The Small Intestine


The small intestine is one of the most interesting and critically important parts of the digestive system. 

This is where the majority of your food gets digested by enzymes and absorbed into the body. It is also where our immune systems get a “taste” of our world. The small intestine isn’t really small at all….if you stretched the tubing out it would extend up to 20 feet. The small intestine is divided into 3 regions: the duodenum, the jejunum and the ileum. The absorption of most of the vitamins, minerals and nutrients are absorbed in the first part of the small intestine. Some sugars and amino acids from proteins are absorbed in the jejunum along with some B vitamins. The last section, the ileum, is where vitamin B12 (with the help of intrinsic factor….remember where it comes from? If not scroll back to the previous post), cholesterol and bile are absorbed.

Remember that this is where your food is broken down (hopefully) and absorbed. What could go wrong? Turns out – a lot!

First we want to appreciate that the wall of this tube is only ONE CELL thick!  The cells that make up the wall of the small intestine have a ton of finger-like projections that increase the surface area tremendously but there is still ONLY ONE CELL thickness that separates what is in that tube from the inside of the body and most importantly the immune system. It turns out that 80% of your immune system lives in your gut!!! Crazy, right??? The inside lining of the tube is called the brush border, and the immune tissue lies just beneath the brush border. The cells that make up the wall of the small intestine are packed together very tightly, they are actually held together by what we call tight junctions. These tight junctions are critical because they keep foreign particles and undigested foodstuff inside the tube and, more importantly, largely away from the immune cells. In addition to the tight junctions, there are structures called desmosomes that act like buttons and hold the cells together. Hopefully it is becoming clear that the integrity of the wall of the small intestine is super critical. When the tight junctions or desmosomes are weakened, we lose the integrity of the wall and it becomes less of a barrier. What sorts of things do you think weaken these structures?

A poor diet, some medications…like NSAIDS, chronic stress, environmental toxins, and inflammation. This inflammation can be a result of eating foods to which you are intolerant.

When this happens, the immune system gets activated and makes antibodies against the contents of the tube…aka your food…and next thing you know we have an inflammatory response happening. This process is often referred to as “leaky gut”.

Common conditions associated with the small intestine:

  • SIBO 

  • IBS

  • IBD


  • Intestinal permeability 

Small Intestinal Bacterial Overgrowth (SIBO): This is an overgrowth of bacteria (can also be fungus or probably even viral overgrowth) in the small intestine.  You might be saying “I thought the intestines are loaded with bacteria with all this talk of the microbiome”. Yes, the large intestine is LOADED with bacteria and you absolutely want a ton of different types of bacteria in the large intestine but you don’t won’t those bugs taken a trip to the small intestine.  That causes all sorts of issues with gas, bloating, and poor absorption of nutrients.

Irritable Bowel Syndrome (IBS): this is a term that is used kinda as a catch all to describe intestinal issues that are not irritable bowel disease.  It can be a frustrating diagnosis to receive because little treatment is often offered. Unless of course you go to a naturopathic doctor…we have a pretty big tool bag for this issue.

Irritable Bowel Disease (IBD): this could be Crohn’s disease, microscopic or lymphogeneous colitis, and Ulcerative colitis. These are inflammatory diseases of the small or large intestine.

Celiac disease: this is an autoimmune condition that affects the tight junctions of the small intestine causing inflammation and activation of the immune system in a major way.

Intestinal Permeability a.k.a “Leaky gut”

What about Leaky Gut?

Remember that the cells that line the small intestine are held together tightly…this creates a barrier and keeps undigested or partially digested food in the tube until it is adequately digested and can be absorbed. This is particularly important when it comes to proteins. Proteins are made up of many amino acids strung together. The enzymes that digest proteins break the bonds in between amino acids. Ideally nothing larger than 3 amino acids are absorbed.  When larger amino acid sequences are absorbed the vigilant immune cells are alerted and they make antibodies to that amino acid sequence. If that is not bad enough, they call more immune cells to the area to beef up the immune response and next thing we know we have a full-blown inflammatory reaction going on. The more robust the immune response, the more “leaky" the intestine and the more pre-digested food gains access to the body.

The person experiencing this may notice that they are reacting to more and more foods. Things they have always eaten are giving them problems. They likely will experience abdominal pain, gas and bloating after meals. They may have mucus or undigested food in their poop (as unpopular as it is, we should all be taking a peep at our poop! It tells us a lot about our digestive health!). Many people also experience symptoms that don’t seem to be related to digestion like joint pain, headaches, nasal congestion and skin conditions.

Can you test for leaky gut?  The answer is yes but often the symptoms are enough to start a gut healing protocol.  There is a test called the lactulose-mannitol test for leaky gut but it misses a lot of cases.  There are some markers on some stool tests that point you toward a leaky gut diagnosis, one of these markers is called zonulin. If someone does a food allergy test and they react to tons of foods that usually means that their gut is “leaky”.

Talk to your naturopathic doctor about this if these symptoms are familiar to you.