The Benefits of Amino Acids for Hashimoto’s

I first became interested in amino acids when I learned about the role of the amino acid tyrosine, which is one of the raw materials required to make thyroid hormones, as well as glutamine, an amino acid that aids in repairing the gut. (1, 2)

Fascinated by these discoveries, I began studying amino acids and came to find that each amino acid has unique and very important functions throughout the body, including supporting many of the imbalances that can occur in people with thyroid conditions.

We get amino acids from eating protein — so when we don’t get enough proteins or digest proteins well, we can become deficient in amino acids, as well as other important thyroid-supportive nutrients like vitamin B12, selenium, and zinc.

Amino acid deficiency can be both a causal factor and a symptom of hypothyroidism. (3, 4)

Because they are involved in so many processes in the body, a deficiency in amino acids can result in a wide range of symptoms that are also associated with Hashimoto’s and hypothyroidism, including hair loss, anxiety, poor liver health, digestive issues, and muscle weakness, to name a few. (5-9)

Learning about how poor protein digestion can result in worsening Hashimoto’s symptoms, was a big “aha” moment for me.

Poor protein digestion is common in those with Hashimoto’s, due in part to the body’s metabolism slowing down (so even digestion happens less efficiently). Many people will also have low stomach acid, leaky gut, blood sugar imbalances, and nutrient deficiencies, all of which can further affect protein digestion and amino acid levels.

Our toxic environment also has a hand in amino acid deficiency, as the body burns through amino acids to help with detoxification.

In this article, you’ll learn:

• Why our bodies need amino acids
• Why amino acid deficiencies may be common in Hashimoto’s
• How amino acids support Hashimoto’s
• My testing recommendations
• The Root Cause approach to getting more amino acids

Why Our Bodies Need Amino Acids

When we eat protein, it is digested and broken down into amino acids. Some amino acids are also manufactured within the body. Amino acids combine together into structures that become the building blocks to make protein in the body. They can help with mood regulation, sleep issues, skin conditions, hair loss, cardiac health, lowering blood pressure, and supporting a healthy pregnancy. (10-18)

The body needs all of this protein because so many vital functions require it, and getting adequate protein can help ensure these functions are carried out. Some vital functions include:

• Enzyme activity – Enzymes are proteins (made up of amino acids) that trigger and accelerate vital chemical reactions throughout the body, supporting everything from digestion to reproductive health.
• Immune response – Amino acids protect the intestinal barrier against pathogens, and are needed for the production of antibodies that the immune system uses to fight infections.
• Structural support for cells – Proteins provide structural support throughout our cells. One example is collagen, which makes up connective tissue and is the most abundant protein in the body.
• Storage and transport throughout the body – Proteins transport blood sugar, cholesterol, and other nutrients. For example, ferritin is a storage protein that stores iron; hemoglobin is a protein transporter used to carry oxygen.
• Hormones and neurotransmitter communication – Proteins and their chemical instructions are necessary for the synthesis of hormones and neurotransmitters. This is important to all aspects of our body’s functioning, including digestion, mood, stress response, reproductive health, immunity, and more.

Deficiencies in amino acids can affect the manufacturing of proteins needed for these functions.

Tyrosine is one example of an amino acid that builds protein and is integral to the synthesis of the thyroid hormone thyroxine. The thyroid gland combines tyrosine and iodine to make thyroid hormone. Tyrosine is also important for our mood and stress response, as it has a direct effect on adrenal neurotransmitter levels, such as dopamine, epinephrine, and norepinephrine.

There are 20 different amino acids that can join together to construct proteins (typically these protein structures contain 50 to 2000 amino acids strung together), as well as polypeptides (a smaller version of a protein structure containing fewer amino acids) in the body. (19, 20)

Essential and Non-Essential Amino Acids

These 20 amino acids are categorized as either essential, non-essential, or conditionally essential. There is some controversy on which essential aminos fall into which category, so as we discuss this, just remember that these are not strict classifications, but instead a way of categorizing them to explain their origins and functions.

Essential amino acids are not more “important” than non-essential ones — the category of “essential” refers to the fact that we need to get them into our bodies via food. Vegetarians and vegans, as well as people eating a more high-carb and processed diet (which I call the Standard American Diet or SAD), may particularly be at risk for deficiencies in essential amino acids, as can individuals with digestive issues.

In cases of deficiency, a few key amino acids can be supplemented.

The essential amino acids that must be taken in through the diet are:

• Tryptophan
• Methionine
• Lysine
• Threonine
• Histidine
• Isoleucine
• Leucine
• Valine
• Phenylalanine

The best food sources of amino acids are quality, clean animal proteins like meat, poultry, and eggs, although you can get them through plant sources as well. (You can read my article on safe protein for Hashimoto’s for more details on this.)

Non-essential amino acids are produced within the body, so there is not as big of an emphasis on needing them from diet or supplements.

The 11 non-essential amino acids include:

• Alanine
• Arginine
• Asparagine
• Aspartic acid
• Cysteine
• Glutamic acid
• Glutamine
• Glycine
• Proline
• Serine
• Tyrosine

These are manufactured within the body, assuming the process is not inhibited in some way — for instance, through a nutrient deficiency caused by gut problems or poor detoxification.

Tyrosine is a non-essential amino acid synthesized within the body from the amino acid phenylalanine (both are critical for thyroid hormone health). Cysteine, a very important amino acid that supports detoxification, is synthesized from methionine and serine. Most of the other non-essential amino acids are synthesized from glucose. (21)

Conditionally Essential Amino Acids

Now let’s talk about amino acids that are considered “conditionally” essential. This means that under certain conditions, our body may not be able to synthesize them.

