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Gut Microbiota, Hashimoto’s, and Hypothyroidism

Understand how the relationship between gut bacteria and your thyroid may help improve treatments for Hashimoto’s and hypothyroidism.
Gut Microbiota, Hashimoto’s, and Hypothyroidism
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In recent years, interest has increased in the relationship between gut microbiota – the bacteria and organisms that populate our gut – and various health conditions. Hypothyroidism – and Hashimoto’s autoimmune disease that frequently causes it –have emerged as a significant area of focus. Hypothyroidism, characterized by an underactive thyroid gland leading to insufficient production of thyroid hormones, can profoundly impact your metabolism, energy levels, and overall well-being. With a greater understanding of the role of gut microbiota in hypothyroidism and Hashimoto’s and new studies that identify the specific beneficial and detrimental gut bacteria, we can gain insight into potential treatment strategies to address the gut-thyroid axis.

Understanding hypothyroidism

Hypothyroidism occurs when the thyroid gland can’t produce enough thyroid hormone, primarily thyroxine (T4) and triiodothyronine (T3). These hormones are crucial regulators of metabolism and influence various processes, including heart rate, body temperature, and energy production. Common symptoms of hypothyroidism include fatigue, weight gain, depression, and sensitivity to cold.

The most common cause of hypothyroidism is the autoimmune thyroid disease Hashimoto’s thyroiditis, where the immune system mistakenly attacks the thyroid gland and ultimately affects levels of thyroid hormone. Other causes include iodine deficiency, some medications, radioactive iodine treatment, and surgical removal of the thyroid gland. Traditionally, the management of hypothyroidism involves thyroid hormone replacement medication, where thyroid hormone is taken to restore normal thyroid levels. However, emerging research suggests that gut health plays a pivotal role in the development and management of an underactive thyroid.

Gut microbiota: an overview

Your gut is home to trillions of microorganisms, collectively known as the gut microbiota. These microorganisms, predominantly bacteria – but also viruses and fungi –play a critical role in maintaining your overall health. Your gut microbiota play a role in digestion, absorption of nutrients, synthesis of vitamins, immune modulation, and protection against pathogens.

A balanced gut microbiota is essential for health, but your diet, antibiotics, stress, infections, and inflammation can disrupt this balance, leading to a state known as dysbiosis. Dysbiosis has been linked to health conditions, including inflammatory bowel disease, obesity, diabetes, and even mental health disorders. Recent studies have also started to explore the connection between gut microbiota and your thyroid, suggesting that the gut-thyroid axis could be a crucial pathway influencing hypothyroidism and autoimmune Hashimoto’s disease.

The gut-thyroid axis

The relationship between gut microbiota and hypothyroidism is bidirectional. This means that gut microbiota can influence thyroid function, and thyroid dysfunction can also alter the gut microbiota composition. This bidirectional interaction is often referred to as the “gut-thyroid axis,” highlighting the reciprocal influence between these two systems.

The relationship between gut microbiota and hypothyroidism is complex and multifaceted, involving various mechanisms and interactions.

Mineral absorption

Gut microbiota play a crucial role in the absorption and processing of essential minerals such as iodine, selenium, and iron, which are important for thyroid function. These minerals are vital for the synthesis and metabolism of thyroid hormones.

Thyroid hormone metabolism

Gut bacteria are involved in the metabolism of thyroid hormones. Specifically, certain gut bacteria produce enzymes that participate in the conversion of thyroid hormone T4 (thyroxine) into T3 (triiodothyronine), as well as the storage of thyroid hormones, potentially affecting their bioavailability and activity. Gut microbiota can also potentially affect the efficacy of medications used to treat hypothyroidism.

Immune modulation

Gut microbiota help to modulate your immune system. Dysbiosis can lead to an overactive immune response, potentially triggering autoimmune conditions such as Hashimoto’s thyroiditis. Studies have shown that people with Hashimoto’s thyroiditis often have changes in gut microbiota composition, with fewer beneficial bacteria and too many more harmful bacteria.

Nutrient absorption

Your ability to produce thyroid hormones requires specific nutrients, including iodine, selenium, and zinc. The gut microbiota facilitates the absorption of these nutrients from the diet. Dysbiosis can impair your ability to absorb nutrients and lead to deficiencies that may worsen hypothyroidism and Hashimoto’s.

Gut barrier integrity

A healthy gut microbiota maintains the integrity of your gut barrier and its ability to prevent harmful substances from entering your bloodstream. Dysbiosis can compromise this barrier, resulting in increased intestinal permeability, better known as “leaky gut.” This condition allows toxins and antigens to cross into your bloodstream, potentially triggering autoimmune reactions, including those against the thyroid gland.

Evidence linking gut microbiota and hypothyroidism

Research provides compelling evidence supporting the link between gut microbiota, Hashimoto’s, and hypothyroidism.

