Leaky gut, microbiome, autoimmunity, and the diseases associated with these terms are coming into relatively common usage.  Few people who use them, however, really know their meaning, how they are related, and how they influence disease, its prevention, and therapy.


A biome is simply any natural community of plants and animals that occupy some major area like a forest, for example.  It seems to have been coined in 1916 by an American ecologist named Frederic Clements.  Joshua Lederberg is thought to be the first to use the term microbiome in 2001.

The word biome comes from two Greek forms: bios meaning life, and -oma, which is a kind of neutral, neuter, word-forming suffix that indicates an entity of some kind.  Western medicine has co-opted this suffix to refer to various kinds of tumor like carcinoma.

Microbiome has come into greater use since about 2008 with the start of the Human Microbiome Project of our National Institutes of Health.  The purpose of this project is to explore the communities of human cells and microorganisms that live throughout your body, and how they affect your health.

These communities exist in various places like your lungs and skin, but most interest has been shown in the microbiome residing in your gut.

What is your gut?

Often called the gastrointestinal tract, GI tract, or alimentary canal, your gut consists of all the organs and structures you use to take in food, digest it, and eliminate the waste products.  That is, your gut includes your mouth, esophagus, stomach, small and large intestines, and anus as well as your pancreas, liver, gallbladder, and more.

The processing of food, digestion, is amazingly complex.  It involves not only the precisely controlled release and absorption of a myriad of chemicals, but also continuous two-way communication between your gut and your brain.  Some suggest that your gut is really a second brain.

What is a leaky gut?

The wall of the small intestine part of your gut may seem impenetrable, but it is, in fact, selectively permeable.  That is, its job is to let through the wall nutrients and other beneficial substances so they can be distributed through your blood to the parts of your body that need them.  At the same time, it needs to keep out of your bloodstream some bacteria and the toxins they produce as well as undigested bits of fats and proteins.

The way it works is that the lining of your intestine, your immune system’s first line of defense, consists of cells (epithelial cells) that are connected to each other by what are called tight junctions.  On the surface of these cells are many tiny projections called microvilli.  Their work is to absorb properly digested nutrients, and carry them through the cells into your bloodstream.

During normal digestion, the tight junctions remain tight, blocking out any substance that can’t be absorbed by the microvilli.  Leaky gut means that the tight junctions loosen up so those larger bits of undigested food can get through into your blood along with yeasts and other waste.


The next line of defense is your liver.  In response to the presence of these strange, foreign bodies in your blood, your liver goes into overdrive trying to screen out the particles your intestine wall was supposed to deal with.  However, no matter how hard it tries, your liver can’t keep up with the constant influx of waste, which begins to build up in your body.

Now the big guns, your immune system, come on to get these intruders out of your body.  In general, the job is too big for your immune system as well, and the foreigners get absorbed into tissues throughout your body, causing them to become inflamed.  Inflammation is also part of your natural immune response.

As this war escalates, other natural processes such as fighting off bacteria, filtering your blood, and regulating your gut tend to be ignored.  The result is your body fighting itself, which is the meaning of autoimmunity.  That is, your body is now producing extra antibodies that wind up responding even to chemicals found normally in your food.

It’s easy to see how such conditions can lead to irritable bowel syndrome, chronic fatigue, and other autoimmune diseases.

What loosens tight junctions?

There is controversy over the causes of leaky gut, but one commonly accepted probable cause is intestinal inflammation.  Whether it’s inflammation because of low stomach acid letting through undigested food or the influx environmental toxins, your tight junctions may be loosened.  In addition, if the mutually beneficial normal balance of yeasts, bacteria, viruses, and other organisms is disturbed, then your gut may be compromised as well.

I have more to say about inflammation in my column from June 2.  If inflammation is chronic, you need to remove the cause.

Diet is commonly cited as causative as well.  Inflammation is associated with diets that are high in refined sugars and processed foods, for example.  In addition, the casein in cow dairy and gluten in refined flour products are known to be inflammatory.

Chronic stress tends to suppress your immune system, leaving it unable to do its job normally.  It gets overburdened by pathogens easily, which leads to inflammation of your gut, and loosening of those tight junctions.

Medications may be complicit as well.  Not only prescription medications, but over-the-counter drugs containing acetominophen or aspirin can irritate the intestinal lining and loosen tight junctions.

How to prevent (or fix) a leaky gut

There are four parts to a program that help to keep leaky gut under control: diet, supplements, probiotics, and some digestive enzymes.

First, and perhaps most important, is to get off sugars, starches, grains, soy, caffeine, and cow dairy.  Eliminating these inflammatory foods will not only reduce intestinal irritation, but will also starve any yeast that has taken over your intestines.  A good diet to consider for these purposes is the Specific Carbohydrate Diet.

I emphasize avoiding cow dairy because it is very high in the troublesome casein.  Sheep dairy is better, and goat is the best.  These days, incidentally, farmers have learned how to make goat dairy taste hardly at all goaty.

Second, consider increasing your nutritional supplements.  One problem with leaky gut is that your body is not making good use of the nutrients you give it.  Fish oils, a multi-vitamin, vitamin D, and zinc are among the more important supplements to try.

Next, you need to repopulate your gut with good bacteria like lactobacillus acidophilus using a probiotic.

Fourth, you might wish to add some digestive enzymes to your diet.  Enzymes are chemical compounds that help chemical reactions to occur.  Lipases, for example, are enzymes that enable the breakdown of fats, and proteases help to breakdown proteins.  There are enzyme supplements, but there are foods as well that provide enzyme support.  These include things like pineapple, grapes, avocado, coconut and extra-virgin olive oil, and raw honey.

What should you do

There are some people who seem to be able to eat as much of anything as they like, and have no unpleasant side effects.  If you are one of those, then God bless you!

However, I urge you to pay attention.  If you begin to have some of these symptoms chronically then consider the possibility that your gut may be in trouble: fatigue, trouble digesting what you eat, pain in your joints, difficulty sleeping, depression, chronic diarrhea or constipation, intestinal gas, or feeling bloated.  You may also think your immune system isn’t up to snuff, you may have rashes, excessive craving for sweets and other carbohydrates, and even some memory problems.  Certainly rheumatoid arthritis, Crohn’s, lupus, and other autoimmune diseases are indicators of likely leaky gut.

In the meantime, bon appetite.



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