Conventional medicine considers arginine, cysteine, glycine, glutamine, proline, and tyrosine as conditional amino acids that may not be produced when a person has catabolic issues, for instance, or in premature babies.

I personally believe that additional amino acids may be conditionally essential in those with Hashimoto’s and other autoimmune conditions. This could be due to genetic variations, nutrient deficiencies, toxins, infections, and/or the digestive issues often present in those with Hashimoto’s.

There are hundreds of other non-protein-associated amino acids which combine in unique ways to perform a number of functions beyond protein synthesis, including tissue growth and repair, central nervous system and neurological function, gut integrity, immune health, gene expression regulation, and detoxification.

Selenocysteine is one such example (sometimes even thought of as the 21st amino acid) and is unique for multiple reasons, specifically that it’s the only amino acid that contains an essential nutrient, selenium. It is not proteinogenic (protein creating), but is important to cellular processes, including selenium homeostasis and thyroid hormone metabolism. (22)

Throughout this article, we’ll talk more about the importance of healthy levels of selenium to the thyroid, and how poor protein digestion can affect these levels. (23)

Research tells us that amino acid deficiencies can contribute to hypothyroidism, the body’s toxic load, and be a trigger for many of the symptoms commonly seen in Hashimoto’s (i.e. anxiety, insomnia, fatigue, muscle wasting, etc.).

Why Amino Acid Deficiencies May be Common in Hashimoto’s

As I mentioned earlier, poor protein digestion was a big “aha” moment for me in my own early Hashimoto’s journey. Only through adequate protein intake can we get the amino acids we need for optimal thyroid function, immune support, and gut health. Animal protein in particular contains many nutrients the body needs (besides amino acids) for healthy thyroid function, including B12, selenium, iron, and zinc.

Unfortunately, many people with Hashimoto’s — even if eating adequate amounts of protein in their diet — don’t digest protein well, nor do their bodies extract these nutrients efficiently. Here are a few reasons for this:

• Proteolysis (protein digestion): Protein digestion is likely to be impaired in hypothyroidism, but tends to be accelerated in hyperthyroidism. (24)
• Low stomach acid and reduced nutrients: Low stomach acid is common in hypothyroidism. This can result in a depletion of amino acids and key nutrients (such as zinc, selenium, B12, and iron/ferritin) needed for thyroid support, as well as for the synthesis of non-essential amino acids. It also can result in common Hashimoto’s triggers, including food sensitivities (many with Hashimoto’s are sensitive to gluten, dairy, and/or soy) and less resistance to pathogenic invasions (which can further impact nutrient absorption, becoming a vicious cycle). I estimate that some 50-70 percent of people with Hashimoto’s are deficient in stomach acid.
• Genetic predisposition: A gene variation of the MTHFR (methylenetetrahydrofolate reductase) gene is common in Hashimoto’s, and results in poor methylation (ability to detoxify). This gene synthesizes the amino acid methionine from the amino acid homocysteine. Methionine (found in animal products and some nuts such as almonds and cashews) is important to the body’s ability to detox. Someone with the MTHFR gene variation will have lower levels of methionine, and homocysteine can build up to toxic levels, which have been associated with inflammation and heart disease. (25) One of the three requirements for developing Hashimoto’s is having a genetic predisposition. You can read more about genes linked to Hashimoto’s (and how genes are only 25 percent of the equation!) at the linked article.
• Leaky gut: One of the other three requirements for developing Hashimoto’s is considered to be having some degree of leaky gut. While a healthy intestine allows for nutrients to be absorbed and blocks the absorption of pathogens and toxins, a leaky gut does not. The gut barrier is supposed to keep potentially inflammatory proteins from entering our bloodstream, where they can trigger an immune response, even contributing to autoimmunity. In my clinical experience, the amino acid glutamine, essential to proper gut barrier integrity and immune function, is usually depleted in people with Hashimoto’s, as well as those experiencing chronic stress. (26, 27)
• Poor detoxification: The liver is vital for protein synthesis, protein breakdown/utilization, and detoxification, as well as amino acid metabolism. An abundance of amino acids such as glutamate, glycine, alanine, aspartate, serine, threonine, and histidine, are active in the liver. (28) An overwhelmed liver can lead to a buildup of toxins, which can deplete our amino acids, as they are required to help us get rid of toxins.
• Infections: Infections such as H. pylori can prevent the absorption of certain amino acids from our foods, while other infections can potentially increase our requirements for amino acids, like lysine. One study found that L-lysine reduced the incidence of recurrent herpes in Brazil. Lysine can be particularly helpful for improving immune function in communities that are deficient in this amino acid (I discuss lysine in more depth below). Additionally, research has shown that infections can lead to decreased protein within the body, but consuming extra protein (20 to 25 percent more than the recommended intake) can be a complementary method in treating infections. (29, 30)

Now we’ll discuss how these amino acids work in the body to help us on our Hashimoto’s healing journey.

How Amino Acids Support Hashimoto’s

While amino acids are supportive of functions throughout the body and multiple conditions, in this article, I will focus on how having adequate amino acid levels, benefits Hashimoto’s by supporting:

• Healthy thyroid hormone levels
• Gut healing and protection
• Improved detoxification within the body

I’ll also talk briefly about a few amino acids that I recommend for common symptoms seen in Hashimoto’s.

