an increase in free T4 from 1.19 to 1.47 ng/dL and a decrease in hs-CRP from 0.98 to 0.9 mg/L. TGA and TPO antibodies remained within the lab reference range. Review of repeat nutritional testing revealed a marked improvement in multiple domains with the only continued nutrient deficiency being B12 and riboflavin, as suggested by elevated methylmalonic acid [29] and glutaric acid [26]. Both methylmalonic acid and glutaric acid, however, had come down dramatically from severe elevations at pre-intervention to just outside the reference range at post-intervention. Previously elevated whole blood lead fell to within normal limits at 0.31 mcg/dL. Urinary amino acids had normalized, suggesting a resolution of the previously suspected catabolic physiology. Suberic and adipic acids were now in the normal range. There was a mild elevation in ketone bodies likely related to the participant’s dietary pattern and weight loss. RBC omega-3 volume remained low and imbalanced compared to omega-6 fatty acid volume.

Repeat stool testing revealed the resolution of previous M. morganii overgrowth with continued insufficiency of beneficial organisms and low SCFAs. There was an isolated elevated fecal phospholipid without other evidence of lipid malabsorption. Fecal calprotectin remained normal and fecal secretory IgA increased to within normal limits.

Case 12

Case 12 involved a 32-year-old female with a past medical history of iron deficiency and eczema who began the program on 125 mcg of levothyroxine. She wanted to decrease stress, improve fatigue and eczema, and address bloating and IBS-like symptoms. She entered the program with a moderately elevated symptom burden (MSQ = 83), with the worst symptoms affecting the HEENT, dermatological, gastrointestinal, genitourinary, musculoskeletal, and neuropsychological systems. Her complaints specifically consisted of headaches, dizziness, dark circles under her eyes, acne, dry skin, hair loss, belching, bloating, joint pain, stiffness, muscle aches, fatigue, tiredness, apathy, poor memory, indecisiveness, anxiety, mood swings, irritability, and depressed mood, as well as frequent/urgent urination. Her initial FFQ revealed a diet low in total animal products, numerous fruits and vegetables, occasional dairy, regular corn, and refined and whole gluten-containing grain products. Her supplements consisted of collagen and iron.

Initial laboratory findings revealed a TSH of 0.73 μIU/mL, TPO antibodies at 438 IU/mL, a TGA of 3.2 IU/mL, and a hs-CRP of 0.29 mg/L. Initial organic acid testing revealed elevated adipic and suberic acids and increased needs for riboflavin [26], vitamin B6 [28], folate [23], and vitamin B12 [29]. RBC analysis of omega-3s was within normal limits and related to the participant’s regular consumption of fatty fish. Urinary amino acids were elevated and suggested catabolic physiology given the participant’s vigorous, regular resistance and cardiometabolic exercise without sufficient rest. Her toxic element screen revealed elevated whole blood mercury at 4.50 mcg/L and lipid peroxides were also elevated, with low serum CoQ10.

Stool testing revealed low SCFAs and pancreatic insufficiency as measured by low fecal elastase [30]. There was also microscopic evidence of Blastocystis hominis, normal fecal calprotectin, and undetectable fecal secretory IgA.

At week six of the program, the participant was counseled to continue the consumption of animal protein, including red meat and organ meats as well as other foods high in thiamine, riboflavin, B6, folate, and B12. Additionally, she was encouraged to explore the inclusion of fermented foods and AIP-compliant bitters to support digestion [27].

Following the program, the participant’s MSQ decreased from 83 to 25, with symptoms of mood swings and her depressed mood improved. On the exit questionnaire, the participant reported complete resolution of eczema and joint complaints, improved energy, and satisfaction with the elimination of grains, including gluten-containing products as well as corn. The participant reported increased resilience amidst continued life stressors. She did not report changes in weight.

A review of her second FFQ documenting the 10-week program revealed strict adherence to the AIP diet, with significantly increased and regular consumption of unprocessed animal protein, coconut, and AIP starches.

Laboratory testing revealed suppression of her TSH to 0.23 μIU/mL. Her hs-CRP remained low at 0.32 mg/L and both TGA and TPO antibodies remained unchanged at 4.8 IU/mL and 452 IU/mL, respectively. Given the stability in the participant’s weight, but decreasing TSH to now suppressed levels, the authors speculated that the improvements in thyroid function were directly related to elements of the dietary and lifestyle intervention positively impacting thyroid hormone production and absorption of the participant’s replacement medication.

Review of repeat nutritional testing revealed normalization of suberic and adipic acids, FIGLU, and glutaric acid as well as xanthurenate. The participant persisted with borderline elevated methylmalonic acid, normalization of urinary amino acids, suggesting a reversal of previous catabolic physiology, and normalization of lipid peroxides. Previously elevated whole blood mercury fell into the normal range from 4.74 to 3.45 mcg/L.

Repeat stool testing revealed a continuation of low fecal elastase, as well as continued microscopic evidence of B. hominis. There was, however, a normalization of fecal secretory IgA, and fecal calprotectin remained within normal limits.

At the conclusion of the study, the participant decreased her thyroid replacement medication to 100 mcg of levothyroxine while seeking evaluation and support for pancreatic insufficiency.

