Skip to content

When in Doubt, Treat the Gut: Elimination Diet, Probiotics, and Stool Testing

June 6, 2016

“Death begins in the colon” –Hippocrates

Everyday exposures to modern processed food may be common, but to our body’s, they amount to extraterrestrial encounters.

Agriculture. In the 200,000 year history of humanity, farming is an astonishing new development. Between 3-10,000 years ago, agriculture popped up around the globe in several disconnected areas: Asia, South America, Europe and The Fertile Crescent (modern day Iraq and Syria). What this means is that for more than 90% of our development as a species, we were not eating grains or or any modern farmed foods. Processed foods with refined sugars, refined grains, preservatives, artificial flavors, etc. are only 50-75 years old. This means that, at most, 99.3% of humanity’s evolution was apart from any processed food.


Hominids, from which human kind evolved and genetically similar, are about 5 million years old. This makes the development of agriculture and processed food, respectively 99.8% and 99.999% new to us. Fast forward to the present. Here we all are living in a society where processed food has become the bizarre but pervasive and rarely questioned normal.

Processed Food

At the same time as grains and processed foods streamed into the food supply, the new norm in modern human health has evolved pervasive “modern epidemics” including: obesity, diabetes, heart disease, cancers, Altzheimers, Parkinsons, ADD, anxiety, depression, insomnia, indigestion, irritable bowel syndrome, fatigue, headaches, and a host of autoimmune diseases. These and many more modern epidemics have become so pervasive that conventional medicine considers them a normal and inevitable part of life and aging. That belief is fundamentally flawed.


A growing group of Functional and Naturopathic providers, naturalists and health proponents are advocating that the path back to optimal health is largely paved by a return to a natural, ancient, whole-foods diet. Although taking this step represents a drastic shift for most people, it is really a return to nature, our own nature.


All of these confections are modern inventions, and s0 it should not really be surprising that although they may be pervasively available and taste good, they are inherently foreign and can be very problematic. No matter what you may be suffering from, returning to a more natural human diet is, by far probably the most important thing you can do to support your return to natural health. Food is medicine.

Let’s talk about our guts? Out GI tract is an impressive 20-25 feet long. What’s more impressive is that when flattened out, our GI tracts have 300 square meters of surface area! That’s the size of a double’s tennis court, and 200x more area than our skin. The GI track is, by far, our greatest exposure to the environment.

GI tract

Our guts are also home to most of the  40 trillion bacterial cells that make up our microbiome –to which we play host. By comparison, an average male has only 30 trillion human cells. When you count the hundreds of trillions more mitochondrial cells (which are basically house-trained bacteria that make 99% of our body’s ATP energy), it’s fair to say that we are not a human hosting a microbiome, we are actually a microbiome hosting a human.


Lets talk about the microbiome: that community of 40 trillion cells in and on our bodies, most of them in the gut. When our guts play host to “unfriendly” microbes (bacteria, yeast & parasites), the result can be chronic immune system activation, leaky gut, and decreased gut surface area, and both GI and systemic inflammation.

good and bad bacteria

Stress, NSAIDS, acid blockers, processed food, pesticides are all things that can  cause leaky gut. also  and decrease the absorptive surface area. This makes the gut “leaky” and allows food, foreign chemicals and microbiome proteins to enter the blood stream where the immune system does its best to protect you from these unexpected invaders. The immune system is quite thorough, often too thorough. Prolonged GI immune activation (i.e. from grains, processed foods, and unfriendly microbiome) is believed to be behind the development of IBD and autoimmune diseases.

The majority of of your body’s immune cells (50%-70% ) live in your gut. Once your gut’s immune system starts reacting to foods, it become like a bad guard dog that not only attacks the food, microbiome and chemicals in your diet, it attacks the gut itself  causing gut inflammation which not only decreases your ability to absorb foods, it promotes leaky gut, new food sensitivities, systemic inflammation. In case you didn’t know, systemic inflammation is at the root of most if not all of the modern epidemics I mentioned earlier–especially autoimmune diseases.


All this is the backdrop for a key primary Functional and Naturopathic intervention: The Elimination Diet. Elimination Diets can be done in many ways, but they always involve removing foods that are potentially contributing to an individual patient’s state of disease for 4-12 weeks, and then reintroducing them one at a time while watching for flareups. A “complete” elimination diet involves reducing food options to a short list of whole foods least likely to be problematic.

In my practice, when I think that an adverse reaction to food (ARF) may be underlying a patient’s symptoms, I often find it most effective to select a more “targeted” elimination of one or more the most likely dietary exacerbates: Wheat/gluten, dairy, sugar, soy, corn, and food additives and preservatives, pesticides of any kind and perhaps the nightshades (tomatoes, peppers, potatoes).

Another way to test for adverse reactions to food is to do a blood food sensitivity test. A true “allergy” to food is mediated by IgE immunoglobulins. These are often, but not always fairly obvious and severe IgE reactions are the classic anaphylaxis: hives, and airway closure requiring a shot of epinephrine. Food “sensitivity” is mediated by the less perilous IgG immunoglobulin, and other more difficult to detect immune reactions to food. Serum IgG testing is an easy way to survey your blood for 90+ foods at once for ~$200. Many patients find this a excellent way to target a trial of an elimination diet.

Genova IgG Food

Here’s how it works: Do eliminate the suspected foods for 4-12 weeks and then sequentially “challenge” the eliminated foods one at a time for a few days each while watching for a return or exacerbation of symptoms such as: headache, brain fog, joint pain, acne, skin rash, acid reflux, loose stools, IBS, anxiety, disturbed sleep, etc. These conditions are all exacerbated by a hyper-activated immune system, and the foreign proteins and chemicals in grains and processed foods can easily overactivate your immune system.

Back to the bugs. One of the other primary interventions I use with patients is Gut probiotics and fermented foods. I am especially likely to recommend probiotics and fermented foods to patients that have more serious gut dysfunction, systemic inflammation, autoimmunity, a weak immune system, a history of a standard American diet (SAD) or taking frequent courses of antibiotics.

For patients with concerted GI issues, I may order a specialized stool test called a Complete Stool Analysis (CSA). For $300, you can learn an awesome amount about your digestion and the community of microbes (both good and bad) living inside your amazing and vitally important GI tract.

No comments yet

Leave a Reply

Fill in your details below or click an icon to log in: Logo

You are commenting using your account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s

%d bloggers like this: