The Thyroid and Immune Benefits of Probiotics

by Mary Shomon Patient Advocate

Probiotics are a hot topic in health today, and it’s common to read that probiotics are recommended for people with autoimmune diseases — including autoimmune thyroid conditions like Hashimoto’s thyroiditis and Graves’ disease. The key question, however, is how can you harness the power of probiotics? Is it enough to eat more yogurt or pop some acidophilus capsules from the grocery store aisle?

I had the opportunity to speak by phone with Kiran Krishnan, a renowned microbiologist, and one of the world’s leading researchers and experts on probiotics. He has spent more than a decade studying various strains of bacteria to assess their effectiveness in probiotic therapy and formulating specialized probiotic products.

Krishnan explained that one trigger for autoimmune diseases — including Hashimoto’s thyroiditis and Graves’ disease — is the ability of toxins to pass through an inflamed intestinal lining and enter your bloodstream. Your intestinal lining becomes inflamed for a variety of reasons:

  • You eat foods that trigger your allergies or sensitivities (like gluten, for example).

  • You eat high-fat, high-calorie foods.

  • You eat foods that are genetically modified, and/or contain hormones and pesticides

  • You eat high amounts of processed foods and simple carbohydrates, such as sugar.

  • You have an imbalance of bacteria in your gut with an overgrowth of “bad” bacteria and/or a deficiency of “good” bacteria, known as dysbiosis, or small intestine bacterial overgrowth (SIBO). This can be a side effect of overuse or chronic use of antibiotic drugs.

According to Krishnan, any sort of autoimmune disease almost always starts with dysfunction in your immune system, and 80 percent of our immune tissue is in the digestive tract. Once you have inflammation, you are at risk of developing a condition known as “metabolic endotoxemia.”

Metabolic endotoxemia is defined as the presence of endotoxins in your blood. These endotoxins can negatively affect your immune system, increase the permeability of your intestinal lining, as well as the makeup of the bacteria in your gut. Endotoxins can also raise your triglyceride levels, and increase levels of cytokines and inflammation. Metabolic endotoxemia is increasingly becoming recognized as a key trigger for obesity, type 2 diabetes, heart disease, inflammatory bowel disease, immune dysfunctions, and autoimmune disease.

Over time, chronic inflammation and metabolic endotoxemia in your intestinal lining can lead to permeability — the ability of larger toxins and particles to cross over that lining and enter your bloodstream. It’s like a window screen that has holes in it. This condition is referred to as “leaky gut.”

While some people with leaky gut have symptoms such as gas, bloating, stomach pain, and digestive issues, not everyone has these symptoms. For some people, the toxins cause immune activation, which can trigger the production of antibodies and an exaggerated immune response that results in an attack on their own organs, glands, tissues or cells — a characteristic of autoimmune disease.

Says Krishnan: “Your gut is the largest source of sampling of the environment around you, and the decisions regarding how to react are often made in the gut. We know probiotic bacteria can affect how the immune system functions. As a result, knowing that autoimmune thyroid is immune-based, and a vast amount of control is coming from the gut, it makes sense for people with autoimmune thyroid disease to include a probiotic supplement.”

One study showed that people with hyperthyroidism have much lower levels of probiotic bacteria compared to healthy people. We also know that since the majority of hypothyroidism is due to autoimmunity, there is a similar immune activation component. SIBO is also common in people with hypothyroidism.

Probiotics for leaky gut and immune protection

Many experts recommend that people with autoimmune thyroid disease eat probiotic-rich fermented foods or take typical probiotic supplements (like acidophilus and bifidobacterium).

Fermented foods are a healthy part of your diet. The fermentation process creates beneficial enzymes and vitamins in the food and by essentially pre-digesting them, makes them more digestible and nutritious. Fermentation also creates probiotic bacteria. Some popular fermented foods include sauerkraut, kimchi, plain yogurt, kefir, kombucha, and miso.

The challenge, however, according to Krishnan, is that most of the probiotic bacteria in fermented foods do not survive the gastric system and stomach acids and are dead on arrival or rapidly die. Says Krishnan: “Probiotic foods are not an effective delivery system for probiotics. They have benefits, but effective delivery of live bacteria is not one of their key benefits.”

According to Krishnan, by scientific standards most probiotic foods and supplements don’t even qualify as “probiotics,” but rather are metabolic response modifiers. They have some benefit in improving digestion and absorption of nutrition from food but don't have a powerful capability to counteract negative strains of bacteria and rebalance gut dysbiosis, reduce inflammation, or effectively heal a permeable gut.

Understanding probiotics

According to Krishnan, there are three categories of probiotic bacteria that are readily available on the market.

Reseeding bacteria: The first category is referred to as “reseeding” bacteria like the acidophilus and lactobacillus found in yogurt and many supplements. They can improve digestion and constipation, but most of them are unable to survive your stomach acid, bile salts, and pancreatic enzymes. This makes them unable to colonize your gut for any length of time, or create any significant metabolic or intestinal lining changes.