How Amino Acids Support Healthy Thyroid Hormone Levels

Research has found that an insufficient intake of dietary essential amino acids for long periods of time alters thyroid axis activity. (31)

In one case study, primary hypothyroidism was caused by a deficiency of amino acids while the patient was on a protein-calorie restricted diet. When the patient’s diet was changed to include full supplementation of amino acids, the patient saw a rapid increase in both T4 and T3 levels, as well as a decrease in TSH. When the amino acid supplementation was changed to one with depleted phenylalanine and tyrosine levels, serum T4 and T3 levels gradually decreased. When those amino acids were subsequently provided, there was again an increase in serum T4 and T3. (32)

Animal studies have shown a variety of effects on thyroid hormone plasma concentration when amino acid-deficient diets are provided. When phenylalanine was examined in chicks, one study found that its deficiency caused reductions in thyroid hormone plasma levels. (33-35)

Several other amino acids are also associated with a reduction in thyroid antibody levels. For example, the amino acid methionine plays a role in the proper absorption of zinc and selenium. We know that adequate levels of selenium have been associated with a reduction in TPO antibody levels; one study found a 40 percent reduction in antibodies in people with Hashimoto’s, with three to six months of therapeutic doses of selenium. In another study, thyroid antibody levels and zinc levels were also significantly positively correlated. (36, 37)

Another example of an amino acid affecting thyroid antibodies is L-cysteine. The nutritional supplement made from L-cysteine is called N-acetyl cysteine (NAC). NAC supports healthy levels of glutathione by providing the body with cysteine, the rate-limiting factor (a factor that prevents the process from happening more quickly) of glutathione production — thus, depleted cysteine can lead to depleted glutathione. In turn, depleted glutathione levels may contribute to Hashimoto’s and cause higher levels of thyroid antibodies. One 2013 study found that patients with Hashimoto’s had 62 percent lower levels of serum glutathione compared to the control group. The lower the glutathione levels, the higher the levels of TSH and thyroid antibodies were found. (38)

There are hundreds of amino acid ramifications on thyroid hormone levels due to the sphere of influence amino acids have throughout the body — take another look at my graphic above!

Since some form of leaky gut is one of the three requirements for having Hashimoto’s, let’s talk about how our amino acids help us protect and heal the gut as well.

Amino Acids’ Role in Protecting and Healing the Gut

Types and levels of amino acids can affect our body’s gut structure and function. They can prevent and heal leaky gut, as well as influence the diversity and activity of bacteria found in the gut microbiome.

The makeup of the microbiome, which is influenced by diet and nutritional intake, can, in turn, affect the activation and metabolism of various amino acids. For example, poorly digested proteins can be fermented by bacteria in the gut to form amino acid-derived metabolites, such as branched-chain fatty acids (BCFAs) and ammonia, which can have toxic impacts on the intestinal tissue, contributing to leaky gut. Gut dysbiosis can lead to a buildup of ammonia, which has been tied to brain fog, trouble staying asleep, and frequent night wakings. (39-43)

To start on the process of removing ammonia, which is a by-product of pathogenic bacteria, I recommend taking Rootcology Carnitine Blend, S. Boulardii, and Magnesium Citrate Powder. For deeper ammonia removal, I recommend targeted amino acids that help with detoxification, such as NOW Foods Ornithine (500-2000 mg) at bedtime.

The amino acids glutamine and NAC (along with the help of zinc) can be helpful in reducing gut inflammation, restoring intestinal health, and repairing the tight junction integrity of the gut lining.

Glutamine’s role in gut health is well studied. Research has shown that this amino acid provides the previously-mentioned benefits by acting as an energy source for the gut mucosal lining, as well as for the immune system’s cells, preventing bacterial translocation (or the movement of bacteria from the gut to sites outside of the intestines). This amino acid also supports muscle-building processes within the body.

Furthermore, animal and clinical studies have shown that glutamine deficiency leads to villous atrophy (destruction of villi) and mucosal ulcerations (sore lesions) in the small intestine, leading to an impairment in the functioning of immune cells, and resulting in greater susceptibility to infections. (44-46)

As a word of caution, in some individuals, glutamine can lead to the production of excess glutamate (this can act as an excitatory neurotransmitter and lead to anxiety, insomnia, and headaches). I have found that this is often due to a deficiency of B6. This is one of the reasons why I generally also recommend taking vitamin B6 in the P5P form, along with magnesium when taking most amino acids, to ensure proper utilization.

The recommended dose of P5P is usually 50-100 mg/day; please do not use more than 300 mg/day, especially if you use B6 in the pyridoxine form. (B6, especially in the pyridoxine form, is one of the few B vitamins that can lead to toxicity when used in excess.)

Threonine is also important to gut barrier integrity in the small intestine, and I have read some reports of it helping with minimizing reactions to gluten, although I have not studied this in great depth… yet.

Lastly, glycine, which is utilized by the small intestine to synthesize the antioxidant glutathione, along with methionine and cysteine, plays a protective role in intestinal immune and anti-oxidative responses. (47)

Amino Acids’ Role in Improved Detoxification

In addition to gut-related issues, people with Hashimoto’s often have impaired detoxification abilities. Phthalates, parabens, and many other toxins commonly found in the home, such as flame retardants, are chemicals that mimic the effect of estrogen. These endocrine disruptors may increase TSH and perpetuate the autoimmune attack on the thyroid. (48)

A buildup of such toxins often also results in liver congestion. When the liver gets congested, toxins are recycled back into the blood, and may then be stored in our fat. This has important implications when we try to support our liver, as detoxification is a two-phased process. In particular, if Phase II of detoxification is not supported with the necessary amino acids and nutrients, we can actually end up releasing stored toxins from our fat and making our toxin levels even worse (remember that elevated toxins can lead to amino acid depletions).

