With Inflammation, We Start With The Gut!


In functional medicine, we always “start with the gut” when investigating the root causes of inflammation and autoimmunity. We do this even if you don’t have actual digestive problems. It’s important to understand why we start with the gut, specifically the small intestine lining.

Autoimmune disease, autoimmunity

Meet the small intestine lining.

The small intestine lining is arguably your body’s most important immune hub. When I think about working with inflammation and regulating the immune system, I think of the small intestine. This may be a new concept to you, to equate small intestine function with immune health. I’d like to help you understand why we think this way. There are four meaningful aspects to think about:

  1. The small intestine is a hollow space organ exposed to the outside world
  2. Its surface is gigantic
  3. Its lining is thin and semi-permeable
  4. The majority of your immune cells are part of the small intestine lining

A hollow-space organ

The parts of your body that are exposed to the outside world are called “hollow-space organs.” This includes your skin, nose, lungs, bladder, vagina, and G.I. tract (gut). Each hollow-space organ has a necessary barrier system for protection and defense against injuries and pathogens.

You may not think of your G.I. tract as exposed to the outside world. However, it’s essentially a hollow tube that starts with your mouth and ends with your anus. Everything that enters your mouth interacts with the whole length of your G.I. tract, but your small intestine gets the most interaction because it’s the largest part of your G.I. tract. So, all day long, your small intestine interacts with the foods, beverages, chemicals, medications, and even supplements that come through. It’s also exposed to the trillions of microbes that reside in your G.I. tract. Between what passes through and what lives there, there are a lot of outsiders to which the small intestine is exposed!

The surface is vast

Not only is the small intestine the largest organ in your G.I. tract, but it’s also the largest of all the hollow-space organs. It’s all folded up and coiled inside your abdomen; however, if we unfolded it, its surface would be the size of a tennis court! This means it has the largest barrier to defend, larger than any other hollow-space organ, including your skin.

Why is the surface so huge? The small intestine is the primary place where you break down and absorb your food. This is an important project that takes time and a lot of surface area. Digestive secretions like enzymes and bile take time to mix with your food and break it down into smaller components for absorption.

The lining is thin and vulnerable.

The epithelial lining of the small intestine is only one cell thick. This lining is thin for a good reason – beneficial nutrients can easily get through and into your circulation. The cells of the lining are called enterocytes, and tight junctions connect them. However, these junctions are semi-permeable, so nutrients can pass between the cells and through them.

This is a great system when it’s functioning well, but when the lining becomes hyperpermeable, it creates a problem in the barrier system. Undigested food proteins, infectious microbes, and toxic bacterial fragments can pass through the lining and cause widespread inflammation and immune havoc throughout your body. This is a breakdown called intestinal permeability or “leaky gut,” which is often a suspect with chronic inflammation and always a suspect with autoimmunity. In functional medicine, we say there are three criteria for an autoimmune disease: a genetic tendency, an original trigger, and a leaky gut.

Inflammation, autoimmunity

The gut immune system

Since the small intestine is the largest hollow-space organ, with a thin and semi-permeable lining, it requires the most robust immune surveillance to protect its border. Fortunately, it has a mucosal layer that houses 70 to 80% of your immune cells. This is called your GALT (gut-associated lymphoid tissue), and it’s your body’s largest and busiest defensive immune hub!

The GALT is the master sorter. All day long, it sorts through food and microbes and tags friends from foes. It helps you tolerate friendly foods and microbes and identifies and attacks suspicious outsiders (antigens). It mounts an appropriate inflammatory immune response against any threatening antigens.

Small intestine, leaky gut, autoimmune, inflammation

The majority of your daily immune activity takes place within the small intestine. So, when there is autoimmunity or inflammation, we want to help regulate the immune system here. There are specific ways that we do this.

The steps to regulate gut-immune health

Hopefully, you better understand why it’s so important to work with the gut and, in particular, the small intestine to de-inflame the body and reverse autoimmunity. To do this, we apply the step-by-step “5 R” approach that we use in functional medicine for gut repair. These steps are often circular rather than linear. We tailor them to the individual because gut health is so unique. These include:

  • REMOVE your triggers, such as high cortisol, food antigens, medications, infections, or alcohol.
  • REPLACE your digestive secretions that are low (like enzymes).
  • REPAIR your gut lining with vitamins, herbs, and nutrients like glutamine and butyrate.
  • REINOCCULATE beneficial gut bacteria by using targeted pro and pre-biotics.
  • REBALANCE your nervous system, is the most important step because stress and emotions deeply affect gut function.

Energetics of the small intestine

In Chinese medicine, we say that autoimmunity is always a disease of the small intestine, the organ that “sorts the pure from the impure.” Your small intestine lining contains your “wei qi” which means your immune defense. In a sense, autoimmunity is when the defensive system is hypervigilant to the point of harming oneself, and it coexists with impaired boundaries with the outside world.

Some people with autoimmunity have larger emotional or energetic challenges with boundaries and being comfortable making choices about what to allow in, or keep out. Healing affirmations could include “I trust my choices, I trust my gut, or I am safe.” Sit with these affirmations and see if they calm your nervous system.

Are you ready to start with the gut to solve inflammation and reverse your autoimmune condition? Please book a discovery call to learn about our Road To Remission monthly program for women’s autoimmune health.


Dr. Laura Paris is an IFM-certified functional medicine practitioner and doctor of acupuncture and Chinese medicine. She helps women rebalance hormones and cycles, reclaim metabolic health, reverse autoimmunity and inflammation, and restore gut health.

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