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Body Basics: Understanding How the Gut Acts as a Protective Barrier


The extraordinary complexity of the human body can make it intimidating to understand. But even though we don’t truly understand all of it, we do know a lot about how it works. And you don’t have to be a physician or have a PhD in physiology to have a basic understanding of how your body works and what you can do to make it as healthy as possible.

This article is part of the Thorne series we call “Body Basics” – and is designed to make it less intimidating to learn about your body. By learning more about how the body works, you can make better decisions about your health – whether you’re at home, the store, your health-care practitioner’s office, or online. Because knowledge is power, let us help you get mighty.



The body is full of protective barriers. The skin is the most obvious barrier, because you can see and touch it, and it’s the primary barrier between you and the outside world.

Although the skin houses specialized structures that perform multiple functions (sweat glands and hair follicles, for example), it has a comparatively simple job – be tough and flexible to prevent damage and keep a tight enough seal that water stays in and viruses and bacteria stay out.

What you might not realize is that your internal body parts that connect with the surface of your body are also exposed to the outside world – they are “outside-in” structures.

So, for example, as you breathe, the air that flows in and out of your lungs is not technically inside your body; it’s just in the middle!

Only the oxygen that leaves the air and enters your blood gets inside your body. In all these outside-in structures, the contents of the hollow space in the center, which is often called the lumen, is technically in the middle of your body but not inside it. To get inside your body the contents must cross a barrier.


The outside-in challenge

Because these outside-in structures are vulnerable to germs and contaminants, just like skin, they also must be effective barriers. The lungs, for example, must be able to exchange oxygen and carbon dioxide with the blood without becoming clogged or damaged by contaminants or letting germs pass into the body.

Your digestive tract is the largest of these outside-in structures. Because it passes through your entire body, it is arguably the one with the toughest barrier job.  

Nearly everything that enters the digestive system is contaminated with a variety of undesirable substances. The mouth and stomach are simpler barriers, in that not much is allowed to pass into the body through these locations, so they needn’t be very selective with what they keep out.

It is in the intestines where the role of being a barrier becomes much more challenging.

The term chyme is used to describe the mixture of food, bacteria and other contaminants, plus digestive secretions (like acid and enzymes) that forms in the stomach.

While desirable substances like nutrients and water must be removed from the chyme and absorbed into the body through the intestines, the undesirable substances (like bacteria and toxins) must be kept in the chyme that remains in the lumen and pass through your body without ever getting inside.

An added complication occurs in the large intestine where trillions of bacteria and other organisms naturally live. Because our health depends on these organisms, they can’t just be killed off. 

The large intestine then, must be able to play nicely with the helpful organisms while not allowing harmful ones to take over, all while absorbing water and nutrients before what remains in the chyme is lost as waste.

And if that’s not enough, the entire digestive tract must coordinate with the immune system, helping it to determine which foreign substances warrant a response and which don’t.  


The intestines as a barrier

Although their jobs are different, the fundamental structures of the small and large intestines are quite similar. It is this structure, and the way the specialized cells within it function, that allows these organs to perform these complicated tasks so effectively.

The intestinal barrier has three major structural components. First, a layer of sticky mucus that contains antibodies and other anti-microbial molecules coats the surface of the lumen.

The mucus is produced by specialized intestinal cells and lies between the chyme and the intestinal wall.

Second, a single layer of long cells (the intestinal epithelium) are connected tightly together by structures called tight junctions.  With this arrangement, all but the very smallest particles are prevented from passing between the cells. 

Even water is limited in its ability to pass. Finally, the lamina propria, a fibrous layer the intestinal epithelium is attached to, contains many different immune cells that monitor substances before the substances can move into the blood or lymph.

When the intestines are healthy, the mucus makes it difficult for large things like bacteria to get to the cells and it slows the movement of smaller things passing through it – like viruses. The anti-microbial molecules in the mucus block undesirable substances from entering the body; they can even kill some bacteria and disable viruses.

Most substances that pass the intestinal barrier pass through a cell, not around it.

These cells, then, selectively carry certain molecules across the barrier into the body while blocking passage of other substances. On the other side of the cells (now inside the body), in the lamina propria, immune cells patrol the space between the intestinal epithelium and the blood and lymph.  These fluids then carry substances away from the intestines and to the rest of the body for use.  

To envision this, imagine you are a molecule of food traveling in a train (the chyme) in a subway tunnel (the lumen) that passes through a high security zone (the body). There is one station (the mouth) where you can enter the subway (the digestive tract) from outside the high security zone.

Once in the subway you are only allowed to exit at the end of the line (the anus) which is outside the high security zone, unless you have clearance to exit at a stop (the small or large intestine) within the high security zone. At every stop along the route there are security barricades that slow your movement (the mucus). 

At these barricades, there are scanners and cameras (anti-microbial molecules) that check your identity and can block you from trying to exit at the wrong stop. 

A solid wall (the intestinal epithelium) between you and the high security zone has locked doorways in it (special channels in the cell membrane).  As food, you have clearance to exit, so you are allowed to pass through a doorway, but this only brings you into a room within the wall (inside an intestinal cell).

In this room, you are processed further before you are allowed to exit a door (another membrane channel) on the high security zone side (inside the body). Once outside the cell you are inside the body, but now security is truly fierce, with more barriers (lamina propria) and constant patrols (immune cells).

But, from here, you can enter an internal subway (blood or lymph) to get to your final destination in the body.

What makes this system particularly astounding is realizing that only one layer of cells, just a few microns thick, separates the contents of the lumen, including those trillions of bacteria in the large intestine, from the inside of your body!  


A healthy barrier 

Thus, a healthy intestinal barrier is critical to good health. When it is healthy, this system is very effective at extracting water and nutrients from food while protecting you from contaminants and toxins.

Although it is an extremely complex system, much more so than described here, there are some relatively simple things you can do to help your gut stay healthy (besides the ubiquitous advice of exercising and drinking water). Two other top tips are:

  • Get plenty of fiber in your diet – whether from food (like beans, whole grains, veggies, popcorn) or from supplements. Fiber keeps fluid in the gut, where it aids digestion, it adds bulk for easier transit of food and waste, and it supports healthy gut bacteria.
  • Replenish lost “good” bacteria – especially after you are ill or use an antibiotic. Eating foods like yogurt, sauerkraut, or miso, and taking a quality probiotic supplement will provide healthy bacteria that compete with the harmful bacteria for space in the gut and help maintain healthy variety and function.


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※ This article is transplanted from Thorne's website and partially edited for Asian region. Original one is here.

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