Case 13

Case 13 involved a 44-year-old female who began the program on 125 mcg of Tirosint and 15 mcg of Liothyronine. She sought to reduce stress, improve fatigue and eczema, and address bloating and IBS-like symptoms. She entered the program with a moderately severe symptom burden (MSQ = 77) with the worst symptoms affecting the HEENT, dermatological, gastrointestinal, musculoskeletal, and neuropsychological systems. Specifically, her complaints consisted of headaches, dark circles under her eyes, dry skin, hair loss, diarrhea, constipation, belching, bloating, joint pain, arthritis, stiffness, muscle aches, fatigue, tiredness, apathy, poor memory, poor concentration, anxiety, mood swings, and irritability. Her initial FFQ revealed a diet high in animal products, including beef and pork, low intake of eggs and fatty fish, no gluten-based grains or dairy consumption, infrequent gluten-free grains, and numerous fruits and vegetables. Her supplements consisted of a probiotic, “adrenal adaptogens,” magnesium, glutamine, vitamin D, vitamin K2, dehydroepiandrosterone (DHEA), 5-HTP, and liposomal glutathione.

Initial laboratory findings revealed a TSH of 0.65 μIU/mL, TPO antibodies of 30 IU/mL, elevated TGA at 826.8 IU/mL, and a hs-CRP of 1.95 mg/L. Initial organic acid nutritional testing revealed mildly elevated suberic acid. There was suspicion for a folate deficiency, as suggested by elevated FIGLU [23]. Lipid peroxides were also elevated. Stool testing revealed no lipid malabsorption or pathogenic overgrowth. There were low normal SCFAs and a normal fecal calprotectin.

At week six of the program, the participant was counseled to continue consumption of fatty fish and organ meats. She was provided with guidance on folate-rich foods and to consider the inclusion of fermented foods.

Following the program, the participant’s MSQ decreased from 77 to 25, with notable improvements in joint pain, cognition, and mood. On the exit questionnaire, the participant reported continued challenges with stress without markedly noticeable changes in her overall health. The participant reported a desire to continue prioritizing stress management practices.

A review of her second FFQ documenting the 10-week program showed strict adherence to the AIP diet, with increased intake of certain fruits and vegetables and the use of AIP-compliant starches. Repeat laboratory testing revealed an elevated TSH of 5.07 μIU/mL while free and total hormones remained within the normal range. On questioning, the participant was surprised by the increased TSH, given some mild improvements in symptoms and no symptoms of worsening hypothyroidism. She reported that she had large fluctuations with her TSH in the past, with difficulty titrating medication and maintaining a stable TSH. Her hs-CRP decreased from 1.95 to 1.63 mg/L, TPO antibodies remained unchanged at 29 IU/mL and TGA rose slightly to 884.3 IU/mL.

Repeat nutritional testing revealed normalized adipic acid but slightly elevated suberic acid. FIGLU remained elevated, however, lipid peroxides normalized. Repeat stool testing revealed no changes outside of a notable overgrowth of K. pneumonie. Given the previous concerns for arthritis and the noticeable presence of K. pneumonie, the participant was counseled on testing for HLA-B27.

Case 14

Case 14 involved a 33-year-old female, with no additional significant past medical history, who began the study taking 120 mg of NP thyroid. She sought to improve energy, decrease inflammation, and lose weight. Initial MSQ was 55, with the worst symptoms affecting the HEENT, dermatological, gastrointestinal, and neuropsychological systems. Complaints consisted of pruritic ears, watery/pruritic eyes, stuffy nose, sinus problems, hay fever, excessive mucus, hyperhidrosis, mild hair loss, diarrhea, constipation, bloating, fatigue, tiredness, infrequent poor concentration, comprehension and memory, and anxiety. Her initial FFQ revealed a diet consisting of a variety of fruits, vegetables, regular unprocessed and occasional processed meats, infrequent dairy with regular use of non-dairy creamer, both refined and whole grain products, rice, daily coffee, and weekly alcohol use. She endorsed taking between 5,000 to 10,000 IU vitamin D daily as well as 100 mcg of vitamin K2.

Initial laboratory findings revealed borderline low TSH at 0.42 μIU/mL and free and total T4 and T3 in the low normal range. Her hs-CRP was slightly elevated at 1.71 mg/L, TPO antibodies were slightly elevated at 99 IU/mL with TGA <0.9 IU/mL. Vitamin D was noted to be high normal at 81.8 ng/mL and serum calcium just outside the normal range at 10.3 mg/dL. Given the concern for hypercalcemia and hypervitaminosis D, the participant was asked to discontinue the use of vitamin D until reassessment at the end of the 10-week study.

Initial organic acid nutritional testing revealed an elevation in adipic acid. The participant had significantly elevated ketone bodies despite not following a low carbohydrate diet, which was concerning for possible cellular insulin resistance. Stool testing revealed very low SCFAs and an overgrowth of Klebsiella oxytoca, Pseudomonas aeruginosa, and Enterobacter cloacae. There was evidence of significant lipid malabsorption, as evidenced by elevated fecal phospholipids and fecal cholesterol. Fecal secretory IgA and calprotectin were within normal limits.

At week six of the program, the participant was counseled to continue consuming animal protein, including organ meats. She was encouraged to explore the inclusion of fermented foods and the use of AIP-compliant digestive bitters to support digestion [27]

Following the program, the participant’s MSQ decreased from 56 to 12 with improvements in sleep, sustained energy, and reduction in HEENT symptoms, bloating, and only occasional loose stools. She reported a 12-pound weight loss and a desire to continue with stress management practices to support her health.