One study published in BMC Microbiology found that patients with Hashimoto’s thyroiditis, an autoimmune condition that can lead to hypothyroidism, exhibited distinct gut microbiota profiles compared to healthy controls. The study observed a lower diversity and richness of gut microbes in Hashimoto’s thyroiditis patients, suggesting a potential link between gut dysbiosis and autoimmune thyroid disorders.

A study published in Endocrinology, Diabetes and Metabolism analyzed the gut microbiota of patients with hypothyroidism. The results showed an increased abundance of Veillonella, Paraprevotella, Neisseria, and Rheinheimera in hypothyroid patients compared to healthy individuals.

Another study published in BMC Microbiology found that patients with Hashimoto’s thyroiditis, the autoimmune thyroid condition that can lead to hypothyroidism, exhibited distinct gut microbiota profiles compared to healthy controls. The study found a lower diversity and richness of gut microbes in Hashimoto’s thyroiditis patients, suggesting a potential link between gut dysbiosis and autoimmune thyroid disorders.

A recent study of beneficial and detrimental bacteria

In a recent study published in 2024 in the journal Frontiers in Nutrition, researchers explored the association between gut microbiota and hypothyroidism.

The study found several types of bacteria, including Akkermansia, Ruminococcaceae, Butyrivibrio, and Holdemania exhibit protective effects against hypothyroidism. At the same time, Anaerostipes, Intestinimonas, and Ruminiclostridium were detrimental to hypothyroidism.

Let’s look at these bacteria in greater detail to understand their role in thyroid function.


The 2024 Frontiers in Nutrition study found that increased Akkermansia levels inhibited the incidence and progression of hypothyroidism.

Akkermansia is a unique strain of bacteria that resides in the human gut and plays a crucial role in maintaining gut health and overall well-being. Akkermansia accounts for up to 4% of the intestinal bacteria in a healthy gut.

Akkermansia has several benefits:

  • It strengthens the intestinal lining, boosts the protective mucus layer, and regulates the immune system.
  • It helps prevent leaky gut and inflammation.
  • The presence of Akkermansia is associated with lean body weight, improved metabolic health, and reduced risk of obesity, diabetes, and inflammatory diseases.

Akkermansia levels can be increased in several ways:

  • Supplementation – some supplements include Akkermansia alone or in combination with other probiotics and prebiotics
  • While Akkermansia is not found in food specifically, it feeds on dietary fibers and polyphenols from plant-based foods, so a diet rich in polyphenols (e.g., fruits, vegetables, nuts, seeds) and prebiotic fibers can help boost Akkermansia levels.

Ruminococcaceae UCG-011

Ruminococcaceae UCG-011 is a bacteria found in the gut microbiome that benefits gut health.

The benefits of Ruminococcaceae UCG-011 include:

  • It helps digest fibrous plant material
  • It ferments fiber into short-chain fatty acids like butyrate, which has anti-inflammatory effects and promotes a strong gut barrier
  • It helps produce compounds known as enterolignans that have antioxidant effects

There are several ways to increase the levels of Ruminococcaceae UCG-011:

  • Eat a diet high in fiber and vegetarian or heavily plant-based diet, with a high intake of fruits, vegetables, whole grains, and legumes
  • Avoid inflammatory foods, like animal products and processed foods
  • Supplementation with broad-spectrum probiotics. Some custom-formulated probiotics may also include strains of Ruminococcaceae.


Butyrivibrio is a type of anaerobic bacteria found in the gastrointestinal system. Butyrivibrio has several benefits:

  • Produces butyric acid, which helps break down plants.
  • Improves the fatty acid profile of milk and meat.
  • It may help protect against weight gain.

There are several ways to increase levels of Butyrivibrio in the gut:

  • Triphala, an ayurvedic herbal medicine used in digestive health, can help increase Butyrivibrio
  • Dietary supplementation with Butyrivibrio fibrisolvens F7, combined with a high linoleic acid diet
  • Pomegranate extract helps boost levels of Butyrivibrio and other helpful bacteria like Lactobacillus and Prevotella


Holdemania is associated with several illnesses, including Parkinson’s disease and delirium. Hypothyroidism, characterized by reduced thyroid hormone levels, can lead to neuropsychiatric symptoms.

Excessive alcohol consumption is associated with elevated levels of Holdemania in the gastrointestinal tract, reducing butyric acid concentration.

Holdemania is an anaerobic bacteria that has some benefits for health:

  • It breaks down sugars
  • It is found in abundance in a healthy human gut microbiome

To increase levels of the gut bacteria Holdemania, you can follow several dietary strategies:

  • Increase your consumption of foods rich in resistant starches. These include:some text
    •    Oats
    •    Rice (especially when cooked and cooled)
    •    Beans and legumes, especially white beans and kidney beans
    •    Lentils
    •    Potatoes (raw or cooked and cooled)
    •    Green bananas and plantains
    •    Whole grains like barley and sorghum
    •    Quinoa
    •    Cashews
  • Consume more polyunsaturated fatty acids – Higher intake of polyunsaturated fatty acids was associated with elevated levels of Holdemania in the gut microbiome
  • Eat a diet rich in fiber, especially from plant sources like nuts, seeds, and vegetables

The detrimental bacteria: Anaerostipes, Intestinimonas, and Ruminiclostridium5

Anaerostipes is an anaerobic bacteria that is generally considered to have positive benefits. While the research has shown that higher levels of Anaerostipes may contribute to the development of hypothyroidism, it’s not clear if reducing this bacteria would be beneficial. More research is needed to determine if regulating the levels of these bacteria could serve a therapeutic function in thyroid disease.