So let’s talk a bit about the two phases of detoxification.

The Phase I Detoxification Pathway

Phase I of liver detoxification involves the clearing out of toxins that are stored inside our fat cells. This phase utilizes chemical processes like oxidation, reduction, hydrolysis, hydration, and dehalogenation of fat-soluble toxins. There are a number of nutrients needed to support this phase, including vitamins B2, B3, B5, B6, B12, folate, glutathione, and flavonoids. These nutrients clear out the toxins from our fat cells and prepare them for elimination in Phase II. These freed-up toxins can worsen the body’s toxic load if Phase II doesn’t appropriately kick in afterwards to remove them.

The Phase II Detoxification Pathway

Phase II is all about removing the freed-up toxic waste created in Phase I. This phase includes sulfation (adding a sulfo group), glucuronidation (adding glucuronide), glutathione conjugation (pairing), acetylation (adding an acetyl group), amino acid conjugation, and methylation. Amino acids play a pivotal role in the efficiency of Phase II. If the body is deficient in certain amino acids, the pollutants freed up in Phase I can become more toxic.

Phase II needs amino acids and other nutrients, including methionine, cysteine, glutamine, glycine, taurine, magnesium, glutathione, alpha-ketoglutarate, vitamins B5 and B12, vitamin C, folate, and choline. (49) Note that methylation, which occurs during Phase II, will be impaired if you have the MTHFR gene variation.

I have found the use of amino acid supplements to be incredibly helpful in addressing multiple symptoms and root causes (in particular leaky gut and liver congestion) shared by many people with Hashimoto’s, and I’ll talk about one of my favorite blends of amino acids supporting these functions in a moment.

First, how do you know if you are deficient in amino acids?

Amino Acid Deficiency Testing

There are amino acid tests available that may be useful in certain scenarios, such as those involving anxiety and depression disorders, where targeted doses of specific amino acids may be helpful. Testing for amino acid deficiency is also valuable if you experience other symptoms such as reduced immunity and mental alertness, blood sugar imbalances, digestive issues, and food sensitivities.

I recommend The Great Plains Amino Acids Urine Test and the Great Plains Amino Acid Plasma Test, which analyze 40 different amino acids (both essential/conditionally essential and non-essential amino acids), as well as several markers of nutrients (magnesium, B6, etc.) needed for amino acid functions. The tests also provide a thorough explanation of the possible causes of listed deficiencies.

The Root Cause Approach to Getting More Amino Acids

The conventional approach and the root cause approach to getting more amino acids overlap in that both recommend consuming a variety of protein sources and supplementing with amino acids, if needed. However, the root cause approach also emphasizes getting the right kind of protein to fulfill our amino acid needs, optimizing low stomach acid levels, as well as addressing nutrient deficiencies and issues related to MTHFR gene variations.

Get Protein and Amino Acids From Your Diet

Protein is important for Hashimoto’s because it promotes healthy immune function, improves detoxification, helps in healthy gut function, and can help reduce symptoms such as muscle weakness and blood sugar dysregulation.

It’s interesting to note that the body has no protein storage site like it has adipose tissue for storing fat. As such, we do need to take in quality and clean protein (and essential amino acids) each day, through our diet or through supplementation.

It’s important, however, to find sources of protein that we are not sensitive to. I learned that I had been consuming the wrong type of protein in my daily “healthy” protein smoothie, using reactive proteins such as dairy, that were making my autoimmune condition and symptoms worse. I’ve found that dairy proteins (whey and casein) are highly reactive for around 80 percent of my clients with Hashimoto’s. I was actually poisoning myself by using dairy products for my daily protein smoothie, before I realized I had a food sensitivity to dairy!

As such, it’s important to find quality sources of protein and amino acids. Some sources that I recommend for people with Hashimoto’s include fatty fish (such as wild salmon) and organic meats (such as chicken and beef). As many individuals with Hashimoto’s are unable to tolerate whey and eggs, I developed hypoallergenic protein powders such as Rootcology Organic Pea Protein and Rootcology AI Paleo Protein. (You can read more about the right types of protein and what to avoid here.)

In addition to finding the right types of protein, it’s important to adjust our protein intake to our needs as well.

Some rodent studies have actually found that animals may self-select between high-protein diets (shown to decrease overall food intake) and low-protein diets (which tend to increase overall intake) in order to meet healthy protein requirements and avoid diets that are imbalanced in amino acids. Researchers have speculated that perhaps amino acids play a role through physiological mechanisms to prompt animals to take in an adequate supply of protein. I find this fascinating. (50)

Focusing on a diet with healthy fats and proteins, and limiting our carbohydrate intake, can help balance blood sugar and keep us from experiencing those blood sugar highs (and lows) associated with anxiety, lightheadedness, nervousness, and fatigue. Plus, some research suggests that up to 45 percent of people with Hashimoto’s have issues with carbohydrate metabolism. (51)

So what’s the right amount of protein for you?

I generally recommend eating about 1-1.2 grams of protein, per kilogram of body weight, per day (roughly 0.5 grams per pound of body weight), which is higher than the RDA of 0.8 grams per kilogram per day. The amount each individual needs depends on various health factors, including their daily activity level. (52)

Those who have higher activity levels may wish to aim for at least 1.2 grams per kilogram of body weight, per day, and bodybuilders may bump that up to 2 grams. Endurance athletes have an even greater protein requirement. Whereas bodybuilders need 1.12 times more protein than sedentary people, endurance athletes require 1.67 times more protein.