A review of her second FFQ documenting the 10-week program revealed strict adherence to the AIP diet, with the elimination of refined carbohydrates, potatoes, eggs, legumes, nuts, seeds, grains, and dairy, as well as the increased consumption of unprocessed meat, vegetables, and fruit and the new, regular inclusion of bone broth, sweet potatoes, fermented foods, and coconut-based products.

Repeat laboratory testing revealed a significantly suppressed TSH at 0.069 μIU/mL, a free T3 increase from 2.3 to 2.9 ng/dL, a decrease of TPO antibodies from 99 to 75 IUI/mL, TGA <0.9 IU/mL, a decrease in hs-CRP from 1.71 to 0.70 mg/L, and a normalization of vitamin D at 50.8 ng/mL.

Repeat stool testing revealed improved, but continued, concern for lipid malabsorption and low SCFAs. There was no growth of any of the previously identified potentially pathogenic organisms. On the exit interview, the participant was instructed to seek digestive enzyme supplement therapy and further work-up for continued lipid malabsorption.

Case 15

Case 15 involved a 43-year-old female, with no additional significant past medical history, who began the study taking 150 mg of Armour. She expressed a desire to improve her diet, improve sleep, lose weight, improve energy and cognition, and begin a structured exercise protocol. She entered the program with a severe symptom burden (MSQ = 103) with the worst symptoms affecting the HEENT, dermatological, gastrointestinal, genitourinary, musculoskeletal, and neuropsychological systems. More specifically, she complained of headaches, dizziness, dark circles under her eyes, pruritic ears and otalgia, acne, dry skin, rashes, hair loss, flushing, constipation, belching, bloating, abdominal pain, joint pain, stiffness, muscle aches, fatigue, tiredness, lethargy, poor concentration, poor coordination, indecisiveness, anxiety, mood swings, irritability, frequent urination, and insomnia. She additionally complained of excessive weight gain, food cravings, and water retention.

Her initial FFQ revealed a diet consisting of a variety of fruits, vegetables, regular unprocessed and processed meats, eggs, infrequent seafood, regular dairy consumption, potatoes, limited refined or whole grains or grain-based products, daily coffee, and weekly alcohol. The participant was not taking any supplements or additional medications.

Initial laboratory findings revealed a markedly suppressed TSH of 0.026 μIU/mL, with total and free hormone levels within normal ranges. TPO antibodies were noted at 141 IU/mL, TGA at 21.8 IU/mL, and hs-CRP was elevated at 1.85 mg/L. The participant was asked given the significantly suppressed TSH, to lower her medication dose to 120 mg.

Initial organic acid nutritional testing revealed borderline elevated methylmalonic acid, suggesting borderline vitamin B12 deficiency [29], as well as elevated suberic and adipic acids. Her toxic element screen revealed a slightly elevated whole blood tin at 0.45 mcg/L. Stool testing showed normal SCFAs, but an overgrowth of C. freundii and E. cloacae.

At week six of the program, the participant was counseled to continue with increased consumption of omega-3 fatty fish and animal protein, including organ meats, and explore the inclusion of fermented foods as tolerated.

Following the program, the participant’s MSQ significantly decreased from 103 to 36 with the only continued symptom of hair loss. She reported a 10-pound weight loss, increased energy, improved sleep, decreased food cravings, improved resilience, decreased bloating, and improved cognitive functioning.

A review of her second FFQ documenting the 10-week program revealed strict adherence to the AIP diet with the elimination of refined carbohydrates, potatoes, eggs, legumes, nuts, seeds, grains, and dairy, as well as increases in the consumption of unprocessed meat, vegetables, fruit, and regular inclusion of coconut products and AIP-approved starches. The participant did report some accidental consumption of gluten in beverages and processed products in the first few weeks of the program with noticeable negative effects on energy and stools that improved after the discovery and elimination of the gluten-containing products.

Repeat laboratory testing revealed TSH of 0.244 μIU/mL, with free and total hormone levels staying within normal limits, hs-CRP decreased to 0.94 mg/L, TPO antibodies decreased from 141 to 111 IU/mL, and TGA remained clinically unchanged.

Repeat nutritional testing revealed continued slight elevation in adipic acid. Methylmalonic acid remained elevated, suggesting B12 deficiency [29], however, previously elevated whole blood tin had normalized. The participant also now had slightly elevated ketones likely related to weight loss and lower carbohydrate diet.

Repeat stool testing revealed no evidence of lipid malabsorption and no overgrowth of previously identified potentially pathogenic organisms, however, there was a reduction in the predominant SCFA butyrate [23]. Upon the completion of the study, the participant decreased her medication from 120 mg Armour to 90 mg. Given the persistently elevated methylmalonic acid in the setting of normal and even increased animal protein intake, the participant was instructed by the study doctor to seek further diagnostic evaluation for potential autoimmune gastritis compromising B12 absorption.

Case 16

Case 16 involved a 26-year-old female, with no additional significant past medical history, who began the study without the use of thyroid replacement medication. She reported the use of the dietary supplement Standard Process Thyrotrophin PMG, which is a bovine protomorphogen devoid of active thyroxine. She sought to improve her dietary patterns, improve energy, cognition, resilience, and become more educated about dietary and lifestyle choices that could support her health. She entered the program with a severe symptom burden (MSQ = 106) with the worst symptoms affecting the HEENT, dermatological, cardiac, respiratory, gastrointestinal, genitourinary, musculoskeletal, neuropsychological and immune systems. More specifically, her complaints consisted of headaches, blurred/tunnel vision, excessive mucus, canker sores, acne, dry skin, rashes, hair loss, flushing, palpitations, shortness of breath/difficulty taking a deep breath, constipation, bloating, abdominal pain, joint pain, stiffness, muscle aches, fatigue, tiredness, lethargy, poor memory and concentration, poor coordination, indecisiveness, anxiety, mood swings, depressed mood, frequent urination and frequent illness. She additionally complained of food cravings and compulsive eating.

