What is an Underactive Thyroid?
The thyroid gland is a butterfly-shaped gland located in the front of the lower part of your neck. It produces thyroid hormones, which control several body functions, the most important being metabolism (aka breakdown of proteins, carbohydrates, and fats), digestion, temperature regulation, brain function, heart rate, and reproduction. An underactive thyroid (called as hypothyroidism in the medical world) fails to produce sufficient amounts of thyroid hormones, slowing down all these functions.
An underactive thyroid is commonly due to the production of antibodies that can no longer distinguish self (your own body) from non-self (aka foreign invaders). These antibodies start attacking body’s own tissues (thyroid gland here) and are, thus, known as “auto-antibodies.” The production of autoantibodies that sabotage the thyroid gland and interfere with its normal production of thyroid hormones is termed as Hashimoto’s disease.
While the primary treatment for an underactive thyroid involves taking prescription thyroid hormones, the use of some alternative adjuncts is also on the rise. One of these trending alternative therapies is probiotics.
To better understand the benefits of probiotics for an underactive thyroid, we’ll first get into the nitty-gritty of the gut mechanisms responsible for Hashimoto’s disease.
How does an Unhealthy Gut contribute to Thyroid Autoimmunity?
A Disrupted Gut Microbiome can provoke Hashimoto’s
Unraveling the effects of probiotics on the thyroid gland, scientists have been able to explore that an out-of-balance gut ecology plays a pivotal part in provoking autoimmune damage whether it’s injury to the thyroid or any other organ/gland of your body.  A disordered microbial population in the gut could mess up with your immune system resulting in its failure to single out self from harmful agents. The ensuing autoimmune mechanisms will then damage the thyroid gland and interfere with its function.
A Leaky Gut Barrier can trigger Hashimoto’s disease
In addition, our gut lining has four layers. The integrity of the outermost layer called mucosa is of utmost importance to prevent the unfriendly bugs from finding their way into the underlying layer called submucosa. This underlying layer is full of immune cells and if breached by and exposed to unwelcoming bacteria, it can overly activate your immune system, culminating in autoimmunity. In 2002, Cindoruk and colleagues were able to demonstrate a link between Hashimoto’s disease and leaky gut barrier. 
Celiac disease and Hashimoto’s may go hand-in-hand
Another factor that accentuates the gut and thyroid link is the co-occurrence of Celiac disease with autoimmune thyroid disease. People with Celiac disease are prone to develop thyroid autoimmunity and vice versa. This is because:
1. Both the diseases are autoimmune and
2. The gut and thyroid cross-talk with each other through the gut-thyroid axis 
The mechanisms responsible for thyroid destruction due to a leaky gut barrier may also account for the connection between the two autoimmune conditions.  
How do Probiotics benefit an Underactive Thyroid?
As opposed to the negative impacts of an unhealthy gut and its microbiome on the thyroid gland, taking probiotic-enriched-foods-or-supplements can heal your gut and may get your thyroid health back on track.
A healthy gut and its beneficial microbiota provide immense benefits to a person with an autoimmune condition.  The ones relevant for thyroid autoimmunity include:
· Building up a healthy gut microbiome
· Forming a gut barrier that is strong enough to keep harmful bacteria and dietary invaders at bay
· Contributing-to-and-fine-tuning the immune system residing in the gut
· Supplying products like butyrate by fermenting dietary fibers in the intestine, which, in turn, can block the cytokines (cell-signaling substances of the immune system) that promote inflammation
Bonus tip: Try healing your gut with probiotic supplements prior to going on a probiotic-rich diet (aka diet rich in fermented foods). This is because the naturally fermented foods contain a multitude of bacterial strains as well as non-digestible fiber (aka prebiotics). To add a scientific terminology, they act somewhat similar to synbiotics (products that are infused with both pro-and-prebiotics). So, it makes sense to restore the balance of the gut bacteria with supplements first and then fuel the growth of these healthy gut bacteria with the fermented foods.
Do Probiotics also restore the Thyroid Hormone Levels in your Blood?
It is important to know for people with an underactive thyroid that probiotic supplementation does not directly raise the thyroid hormone levels. With that said, a well-balanced gut microbiome can help support thyroid function by increasing the fraction of the prescription thyroid hormone (such as levothyroxine used to treat an underactive thyroid) reaching the blood.  This, in turn, may help the thyroid gland resume its function.