Semi-transient bacteria: The second category is semi-transient bacteria. These bacteria are designed to colonize your gut for a period of time, have a metabolic effect, and then naturally leave your body. Says Krishnan: “It’s as if they come to your house, stay a little while, fix it, clean up, and leave.”

Spore-based bacteria are semi-transient bacteria, which over millions of years have developed a natural ability to survive the gastric system. According to Krishnan: “In the past, people got their probiotics from food they ate. Most of the bacteria died as they passed through the gastric system, but some didn't.

These strains developed protective shells, known as spores, that enabled them to survive inside and outside the body and to reach the intestines. They are typically found in the soil. Today's food, however, is highly sterilized, and our exposure to these spore-based bacteria is very limited in the modern diet.”

Spore-based strains of bacteria have the ability to kill bad bacteria and fungus and modulate your immune system. According to Krishnan, the biggest advantage of spore-based probiotics is that they are resistant to stomach acids, are stable at room temperature, don’t require special handling or refrigeration, and deliver more viable bacteria to the small intestine.

Transient bacteria: The third category is completely transient bacteria. They don't colonize, but as they pass through your system, they stimulate and upregulate the immune system and then leave the body.

Spore-based bacteria and probiotics

Most of the market for probiotics is focused on creating supplements that have more of the reseeding or transient bacteria, or higher numbers of bacteria, known as CFUs. According to Krishnan, however, the most promising and underutilized area of probiotic therapy for autoimmune disease patients is spore-based semi-transient bacteria. Spore bacteria have been used in the pharmaceutical market for more than 50 years, including in some drugs used to effectively treat intestinal problems like dysentery.

A recent study done at the University of North Texas evaluated the effectiveness of spore-based probiotic supplements in combating metabolic endotoxemia. The study took a group of 100 otherwise healthy, normal-weight adults and found that a surprising half of them had an exaggerated endotoxin response to a high-calorie, high-fat meal, with levels of endotoxins five times higher than normal as long as five hours after eating.

In a randomized trial, half the group of “responders” had a placebo and the other half took a spore-based probiotic for 30 days. The results were promising:

  • A 42 percent reduction in the endotoxins response, reducing inflammation and helping to heal the intestinal lining

  • A 24 percent reduction in triglyceride levels

  • Restoration of better brain-body connection in terms of hunger and satiety hormones

  • Better insulin response

This is the first time that a probiotic has been shown to significantly reduce endotoxins, leaky gut, and all the associated immune activation, in humans.

Anecdotally, some autoimmune thyroid patients who have taken spore-based probiotics have reported a reduction in their thyroid antibodies, and a reduction in food sensitivities and allergies after even one to three months of therapy.

If you want to try a probiotic

If you are interested in trying a probiotic, keep in mind that while probiotics are generally safe, side effects can include mild gas or bloating. You should always discuss any probiotic supplement use with your healthcare provider if you are immune-compromised, have a chronic illness, are pregnant, or are considering their use in infants or children.

Krishnan advises that you choose a probiotic that contains verified strains of bacteria because many products do not actually contain the number of bacteria advertised. A University of California San Diego study published in the journal Pediatrics Research in 2015 found that only 1 in 16 bottles of probiotics studied actually contained the strains and the potency listed on the label.

The only way to verify the strains is if the manufacturer commissions independent DNA analysis and makes that information available to the public. Look for “DNA-verified” on a product’s label or website, or contact the manufacturer.

If you want to try a spore-based probiotic, there are several brands on the market. Look for DNA-verified products that include bacteria such as bacillus indicus, bacillus subtilis, bacillus coagulans, bacillus licheniformis, and bacillus clausii. Krishnan was also on the team of scientists that formulated two spore-based probiotic products, MegaSporeBiotic, which is only available through health professionals, and the consumer version of the product, JustThrive, which is available at health food stores and online.


Interview with Kiran Krishnan, October 24, 2017

McFarlin, B et. al. "Oral spore-based probiotic supplementation was associated with reduced incidence of post-prandial dietary endotoxin, triglycerides, and disease risk biomarkers." World Journal of Gastrointestinal Pathophysiology. 2017 August 15; 8(3): 117-126

Yan F, et al. “Probiotics and immune health.” Current opinion in gastroenterology. 2011;27(6):496-501.

Mary Shomon
Meet Our Writer
Mary Shomon

Mary Shomon is a patient advocate and New York Times bestselling author who empowers readers with information on thyroid and autoimmune disease, diabetes, weight loss and hormonal health from an integrative perspective. Mary has been a leading force advocating for more effective, patient-centered hormonal healthcare. Mary also co-stars in PBS’ Healthy Hormones TV series. Mary also serves on HealthCentral’s Health Advocates Advisory Board.