For those with illness or older adults, you may focus on eating 1.2 to 1.5 grams of protein, per kilogram of body weight, per day. (Note that older people with severe kidney disease, estimated GFR <30 mL/min/1.73 m2, but who are not on dialysis, are an exception to this rule; these individuals may need to limit their protein intake.)

Rather than increasing protein intake past appropriate weight and activity levels, taking pure amino acids may be a more viable option for many people. I’ll talk about that in a moment.

First, I did want to at least introduce a specialized (and fairly extreme) diet focused on introducing free amino acids that a practitioner might recommend for someone with more significant protein-related deficiencies.

The Elemental Diet

The Elemental Diet has been traditionally used for rehabilitation of se­verely malnourished individuals, bowel inflammation, and diarrhea.

It is a liquid diet that is free of non-digestible substances such as fiber, complex carbohydrates, and protein structures. It contains our es­sential macronutrients in a state that requires little to no digestion, and results in complete absorption.

It is also composed of free amino acids and fat in liquid form. Amino acids, glucose, fat, and vitamin/mineral supplements are utilized instead of food.

This diet results in reduced secretion of pancreatic and gastric juices, giv­ing the stomach and pancreas a rest from activity, and allowing for heal­ing and reduction of inflammation to take place. As the diet has little residue, it results in slower movements of the GI tract, which speeds up healing.

Additionally, free-form amino acids allow for the body’s own protein to be spared, helping the rest of the body to heal quicker. It also provides no food to pathogenic bacteria, basically starving them. This diet causes a rapid shift in bacte­rial flora within one to two weeks.

Clinical trials have shown this diet is effective in reducing SIBO within two weeks in people with IBS, resulting in a substantial improvement of symptoms. I use it from time to time to expedite healing, especially in people with IBS or small intestinal bacterial overgrowth (SIBO).

The drawbacks of the diet are that amino acids are expensive and taste pretty disgusting if not properly prepared. People report feeling nause­ated after drinking the solution, and aspiration has resulted when people lie down too quickly following ingestion.

Furthermore, commercially available formulas (such as Vivonex®) contain a lot of arti­ficial ingredients that people with Hashimoto’s may not tolerate. They also include loads of carbohydrates, which can cause high blood sugar spikes and may harm adrenal function. Additionally, many of the elemental formulas have added iodine, which can exacerbate Hashimoto’s in excess amounts.

In recent times, the company Integrative Therapeutics came up with a cleaner version of the elemental diet — the Physician’s Elemental Diet. This formulation has become my go-to recommendation for people with Hashimoto’s who are interested in the elemental diet. Please note, Integrative Therapeutics has removed the distribution of this formula from retail channels, as it is an FDA-regulated medical food. As always, I do recommend working with your personal health care provider to ensure this (or any other) intervention is appropriate for you. However, if you and your practitioner are having trouble obtaining this elemental formula, Dr. Siebecker’s homemade elemental diet may be a suitable alternative.

A modified homemade elemental diet is also available in the Companion Guide to my Hashimoto’s: The Root Cause book. However, as this diet requires the purchase of expensive amino acids, it can be quite pricey.

Some critics of the elemental diets also noticed that symptoms sometimes return after a period of time, ranging from months to years. I think this is likely because people go back to their junk food diets too soon. However, if an elemental diet is followed by a grain-free Low FODMAP diet, SCD diet, or similar diet, this could result in permanent remission.

Another option that I have recommended is to try a semi-elemental diet and gradually introduce the elemental diet into your life. For example, you could start off with an elemental smoothie for breakfast, followed by a regular meal at lunchtime and dinner. The next day, you could replace both breakfast and lunch with an elemental smoothie, and move forward from there. My Root Cause Companion Guide contains more information on how to transition to an elemental diet, along with recipes and modifications — and it’s free to download!

If the Elemental Diet resonates with you, it may be something for you to discuss with your doctor depending on your own symptoms, and how other interventions have worked for you.

Address Causes of Low Stomach Acid

Insufficient stomach acid was a huge issue for me, and is common in Hashimoto’s. Without proper amounts of stomach acid, we can’t break down the protein we consume and extract the amino acids from it.

In a 2015 survey I did of 2232 people with Hashimoto’s, some 59 percent of respondents said they felt better after addressing their low stomach acid, by taking betaine HCL with pepsin. Years ago, when I first tried Betaine HCL with pepsin, I felt better after one day!

Note that an H. pylori infection, which is a common root cause trigger in Hashimoto’s, promotes gastric atrophy and can lead to diminished stomach acid levels as well. (53)

So, you may need to dig a little deeper into the cause of your low stomach acid if you find the Betaine HCL doesn’t help. Learn more about betaine with pepsin here.

Address Nutrient Deficiencies

Remember that there are many nutrients that help non-essential amino acids synthesize other amino acids and nutrients. Magnesium and B6 are examples of such nutrients. I always suggest taking these two along with amino acids (be sure to only have up to 300 mg per day of vitamin B6, as higher doses can be neurotoxic). Pyridoxal-5-Phosphate, or P5P, is the active form of B6 – this form may be safer for use with children (but be sure to discuss this with your practitioner to determine dosage recommendations for little ones).

As part of your routine labs, I do suggest people have basic blood testing for some of the common deficiencies we see in Hashimoto’s (including B12, ferritin, zinc, and vitamin D). Please note that tests may not always flag vitamin and mineral deficiencies until our body becomes extremely depleted. I like the NutrEval test for testing multiple nutrient deficiencies. SpectraCell labs offers an advanced mineral testing option as well.