Her initial FFQ revealed a largely vegetarian-based diet with infrequent chicken and egg consumption, a large variety of fruits, numerous whole grains, pea protein, coffee and tea with no alcohol consumption. Outside of the previously mentioned dietary supplement, she was taking zinc, selenium, vitamin D, vitamin K2 and cod liver oil.

Initial laboratory findings revealed a TSH of 1.49 μIU/mL with total and free hormone levels within normal ranges. She was noted with initial TPO antibodies of 120 IU/mL, TGA of <0.09 IU/mL, a hs-CRP of 1.06 mg/L, and a low WBC count of 3.3 x 103 / μL.

Initial organic acid nutritional testing revealed no concerning vitamin or mineral deficiencies. Toxic element screen revealed no concerning findings. RBC analysis for RBC PUFA volume showed high normal omega-3 volume with a normal omega-3: omega-6 ratio.

Stool testing no bacterial overgrowth with slightly low SCFAs. There was no evidence of lipid malabsorption.

At week six of the program, the participant was counseled to continue the consumption of omega-3 fatty fish and increase animal protein consumption, including organ meats, and well as fermented foods.

Following the program, the participant’s MSQ significantly decreased from 106 to 23 with the only continued significant symptoms of hair loss (improved), headaches (improved), and hyperhidrosis. She reported significantly increased energy, improved sleep, fewer food cravings, improved resilience, resolved joint pain, decreased depression, less frequent and severe migraines, no significant gastrointestinal symptoms, and marked improvements in dry skin/ acne, and improved cognitive functioning. She reported significantly improved functioning in her job as a healthcare provider.

A review of her second FFQ documenting the 10-week program revealed strict adherence to the AIP diet with the elimination of refined carbohydrates, potatoes, eggs, legumes, nuts, seeds, grains, and dairy, as well as increases in the consumption of vegetables and fruit, and the new regular inclusion of chicken, kombucha, fermented foods, coconut products, such as coconut yogurt, and AIP starches such as cassava.

Repeat laboratory testing revealed a post-intervention TSH of 3.48 μIU/mL, with very slight increases in free and total hormone levels. hs-CRP decreased from 1.06 to 0.16 mg/L. TPO antibodies decreased from 120 to 105 IU/mL, and TGA remained clinically unchanged <0.9 IU/mL. Interestingly, the patient’s previously low WBC count of 3.3 x 103/μL increased at post-intervention to 4.0 x 103/μL. Her monocyte percentage decreased from an elevated 14% to within normal limits at 9% and her lymphocytes increased from 36% pre-intervention to 42% post-intervention.

Repeat nutritional testing revealed overall balanced vitamin and minimal markers with the exception of a now elevated FIGLU, suggesting folate deficiency [23]. She remained with ideal RBC volume of omega-3 fatty acids as well as no concerning levels of whole blood heavy metals. Repeat stool testing revealed no identifiable potentially pathogenic organisms as well as low normal SCFAs. There were still no signs of lipid malabsorption.

Upon completion of the study, the participant remained without the use of thyroid hormone replacement medication.

Case 17

Case 17 involved a 27-year-old female, with a significant past medical history within the past year of a severe varicella zoster infection, slight elevation in anti-CCP antibodies, without clinical evidence of rheumatoid arthritis, and a diagnosis of HT three months prior to study onset, who began the study on a small dose of Armour (15 mg). She sought to improve her dietary patterns, improve energy, cognition, resilience, and become more educated about dietary and lifestyle choices that could support her health. She hoped to alleviate the most troubling symptoms of fatigue, moodiness, hair loss, and dry skin and reverse HT such that she would no longer need replacement medication.

She entered the program with a moderate symptom burden (MSQ = 75), with the worst symptoms affecting the HEENT, skin, gastrointestinal, genitourinary, neuropsychological, and immune parameters. More specifically, her complaints consisted of watery or itchy eyes and swollen red eyelids, stuffy nose, excessive mucus, stuffy nose, sinus problems, canker sores, acne, dry skin, rashes, hair loss, flushing, constipation, bloating, abdominal pain, fatigue, tiredness, lethargy, poor memory and concentration, indecisiveness, anxiety, mood swings, irritability, frequent urination, and frequent illness.

Her initial FFQ revealed a diet transitioning from a vegetarian template to now regular chicken, egg, and fish consumption, non-dairy creamer with no regular dairy consumption, a large variety of fruits, unrefined whole grains, infrequent rice, numerous nuts and seeds, coconut, decaf coffee, occasional tea, with no alcohol consumption. She had discontinued supplementation prior to the study but reported previous use of a B complex, vitamin D, iron, collagen, oregano, quercetin, and magnesium.

Initial laboratory findings revealed a TSH of 1.77 μIU/mL, with total and free hormone levels within normal ranges. Her additional initial labs included TPO antibodies of 138 IU/mL, TGA of 66.6 IU/mL, hs-CRP of 0.88 mg/L, and a borderline low WBC count of 3.5 x 103/μL and 10% monocytes.

