• Sue

Gut Health - The Immune System in Your Gut - Part I


The gut is a magical place. This long tube is not just where we breakdown and assimilate food it is also the gatekeeper to the outside world. Because it is directly in contact with the outside world the gut must sift through what is beneficial for the body and what is not. This is why it houses the largest majority of the body’s immune system and why it is the largest immune organ. In this blog series we are going to learn about the immune system.




The immune system is made of up cells, tissues, and organs and just as I mentioned the gut is the largest immune organ in the body. To be exact, 70 to 80% of the immune system resides in the gut. For things to work properly the immune cells in your gut need to be able to sort through all you ingest and tell the difference between healthy bacteria and pathogens, toxins and nutrients and protect against anything else you do not want in your body. Immune function is one of the main jobs of the gut.


The epithelial layer of the gut provides a physical barrier, in addition to that, the epithelial layer is lined with immune cells that are constantly surveying the land making sure we are healthy and thriving. To properly do their job, the intestinal wall must be permeable enough to let in nutrients and fluids but strong enough to keep out unwanted particles, toxins and pathogens. It also needs to keep the good bacteria in the places it should be and out of the places it shouldn’t. Not an easy job.


Goblet cells in the epithelial layer produce mucus, Goblet cells serve to protect the gut wall from unwanted bacteria. This mucus lines the walls that contain pathogen killing substances called defensins. The immune system starts in the mouth and runs along the length of the digestive system. At the root of the tongue are dome like structures what we know as the tonsils. Many people think that the tonsils don’t do much except get us sick but they are actually full of immune cells. The tonsils also seem to communicate with the immune system at large educating it on what is friend and what’s foe. This is also why they are likely to get infected as all immune cells are more vulnerable to flareups. Don’t worry if you have had your tonsils out, we have tons of backup. Beyond the tonsils you have your immune tissue surrounding your entire throat. There are more dome like immune filled tissues along your gut lining and your small intestine called Peyer Patches. Peyer Patches are right below the epithelial layer in the Lamina propria. Their like security guards monitoring all the happenings and the bacterial population of the gut so that the body is on full alert if anything or anyone suspicious shows up.


In addition to functioning as a physical barrier, the immune system in the gut sends out chemical signals to identify and fight off unwanted substances. This is important to understand when considering gut problems because it’s the immune system that triggers inflammation or autoimmune reactions in response to these signals it picks up from the immune cells in the gut. There are three things immune cells do.

  1. Make more immune cells

  2. Produce cytokines – which are signals that communicate between cells that can trigger inflammation and can also turn genes on and off

  3. Produce antibodies called adhesion molecules – that can attach to a pathogen or an unwanted substance and lead it out of the body via the liver and spleen.

An easy way to remember how antibodies work is to imagine them as plugs. When they do their job, they essentially plug up the antigen or unwanted substance so that it can’t activate or attach to anything in the body.


With so many conditions being tied back to the gut, we can begin to understand why through the gut we take in the building blocks of cellular life and where we protect ourselves against illness. In Part II we will discuss the two parts of the immune system, the innate system, the one we are born with and the adaptive immune system, the one that learns and gets smarter over time.


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