If you are indeed deficient in nutrients such as selenium, zinc, and B12, check out the linked articles on each of them to learn about what you can eat and how you can supplement, to get more of these important thyroid-supportive nutrients and optimize your levels.

Address MTHFR Gene Issues

When I see clients with symptoms such as multiple chemical sensitivities, anxiety, depression, irritability, and brain fog, I will sometimes suspect impaired methylation and may recommend testing for the MTHFR gene variant.

Should you test positive for this gene variation, and find that you do indeed have issues relating to methylation, I recommend taking Rootcology MTHFR Pathways, as it contains nutrients (B vitamins, trimethylglycine, or TMG, NAC) that can help lower homocysteine levels and support healthy homocysteine metabolism.

In my 2015 survey, 45 percent of people with Hashimoto’s said they felt better after adding methylation-supporting supplements to their regimen. Having a healthy homocysteine metabolism helps ensure we have adequate amounts of other amino acids such as cysteine and taurine, as well as neurotransmitters norepinephrine and dopamine, on board. You can read more in the linked article.

Again, I generally assume most people with Hashimoto’s may need some support in the areas of protein digestion, leaky gut, and detoxification. As such, addressing these areas is a good place to start.

Amino Acid Supplementation for Improved Liver Detoxification and Gut Health

Along with having people eat the right protein and address potential root causes of amino acid deficiency such as low stomach acid and nutrient deficiencies, I always recommend that readers and clients initially prioritize supporting their liver and their gut health. These two things can make a world of difference to one’s thyroid health and how one feels each and every day. (Learn more about both of these in the linked articles above.)

Additionally, I like a product from Rootcology called Amino Support.

This supplement blend contains L-glutamine and NAC, which protect and heal the gut. It also provides the amino acid support necessary for optimal Phase II detoxification in the liver. (Amino Support does not contain B vitamins, botanicals, or minerals that stimulate Phase I metabolites that could cause increased toxin overload or sensitivity reactions.)

Rootcology Amino Support also helps the body bind and remove heavy metals.

Here are the nutrients found in Rootcology Amino Support:

• L-glutamine – L-glutamine protects and heals the intestinal barrier and gut function. It also helps support immune function. It is the precursor in the synthesis of other amino acids such as arginine, as well as the antioxidant glutathione. L-glutamine is vital to supporting optimal Phase II detoxification and helps stabilize blood glucose levels. Like many amino acids, it also has a role in gene expression. In one study, glutamine increased the intestinal expression of genes (by 120-124 percent) that are necessary for cell growth and the removal of oxidants, while reducing the expression of genes (by 34-75 percent) that promote oxidative stress and immune activation. (54)

• Glycine – Glycine helps with improving sleep. A study found that glycine subjectively and objectively improved sleep quality in people who suffered from insomnia. It also regulates neurological function, supports the production of the antioxidant glutathione, and has been associated with improved insulin sensitivity. Better sleep means a better mood and less brain fog. (55, 56)

• Methylsulfonylmethane (MSM) – Although not an amino acid, MSM helps with sulfation in phase II of liver detoxification — it acts as a sulfur source for the production of the amino acids methionine and cysteine, which are involved in the detoxification process (more on that later on). MSM has been shown to exhibit anti-inflammatory, antioxidant, and anti-cancer activity. In animal studies, MSM inhibited cortisol-induced stress in skeletal muscle cells. (57)

• N-Acetyl-L-Cysteine (NAC) – The sulfur-based amino acid L-cysteine is important for healing leaky gut as well as supporting Phase II detoxification (via sulfation). NAC, a derivative of L-cysteine, has been shown in research to protect the liver from toxic effects due to acetaminophen poisoning and alcohol. As mentioned previously, cysteine is critical in the production of glutathione. NAC raises glutathione levels (depleted glutathione levels have been associated with higher levels of thyroid antibodies) and prevents oxidative damage. It is also effective in detoxing heavy metals such as mercury from the body. (58)

*A note about NAC:

Per a July 2020 warning letter from the FDA, there is currently some debate on whether or not NAC can be sold as a supplement, because it was approved for use as a drug in 1963.

Last year, Amazon removed NAC-containing products from its website, presumably in response to the warning letter.

In response, the Natural Products Association (NPA) reached out to Amazon to let them know that the issue was not closed with the FDA, and that NAC is a product that has dual uses as both a drug and a supplement, like many other products on the market (such as niacin, fish oil, and potassium, which can be sold as over-the-counter supplements, or prescribed by a medical professional). The Council for Responsible Nutrition filed a citizen petition on June 1st, 2021 asking the FDA to reverse its position that NAC cannot be lawfully marketed in dietary supplements. 

On March 31st, 2022, the FDA denied the NPA petition as well as another one submitted by the Council for Responsible Nutrition (CRN). However, the FDA has still not decided whether to create new rules around the use of NAC in dietary supplements. That request from the petition is still in review. At the time of writing, the FDA has so far noted an “absence of safety concerns based on their review to date” and is “considering exercising enforcement discretion” regarding the sale and distribution of (at least some) NAC-containing supplement products. (59-62) 

I’ll be sure to let you know when I learn more about the status of NAC on the market. In the meantime, I am stocking up on NAC-containing supplements, and telling friends and family to do the same!