Initial organic acid nutritional testing revealed no concerning vitamin deficiencies. Zinc levels were borderline low and significantly lower than plasma copper, resulting in a depressed copper to zinc ratio. Toxic element screen revealed no concerning findings with only a high normal whole blood mercury at 2.64 mcg/L. RBC analysis for RBC PUFA volume showed high normal omega-3 volume with a normal omega-3/6 ratio.

Stool testing revealed numerous imbalances, including mild lipid malabsorption, low butyrate, and an overgrowth of Citrobacter freundii and Morganella morganii.

At week six of the program, the participant was counseled to continue the consumption of omega-3 fatty fish, animal protein, including organ meats, as well as the inclusion of fermented foods. She was provided with education to explore the exclusion of high FODMAP-containing foods, given her symptoms of constipation and bloating [25]. She was additionally supported with information regarding the use of AIP-compliant digestive bitters to support improve the digestion and absorption of nutrients [27].

Following the program, the participant’s MSQ significantly decreased from 75 to 25, with the only continued severe symptoms of hair loss (which had become less frequent and overall improved). She reported significantly increased energy, improved sleep, improved resilience, improved sinus and allergic symptoms, more stable mood, less severe and frequent gastrointestinal symptoms, and improved cognitive functioning. She reported significantly improved functioning in her job as a healthcare provider.

A review of her second FFQ documenting the 10-week program revealed strict adherence to the AIP diet, with the elimination of refined carbohydrates, potatoes, eggs, legumes, nuts, seeds, grains, and dairy, as well as increases in the consumption of unprocessed meat, vegetables, and fruit, and the new, regular inclusion of more animal protein, fermented foods, and AIP starches.

Repeat laboratory testing revealed a post-intervention TSH of 2.2 μIU/mL, with continued stability in free and total hormone levels. hs-CRP decreased from 0.88 to 0.80 mg/L. TPO antibodies increased slightly from 138 to 155 IU/mL with TGA also slightly increasing from 66.6 to 76.9 IU/mL. Interestingly, the patient’s previously borderline low WBC count of 3.5 x 103/μL had only increased slightly to a post-intervention level of 3.6 x 103/μL. Her monocyte percentages remained at 10%.

Repeat nutritional testing revealed balanced vitamin and mineral markers improved minimal markers, with the exception of a now slightly elevated FIGLU, suggesting folate deficiency [23]. She remained with an ideal RBC volume of omega-3 fatty acids as well as no concerning levels of whole blood heavy metals. Interestingly her plasma copper had decreased from high normal ranges and was now in a nearly 1:1 ratio with plasma zinc.

Repeat stool testing revealed a marked improvement and increase in butyrate. She continued with an overgrowth of C. freundii but now had no evidence of M. morganii. Previously noted mild lipid malabsorption had resolved.

Upon completion of the study, the participant remained using only 15 mg of Armour but was going to seek changing medications to 25 mcg of Tirosint, removing the T3 component, with future considerations for titrating off medication entirely.

Raw data tables

Table 7 includes the baseline laboratory data for the 17 participants completing blood chemistry testing pre-intervention.

