The Gut-Immune Connection
Have you ever though about the primary functions of the gut?
It's primary function is the digestion and absorption of nutrients and the excretion of waste.
However, it also has a major influence on both the development and function of the immune system, as well as on gut-brain communications. 
But more important than digestion, absorption and elimination is the protective barrier that our digestive tract offers.
If you really think about it, the contents of your gut are outside of the body!
In other words, from your mouth to your anus, this long tube that we think of as our gut, is actually outside of our body's internal cavities and blood stream.
So anything that doesn't get digested and absorbed, simply passes through.
And it's designed this way because the digestive system helps to keep foreign substances, toxins and anything harmful from actually entering your body.
Adding to this layer of protection is the GALT system. GALT or gut associated lymphoid tissues make up between 70-80% of the immune tissues in the body.
Again, this is important because all sorts of bad bugs and harmful chemicals can enter our body via the mouth.
When these protective mechanisms are compromised (i.e. leaky gut or intestinal permeability), then undigested food and various molecules can enter the blood stream and cause our body to go on the defense.
This is one of the driving mechanisms behind all autoimmune conditions.
The Gut-Thyroid Connetion
The gut plays a strong role with thyroid function.
As we just discussed, the gut is a protective barrier that keeps bad bugs and chemicals from entering your body.
But if this barrier is broken, then you'll have serious problems develop over time.
Part of the protective barrier are structures called tight junctions.
The tight junctions are areas where the membranes of two adjacent gut cells join together to form a barrier.
We now know that thyroid hormones strongly influence the tight junctions in the stomach and small intestine.
T3 and T4 have been shown to protect the gut mucosal lining during times of stress. 
We also know that damaged tissue in the gut results in lower levels of T3, T4 and abnormal levels of reverse T3. 
In addition, beginning in the brain, we know that thyrotropin releasing hormone (TRH) and thyroid stimulating hormone (TSH) influcent the development of GALT.
All of this is part of the growing body of research that connects thyroid hormones to the gut and immune system. 
Now if you have any interest in optimizing thyroid hormones, you need to know your numbers.
There are several thyroid hormones that we could talk about, but for the purposes of this article, let's discuss 4:
- TSH – Thyroid Stimulating Hormone
- T4 – The Inactive Thyroid Hormone
- T3 – The Active Thyroid Hormone
- Reverse T3 – Another Inactive Thyroid Hormone
In short, your brain sends a signal to the thyroid to production thyroid hormone.
This is TSH (the signal) telling your thyroid to release thyroid hormone (T4).
But remember, T4 is the inactive thyroid hormone. So what has to happen here is that your body needs to convert T4 (inactive) to T3 (active).
There are all sorts of reasons why someone might not be converting T4 to T3 and a big one is nutrient deficiency.
Can you take a wild guess what else contributes to the conversion of T4 to T3?
Or at least the bacteria in your gut assist in converting inactive T4 to the active thyroid hormone T3.
This is why dysbiosis or imbalances in good and bad bacteria can be a root cause of thyroid dysfunction.
These bacteria help to produce an enzyme called intestinal sulfatase, which is necessary for T3 conversion. 
Inflammation also reduces T3 by raising cortisol.
Cortisol decreases active T3 levels while increasing inactive T3 or reverse T3. 
Not only do good bacteria influence T4 to T3 conversion, but there are bad bacteria whose cells walls known as lipopolysaccharides (LPS), negatively effect thyroid metabolism.
LPS has been shown to:
- Reduce thyroid hormone levels as a whole
- Decrease sensitivity to thyroid hormone
- Increase inactive T3 (reverse T3)
- and promote autoimmunity
For anyone experiencing thyroid disorders or disease, it's important to consider the gut and digestive system as a potential root cause.
This is really what sets Functional Medicine apart from conventional medicine.
The first step is always to figure out what’s causing the gut dysfunction and this takes a comprehensive stool panel.
Potential causes of gut problems can include low stomach acid, pathogenic infections, deficiencies of good bacteria, food sensitivity (especially gluten), and stress.