Intestinimonas is an anaerobic, butyrate-producing bacteria found in the gastrointestinal tract. Its primary function is to break down and ferment sugars. It’s considered a beneficial bacteria,

Ruminiclostridium is an anaerobic bacteria that uses cellulose, glucose, and xylose as energy sources. An abundance of this bacteria has been linked to obesity, cardiometabolic traits, and insulin irregularities.

Ruminiclostridium can be reduced with various dietary interventions, including:

  • Increasing resistant starch intake
  • Following a Mediterranean diet
  • Consume prebiotic foods, including garlic, onions, leeks, asparagus, and Jerusalem artichokes
  • Increase fiber intake
  • Reduce processed and high-fat foods
  • Stay hydrated
  • Manage stress and improve sleep

Other potential treatment implications

Understanding the relationship between gut microbiota and hypothyroidism opens up new avenues for potential treatments. In addition to focusing on increasing the beneficial bacteria and reducing the detrimental bacteria discussed earlier, other strategies can be explored.

Other probiotics and prebiotics

Supplementing with other probiotics and prebiotics (non-digestible fibers that feed beneficial bacteria) can help restore a healthy and balanced gut microbiota. Specific strains of probiotics, such as Lactobacillus and Bifidobacterium, have shown promise in improving general gut health and immune function, potentially benefiting individuals with hypothyroidism.

Dietary interventions

Diet plays a crucial role in shaping the gut microbiota. A diet rich in fiber, fruits, vegetables, and fermented foods can promote a diverse and balanced gut microbiota. Additionally, reducing the intake of processed foods, sugars, and artificial additives can help prevent gut dysbiosis.

You’ll also want to read a helpful article on the Paloma blog, How To Starve Bad Gut Bacteria For Better Thyroid Health.

Nutrient supplementation

Ensuring you get an adequate intake of essential nutrients involved in thyroid hormone synthesis and regulation, such as iodine, selenium, and zinc, can support your thyroid function. Supplementing may be particularly beneficial for people who have absorption issues due to gut dysbiosis.

Targeted antibiotics

In cases of severe dysbiosis, targeted antibiotic therapy may be needed to reduce harmful bacteria and allow beneficial bacteria to thrive. However, this approach must be carefully managed to avoid further disrupting the gut microbiota.

Fecal microbiota transplantation

Fecal microbiota transplantation (FMT) involves transplanting fecal matter from a healthy donor into the gut of a patient with dysbiosis. FMT is a promising therapeutic approach that is currently being explored as a way to restore a disrupted gut microbiome in patients with Hashimoto’s and hypothyroidism. The goal is to potentially halt disease progression and dampen autoimmunity. Currently, the IMITHOT trial is being conducted to evaluate the effectiveness of FMT for autoimmune hypothyroidism. If successful, this study could provide high-quality evidence for distinct patterns within the gut microbiota associated with improved thyroid function. This may open avenues for future clinical applications of microbial-targeted therapy in at-risk people.

A note from Paloma

The relationship between gut microbiota, hypothyroidism, and Hashimoto’s represents a fascinating and rapidly evolving field of research. The gut-thyroid axis underscores the importance of gut health in maintaining thyroid function and highlights the potential for innovative therapeutic approaches. While more research is needed to fully understand the mechanisms underlying this relationship, current evidence suggests that maintaining a healthy gut microbiota through diet, probiotics, and other interventions could play a significant role in managing hypothyroidism.

The emerging understanding of the gut-thyroid axis is also opening up new avenues for potential therapeutic interventions in hypothyroidism. Strategies aimed at modulating the gut microbiota, such as the use of probiotics, prebiotics, or fecal microbiota transplantation, may hold promise in managing or preventing hypothyroidism.

Paloma’s team of practitioners, nutritionists, and health coaches consider nutrition and gut health important factors in people’s overall health and wellness with Hashimoto’s and hypothyroidism. Consider becoming a Paloma member to explore how to best integrate the latest nutrition and gut health findings into your wellness plan.


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Mary Shomon

Patient Advocate

Mary Shomon is an internationally-recognized writer, award-winning patient advocate, health coach, and activist, and the New York Times bestselling author of 15 books on health and wellness, including the Thyroid Diet Revolution and Living Well With Hypothyroidism. On social media, Mary empowers and informs a community of more than a quarter million patients who have thyroid and hormonal health challenges.

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