Lab AIP 001 (*,** ) AIP 002 (***) AIP 003 (**) AIP 004 AIP 005 (#) AIP 006 AIP 007 AIP 008 AIP 009 AIP 010 AIP 011 AIP 012 AIP 013 (****) AIP 014 AIP 015 (**) AIP 016 AIP 017 TSH (μIU/mL) 0.424 (*,** ) 4.75 3.55 (**) 2.85 1.48 1.64 1.06 13.45 2.79 2.09 4.08 0.736 0.653 0.42 0.026 (**) 1.49 1.77 total T4 (μg/dL) 12.3 (*,** ) 6.5 2 (**) 8.3 7.6 8.1 6.5 6.1 4.7 6.5 7.8 7.4 7.6 5.5 6.8 (**) 6.4 8.2 total T3 (ng/dL) 149 (*,** ) 106 131 (**) 101 118 82 80 137 84 90 95 98 142 78 138 (**) 97 115 free T4 (ng/dL) 2.9 (*,** ) 2.6 0.31 (**) 1.4 1.29 1.48 1.11 1.02 0.82 1.02 1.19 1.41 1.31 1.05 1.07 (**) 1.07 1.26 free T3 (pg/mL) 1.36 (*,** ) 0.91 3.3 (**) 2.7 3.3 2.2 2.2 3.1 2.2 2.3 2.6 3 3.4 2.3 3.4 (**) 2.6 2.8 reverse t3 (ng/dL) 28.2 (*) 17.1 <5.0 (**) 24.7 14.7 27.3 15.9 12.9 15.7 13.4 15.9 15.4 16.1 16.5 15.9 (**) 13.2 17.1 TPO (IU/mL) 477 (*) 374 135 180 365 135 273 185 471 >600 16 438 30 99 141 120 138 TGA (IU/mL) 5.7 (*) 0 2 603.5 200.7 0 4.7 1.8 3.4 2.1 0 3.2 826.8 0 21.8 0 66.6 WBC (x103 / μL) 8.3 (*) 7.9 5.8 4.8 4.5 6.9 4.8 9 6 6.8 7.3 4.6 6.4 (****) 4.9 4.8 3.3 3.5 Neutrophils (%) 50 (*) 63 59 57 40 69 57 70 55 58 68 58 49 58 63 47 49 Lymphocytes (%) 39 (*) 28 30 33 50 21 28 21 33 37 21 30 34 32 29 36 39 Monocytes (%) 9 (*) 8 7 6 8 8 8 6 8 5 9 9 12 7 7 14 10 Eosinophils (%) 2 (*) 1 4 3 2 1 6 2 3 0 2 2 4 3 1 2 1 Basophils (%) 0 (*) 0 0 1 0 1 1 1 1 0 0 1 1 0 0 1 1 Absolute Neutrophils (x103 / μL) 4.2 (*) 5 3.4 2.8 1.8 4.8 2.8 6.3 3.4 3.9 4.9 2.6 3.2 2.8 3 1.5 1.7 Absolute Lymphocytes (x103 / μL) 3.2 (*) 2.2 1.7 1.6 2.2 1.4 1.3 1.9 2 2.5 1.6 1.4 2.2 1.6 1.4 1.2 1.4 Absolute Monocytes (x103 / μL) 0.7 (*) 0.6 0.4 0.3 0.4 0.5 0.4 0.5 0.5 0.4 0.6 0.4 0.8 0.3 0.3 0.5 0.4 Absolute Eosinophils (x103 / μL) 0.1 (*) 0.1 0.2 0.1 0.1 0.1 0.3 0.1 0.2 0 0.2 0.1 0.2 0.1 0 0.1 0 Absolute Basophils (x103 / μL) 0 0 0 0 0 0.1 0 0.1 0 0 0 0 0.1 0 0 0 0 hs-CRP (mg/L) 14.07 (*) 6.97 (***) 0.23 2.64 0.65 0.72 0.43 2.59 0.67 2.42 0.98 0.29 1.95 1.71 1.85 1.06 0.88 Table 7: Pre-intervention laboratory data including thyroid parameters, thyroid antibodies, WBC, and differential cell count. Note: TGA <0.9 IU/mL was reported as 0 in the table and treated as 0 in the statistical analysis. TPO antibodies >600 IU/mL were treated as 600 IU/mL in the statistical analysis. AIP (autoimmune protocol), TSH (thyroid stimulating hormone), TPO (thyroid peroxidase antibodies), TGA (anti-thyroglobulin antibodies), WBC (white blood cell), hs-CRP (high sensitivity C-reactive protein), (*) acutely sick, (**) decreased or changed thyroid medication during the study because of the pre-intervention result or because of irregular medication dosing, (***) hs-CRP outlier, (****) WBC count outlier, (#) did not complete post-intervention testing

Table 8 includes baseline HRQL for the 17 participants completing the SF-36 pre-intervention.

SF 36 Score AIP 001 AIP 002 AIP 003 AIP 004 AIP 005 AIP 006 AIP 007 AIP 008 AIP 009 AIP 010 AIP 011 AIP 012 AIP 013 AIP 014 AIP 015 AIP 016 AIP 017 SF 36 Physical Functioning 65 80 95 75 100 95 85 80 55 90 85 90 60 95 75 55 15 SF 36 Physical Role Functioning 0 50 100 25 100 0 25 25 0 50 25 100 0 100 100 0 0 SF 36 Emotional Role Functioning 0 33.3 33.3 100 33.3 0 0 33.3 0 33.3 100 100 100 100 66.7 33.3 0 SF 36 Vitality 10 20 25 30 75 40 25 30 5 20 15 25 0 50 10 10 25 SF-36 Mental Health 56 68 44 72 76 52 36 36 60 40 48 40 60 68 72 44 60 SF 36 Social Role Functioning 62.5 62.5 62.5 62.5 75 50 62.5 50 37.5 25 37.5 100 50 87.5 87.5 50 75 SF 36 Bodily Pain 67.5 45 67.5 67.5 90 67.5 47.5 67.5 32.5 32.5 35 80 67.5 77.5 47.5 55 90 SF 36 General Health 20 35 40 45 75 80 40 35 10 10 30 60 25 65 55 40 40 Table 8: Pre-intervention SF-36 subcale scores SF-36 (36-Item Short Form Health Survey); AIP (autoimmune protocol)

Table 9 includes the baseline clinical symptom burden for the 17 participants completing the MSQ pre-intervention.

MSQ AIP 001 AIP 002 AIP 003 AIP 004 AIP 005 AIP 006 AIP 007 AIP 008 AIP 009 AIP 010 AIP 011 AIP 012 AIP 013 AIP 014 AIP 015 AIP 016 AIP 017 MSQ Head Score 9 4 2 4 2 7 5 7 4 9 10 8 2 1 6 5 1 MSQ Eye Score 6 3 4 0 3 0 10 3 8 1 9 4 5 3 3 4 5 MSQ Ear Score 3 2 0 0 0 0 2 2 9 5 7 0 1 4 7 0 0 MSQ Nose Score 16 5 13 0 1 0 13 2 16 3 9 0 1 7 0 2 13 MSQ Mouth/Throat Score 3 5 1 0 0 0 6 1 0 9 5 0 1 1 3 1 4 MSQ Skin Score 9 12 7 7 3 0 11 8 6 9 12 8 7 5 11 12 8 MSQ Heart Score 0 1 0 0 1 2 1 2 3 1 4 1 2 0 0 6 0 MSQ Lung Score 1 1 0 0 0 0 1 1 0 0 4 0 1 0 0 4 0 MSQ Digestive Score 14 3 10 9 6 6 12 11 9 14 9 7 5 11 11 10 8 MSQ Joint/Muslce Score 11 13 4 12 1 13 5 15 16 8 18 20 15 3 15 12 5 MSQ Weight Score 16 20 15 7 15 0 10 16 1 10 8 4 3 10 12 10 1 MSQ Energy/Activity Score 12 7 8 4 3 6 12 9 6 10 10 10 11 2 7 9 9 MSQ Mind Score 12 4 12 5 0 13 14 16 28 2 9 4 12 4 12 14 5 MSQ Emotion Score 11 11 4 3 2 9 8 12 7 8 13 13 10 4 11 11 6 MSQ Other Score 3 7 3 4 0 0 4 3 6 0 5 4 1 0 5 6 10 MSQ Total Score 126 98 83 55 37 56 114 108 119 89 132 83 77 55 103 106 75 Table 9: Pre-intervention MSQ scores (subscales and total) MSQ (Medical Symptoms Questionnaire), AIP (autoimmune protocol)

Table 10 includes the post-intervention laboratory data for the 16 participants completing blood chemistry testing following the 10-week dietary and lifestyle intervention. Note: Participant AIP 005 did not complete the study and, as such, there is no data presented in the table below.

Lab AIP 001 (*,**) AIP 002 (***) AIP 003 (**) AIP 004 AIP 005 (#) AIP 006 AIP 007 AIP 008 (*) AIP 009 AIP 010 AIP 011 AIP 012 AIP 013 (****) AIP 014 AIP 015 (**) AIP 016 AIP 017 TSH (μIU/mL) 0.92 (*,**) 2.32 7.35 (**) 2.06 1.55 1.13 31.92 (*) 3.06 0.535 2.15 0.23 5.07 0.069 0.244 (**) 3.48 2.2 total T4 (μg/dL) 13.1 (*,**) 6.1 5 (**) 9.8 8.3 6.6 8.3 (*) 5.2 6.9 8.8 8 7.1 5.4 6.4 (**) 6.6 6.4 total T3 (ng/dL) 98 (*,**) 93 107 (**) 84 78 84 154 (*) 83 79 78 99 92 101 88 (**) 96 101 free T4 (ng/dL) 1.8 (*,**) 2.3 0.77 (**) 1.59 1.49 1.19 1.1 (*) 0.86 1.23 1.47 1.53 1.14 1.07 0.91 (**) 1.11 1.21 free T3 (pg/mL) 1.61 (*,**) 0.91 2.5 (**) 2.6 2.2 2.5 3. 1(*) 2.3 2.4 2.4 2.8 2.4 2.9 2.2 (**) 2.8 2.8 reverse t3 (ng/dL) 54.7 (*,**) 15.9 10.9 (**) 30.5 27.7 17.9 17.5 (*) 13 14.8 23.3 20.6 18 16.3 20.3 (**) 13.6 17.2 TPO (IU/mL) 598 (*) 409 107 177 160 190 123 (*) 481 >600 14 452 29 75 111 105 155 TGA (IU/mL) 3.1 (*) 0 0.9 735.7 0 4.8 4.5 (*) 3.6 1.7 0 4.8 884.3 0 20.7 0 76.9 WBC (x103 / μL) 6.1(*) 6.6 4.4 3.8 5.9 3.9 11.1 (*) 5.5 4.6 6.7 4.5 8.3 (****) 4.2 5.6 4 3.6 Neutrophils (%) 58 (*) 66 57 51 59 55 76 (*) 44 48 71 57 52 61 66 44 51 Lymphocytes (%) 32 (*) 28 31 38 32 34 17 (*) 44 46 19 32 37 29 27 42 37 Monocytes (%) 10 (*) 5 8 7 7 6 5 (*) 7 6 8 9 7 7 7 9 10 Eosinophils (%) 0 (*) 1 4 3 1 4 1 (*) 4 0 2 2 2 3 0 3 1 Basophils (%) 0 (*) 0 0 1 1 1 1 (*) 1 0 0 0 1 0 0 2 1 Absolute Neutrophils (x103 / μL) 3.5 (*) 4.3 2.5 2 3.5 2.1 8.4 (*) 2.4 2.2 4.7 2.5 4.4 2.6 3.6 1.8 1.8 Absolute Lymphocytes (x103 / μL) 1.9 (*) 1.9 1.4 1.5 1.9 1.3 1.9 (*) 2.4 2.1 1.2 1.4 3.1 1.2 1.5 1.7 1.3 Absolute Monocytes (x103 / μL) 0.6 (*) 0.3 0.4 0.3 0.4 0.2 0.6 (*) 0.4 0.3 0.6 0.4 0.6 0.3 0.4 0.4 0.4 Absolute Eosinophils (x103 / μL) 0 (*) 0.1 0.2 0.1 0 0.2 0.1 (*) 0.2 0 0.1 0.1 0.2 0.1 0 0.1 0 Absolute Basophils (x103 / μL) 0 (*) 0 0 0 0 0 0.1 (*) 0 0 0 0 0.1 0 0 0.1 0 hs-CRP (mg/L) 11.7 (*) 5.02 (***) 0.42 2.9 0.76 0.38 6.52 (*) 0.36 0.84 0.9 0.32 1.63 0.7 0.94 0.16 0.8 Table 10: Post-intervention laboratory data, including thyroid parameters, thyroid antibodies, WBC, and differential cell count. Note TGA <0.9 IU/mL was reported as 0 in the table and treated as 0 in the statistical analysis. TPO antibodies >600 IU/mL were treated as 600 IU/mL in the statistical analysis. AIP (autoimmune protocol), TSH (thyroid stimulating hormone), TPO (thyroid peroxidase antibodies), TGA (anti-thyroglobulin antibodies), WBC (white blood cell), hs-CRP (high sensitivity C-reactive protein), (*) acutely sick, (**) decreased or changed thyroid medication during the study because of the pre-intervention result or because of irregular medication dosing, (***) hs-CRP outlier, (****) WBC count outlier, (#) did not complete post-intervention testing