• Taurine – Taurine is a multi-tasking amino acid that is also an antioxidant, a neurotransmitter, and an osmoregulatory molecule that facilitates the retention of magnesium and potassium. This sulfur-containing amino acid is a component of bile and can increase bile flow, helping to ensure healthy liver function. It also supports the sulfation pathway of detox and is involved in immune system regulation and anti-oxidation functions. Animal studies have shown taurine to be able to reverse both thyroid and kidney damage in rats that have been chronically exposed to high levels of fluoride (and we know fluoride is a trigger for Hashimoto’s). One review paper found taurine reduced thyroid damage due to exposure to industrial insecticides and lead; taurine was also found to play a protective role against neurodegeneration by reducing the toxic effects of some metals. (63)

• Alpha-Ketoglutarate (AKG) – AKG has antioxidant properties and is a major source of energy for the body. It plays an important role in general immune system metabolism. AKG is also a precursor of glutamine and glutamate, which stimulate protein synthesis. Furthermore, AKG can decrease protein degradation in muscles, and plays a protective role in the gut. (64)

• L-glutathione – L-glutathione is the body’s master antioxidant and is involved in numerous critical functions, including immune response, antioxidant defenses, gene expression, nutrient metabolism, and other cellular functions. It is a free-radical scavenger and protects the body against oxidative stress. Chronic inflammation (due to poor diet, infections, stress, etc.) can deplete levels and has been implicated with higher levels of TPO antibodies, as well as higher TSH. Precursors to L-glutathione are NAC and glutamine. (65)

• L-methionine – This is a sulfur-containing amino acid that helps build protein, synthesizes other critical amino acids (cysteine and taurine), and produces important molecules in the body, including glutathione and a naturally-occurring antidepressant called S-Adenosyl-L-methionine (SAMe – low levels have been found in liver disease and depression). SAMe is a methyl donor for several molecules such as homocysteine, serine, creatine, and epinephrine. Methionine and the amino acid lysine combine to form carnitine (more on the importance of carnitine later on in the article). Methionine is important for Phase II detoxification (it supports the sulfation pathway) and helps with the absorption of two vital thyroid nutrients, selenium, and zinc. It also reduces levels of histamine, which can help promote sleep. Methionine can help support mood by supporting healthy levels of SAMe. Methionine metabolism is dependent on adequate levels of B12, B6, magnesium, and folate. People with methionine deficiency may have poor detoxification of xenobiotics and sulfhydryl reactive metals (mercury, lead, arsenic, and cadmium), or present with fatty liver or biliary insufficiency occlusive arterial disease. Other symptoms of deficiency may include inflammation, headaches, skeletal disorders, and nearsightedness. (66)

• L-ornithine – L-ornithine has been found to enhance the detoxification of ammonia in the body. Ammonia is a waste product made by the body during protein digestion and can be made by certain pathogens common in Hashimoto’s. (Ammonia is normally processed by the liver and transformed into another waste product called urea; urea is removed from the body in urine; a congested liver may result in an ammonia backlog.) L-ornithine has also been found to relieve stress, reduce fatigue and improve sleep quality, boost growth hormone (which happens mainly after the onset of sleep), and have a positive effect on the body’s cortisol/stress response. It may help maintain the body’s circadian rhythm as well. (67, 68)

• Calcium-D-Glucarate (CDG) – CDG is a modified version of glucuronic acid. Glucuronic acid supports Phase II detoxification by preventing the recycling of certain hormones (such as estrogen) and undesirable fat-soluble toxins (via the glucuronidation detox pathway), and excreting them through the bile or urine. Elevated beta-glucuronidase activity has been associated with an increased risk for various hormone-dependent cancers such as breast, colon, and prostate cancers. The supplement CDG is viewed as a potential clinical application for the regulation of estrogen metabolism and as a lipid-lowering agent (it helps maintain normal cholesterol levels). (69)

Precautions for Rootcology Amino Support

Amino Support should not be used by those with a sulfur sensitivity. Do not use if pregnant or breastfeeding (in these cases, it may be beneficial to consume a variety of whole foods and/or animal protein sources to get beneficial amino acids such as arginine; please discuss with your healthcare practitioner if unsure), if you plan to consume alcohol, or if you are allergic or sensitive to any of the ingredients in this supplement.

Do not take this product if you are taking the following medications: ACE inhibitors, anticoagulant/antiplatelet drugs (including warfarin), anticonvulsants, antihypertensive drugs, blood thinners, chloroquine, clozapine, glucuronidated drugs, lactulose, lithium, and/or nitroglycerin.

Amino Support is often used in conjunction with other supplements, to support detoxification — I typically use it as part of my Liver Reset Protocol. In some cases, I may also recommend binders like activated charcoal, with detox protocols. While the two can be used together on the same day, it’s important to space them out by at least three hours, as activated charcoal can impair the absorption of amino acids (and everything else, for that matter!).

Other Noteworthy Amino Acids

While I can’t go through the hundreds of other amino acids and their many health benefits here in this article, let me just point out a few additional ones that I have successfully used for clients.

Arginine – Because L-arginine acts as a vasodilator, dilating or opening up blood vessels, many people take L-arginine to treat heart conditions, high blood pressure, and erectile dysfunction. I have used it to treat resistant Blasto infections, but be aware that it may reactivate the Epstein-Barr virus and should always be taken with lysine and under the guidance of a practitioner.

• The amino acid arginine lowers blood pressure. It is used to make a potent vasodilator called nitric oxide. Vasodilators relax the inner muscles of our blood vessels, causing the vessels to widen. This increases blood flow and lowers blood pressure (both markers of improved vascular health).
• Arginine (alongside L-citrulline) may help improve outcomes related to pregnancy. Some studies have shown that L-arginine infusions may lower blood pressure in pregnant women who develop high blood pressure. This is due to arginine’s role in nitric oxide production (explained above) — improved vascular health in pregnancy will help with healthier, less inflamed placentas, leading to an improvement in growth restriction and low birth weight.
• Low arginine appears to play a role in the pathogenesis of a number of varied diseases, including cardiovascular disease, acute asthma, pulmonary hypertension, cystic fibrosis, sickle cell disease, trauma, and certain cancers, among others.
• Arginine is essential for maximum neonatal growth and embryonic survival. It’s also important in infancy, as it provides intestinal barrier integrity. (70-72)

Lysine – Lysine is a component of several structural proteins and enzymes. As mentioned previously, this amino acid can help prevent the recurrence of herpes. Additionally, it is required for several processes such as the transamination (or relocation) of amino acids. A deficiency in this amino acid can limit the activity of vitamin B6. In some cases, individuals who show signs and symptoms (poor dream recall, loss of muscle tone, weight loss, poor appetite, as well as muscle weakness) of B6 deficiency, may actually be deficient in lysine instead. Lysine is mainly found in animal protein sources. While lysine is found in some legumes, most plant sources are lacking in this amino acid, making vegetarians and vegans more susceptible to lysine deficiency. This can be detrimental, especially for children who generally require 10 mg per kg of body weight of lysine.

Tyrosine – The amino acid tyrosine is a precursor of the thyroid hormone thyroxine and several neurotransmitters (dopamine, norepinephrine). L-tyrosine has been found to enhance positive mood and cognitive function, especially in situations involving stress. (Because tyrosine can be beneficial to our health in a multitude of ways, I added it to Rootcology Adrenal Support.)

However, please note that the use of tyrosine supplementation is a bit controversial in Hashimoto’s.

While tyrosine may increase the production of thyroid hormones, it may also increase adrenal hormone production, which can be problematic if a person has overactive adrenals and excessive cortisol stress hormone levels (which most people do). Small amounts of tyrosine from protein food sources or elemental diet formulas might not cause problems, but I would recommend exercising caution with taking high-dose tyrosine supplements, and you should definitely discuss with your doctor before considering tyrosine supplementation.

Lastly, tyrosine (along with other nutrients) is used to make the antioxidant COQ10. This antioxidant, especially when taken with other beneficial amino acids such as L-carnitine, has many benefits such as supporting mitochondrial function and heart health. I recommend 200-500 mg per day of COQ10.

Tryptophan – Tryptophan is a precursor to the neurotransmitter serotonin. Inflammation can trigger your brain to convert it into anxiety-provoking chemicals instead of serotonin (happy!) and melatonin (sleep!) neurotransmitters. Tryptophan requires that vitamin B6 be converted to serotonin, and as such, some people with low B6 levels may be deficient in this amino acid.

One study found that subjects consuming higher levels of tryptophan had significantly less irritability and depression and decreased anxiety than when they consumed lower levels. It is sometimes used in treating people with seasonal affective disorders. (73)

I am finding more and more research relating to mood, anxiety, depression, and psychiatric conditions, where doctors are using amino acids as a therapy to help support mental health. (74)

To me, this is fascinating — and makes complete sense, given the role of amino acids in neurotransmitter metabolism. (I may add this topic to my growing list for future articles… stay tuned!)

Let me know if your doctor has recommended amino acid therapy for mood-related conditions and how it has worked for you.

Final Thoughts on Amino Acids

Amino acids are found in the protein we eat and are manufactured in our bodies from other amino acids, as well as key nutrients such as B12, selenium, and zinc. People with Hashimoto’s are often affected by poor protein digestion, either due to diet choices (high carb diets or inflammatory protein choices such as dairy), low stomach acid, or nutrient deficiencies. (As discussed, certain deficiencies affect the health of our gut microbiome or our body’s ability to detox.)

Amino acids are vital for many different processes and bodily functions, and detoxification is one of them. Poor detoxification is a common issue in Hashimoto’s. In particular, we need to support our liver’s Phase II detoxification pathway to ensure toxins released from our body’s fat storage in Phase I are not released and recycled, adding to our liver’s already toxic load. Upping our amino acid levels can help support this process of detoxification.

Along with eating the right diet with the right amount of protein, we can take in amino acids such as those found in the Rootcology Amino Support blend. This supplement is designed to target several key health issues likely contributing to your Hashimoto’s, including gut health and poor liver detoxification. It’s a supplement I have found to be very helpful with my clients and readers. Depending on your own unique health situation (such as having the MTHFR gene variation or being deficient in a nutrient like selenium or B12), you may benefit from additional supplementation support.

Always discuss new supplements with your doctor, as they know your particular health situation and will know whether taking additional amino acids would be appropriate for you.

Remember to take your healing journey one step at a time — making a series of small changes and paying close attention to what your body needs will help you understand what’s working best to help you heal. Also remember that the journey may look different for everyone.

If you feel frustrated along the way, please don’t give up… you’ll get there. I know you can do it.

Let me know if you find that poor protein digestion has been an underlying issue for your healing, and what strategies you have found to be useful. I love to share people’s successes with our community so that others can benefit.

For future updates, make sure to follow us on Facebook and Instagram!

P.S. You can also download a free Thyroid Diet Guide, 10 thyroid-friendly recipes, and the Nutrient Depletions and Digestion chapter of my first book for free, by signing up for our newsletter. You will also receive occasional updates about new research, resources, giveaways, and helpful information.

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Originally published in 2021, this article has been revised and updated for accuracy and thoroughness.