Table 11 includes post-intervention HRQL for the 16 participants completing the SF-36 survey following the 10-week dietary intervention. Note: Participant AIP 005 did not complete the study and, as such, there is no data presented in the table below.

SF 36 Score AIP 001 AIP 002 AIP 003 AIP 004 AIP 005 (#) AIP 006 AIP 007 AIP 008 AIP 009 AIP 010 AIP 011 AIP 012 AIP 013 AIP 014 AIP 015 AIP 016 AIP 017 SF 36 Physical Functioning 70 95 100 90 95 95 95 95 100 95 100 75 95 80 100 100 SF 36 Physical Role Functioning 100 100 100 100 75 50 25 50 100 100 100 25 100 100 50 100 SF 36 Emotional Role Functioning 33.3 100 100 100 66.7 100 0 100 100 100 100 100 100 0 100 0 SF 36 Vitality 30 70 40 65 70 45 35 35 85 70 75 15 80 55 55 60 SF-36 Mental Health 72 88 76 88 80 60 52 84 100 84 68 68 92 76 64 80 SF 36 Social Role Functioning 87.5 87.5 50 75 100 75 50 75 100 100 87.5 75 100 75 87.5 75 SF 36 Bodily Pain 77.5 77.5 100 90 35 90 75 77.5 100 90 90 67.5 100 67.5 77.5 67.5 SF 36 General Health 50 65 85 55 95 60 35 40 90 75 85 50 85 70 80 70 Table 11: Post-intervention SF-36 subscale scores AIP (autoimmune protocol), SF-36 (36 Item Short Form Health Survey), # (did not complete post-intervention testing)

Table 12 includes the post-intervention clinical symptom burden for the 16 participants completing the MSQ following the 10-week dietary intervention. Note: Participant AIP 005 did not complete the study and, as such, there is no data presented in the table below.

MSQ AIP 001 AIP 002 AIP 003 AIP 004 AIP 005 (#) AIP 006 AIP 007 AIP 008 AIP 009 AIP 010 AIP 011 AIP 012 AIP 013 AIP 014 AIP 015 AIP 016 AIP 017 MSQ Head Score 6 0 1 2 2 6 9 1 0 0 0 0 0 1 2 0 MSQ Eye Score 2 3 2 0 1 7 6 3 0 0 0 3 0 3 2 2 MSQ Ear Score 0 0 0 0 0 0 0 0 1 0 0 1 1 0 0 0 MSQ Nose Score 11 1 0 0 0 7 1 1 0 0 0 0 1 1 0 5 MSQ Mouth/Throat Score 2 0 0 0 0 2 1 0 1 0 0 0 0 2 1 0 MSQ Skin Score 4 0 1 5 0 5 9 5 3 1 2 3 1 4 7 3 MSQ Heart Score 1 0 0 1 2 0 4 0 0 0 0 0 0 0 2 0 MSQ Lung Score 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 MSQ Digestive Score 4 1 1 3 9 9 11 6 0 2 3 4 2 5 3 4 MSQ Joint/Muslce Score 1 3 0 4 4 1 9 2 0 2 4 5 1 4 0 4 MSQ Weight Score 3 2 2 4 4 4 9 1 0 1 3 1 3 4 4 1 MSQ Energy/Activity Score 4 0 0 2 0 3 8 2 0 1 4 2 1 2 0 1 MSQ Mind Score 1 1 2 2 6 7 8 5 1 0 1 3 1 8 1 0 MSQ Emotion Score 3 0 0 3 4 4 7 4 0 1 8 3 1 2 1 3 MSQ Other Score 1 1 1 1 1 1 3 2 0 0 0 0 0 0 0 2 MSQ Total Score 43 12 10 28 33 56 85 32 6 8 25 25 12 36 23 25 Table 12: MSQ subscale and total scores post-intervention AIP (autoimmune protocol), MSQ (Medical Symptoms Questionnaire), (#) did not complete post-intervention testing

Table 13 depicts the originally calculated p-values, ordered from lowest to highest matched with corresponding corrected p-values for statistical significance following the use of a false discovery rate correction, given the study's multiple hypotheses. The corrected p-values of significance for n = 27 tests were calculated assuming a false discovery rate d = 0.05 using the formula p i = d * (i/n), where n is the number of tests, i is an integer between 1-27, and p i is the corrected p-value for the given ordered integer. After performing the correction and matching the ordered and previously calculated p values with its respective p i , the only original p-value affected corresponded to a change in the mean lymphocyte count from pre- to post-intervention. Given this correction, the study authors could not reliably state that there was a significant difference between the mean lymphocyte count from pre- to post-intervention. No other p-values were affected by the false discovery rate correction.