Pre Class Homework



Autoimmune Paleo Cookbook - Mickey Trescott



The Gut has multiple actions

Digest - break down food into absorbable components that are small enough for the rest of our body to use. Stomach acid, enzymes in saliva, enzymes from our pancreas, bile from our liver (stored in the gallbladder and used when we need it, which is why we do really need our gallbladder). The motion of our intestines constantly moving helps to break food down.

Absorb - get good nutrients in. The lining of the gut is like a cheesecloth filter that keeps out big or bad particles, but allows the important things in.

Detox - excrete the bad stuff. The liver helps by packaging toxins and natural waste products in ways that they should stay in the gut and not get reabsorbed.

Protect - keep out bad things - we don’t want to absorb the bad stuff from our foods and we also don’t want to reabsorb waste products and toxins that our liver has packaged to be excreted.


The gut is the soil from which the brain grows!

GI Effects Stool Test - helps us to look at the following: 

Infection - clear cause of inflammation and chronic disease. Infection can affect all of the actions of the gut.

Inflammation - can sometimes show signs of parasites, food allergies, chronic inflammatory bowel disease (such as Crohn’s and ulcerative colitis). Some markers tell us if we need to be especially vigilant with colonoscopies to screen for colon cancer.

Digestion - tests for pancreatic enzyme function and whether we are breaking down fats and proteins. If we aren’t it can be a sign of low stomach acid, pancreatic enzymes, stomach acid or bile salts. We can replace these with supplements.

Imbalance - tests for how well our good bacteria counts are compared to potentially bad bacteria (PP bacteria stands for potential pathogen). We also look for markers such as SCFA (short chain fatty acids), which are signs of how well our good bacteria are working to get our gut cells the fuel that they need to work properly. We often treat with herbs for PP bacteria, or treat with probiotics and prebiotics if our good bacteria levels are low.

Probiotic Diversity - humans normally have 75-150 different types of healthy bacteria in the gut. There is no way that we can completely replace these with probiotics. Probiotics help build the soil for a fertile microbiome, but we also need fertilizer.

Probiotics aren’t enough because they don’t stick around more than a few days so we really have to grow our natural garden.

Prebiotics = fertilizer. Fruits and vegetables and natural fibers are prebiotics. My favorite supplement is arabinogalactan because it works as a prebiotic and also as an immune booster.

Sugar is like fertilizer for the weeds, the bad bacteria.

Leaky Gut

Leaky gut is when the lining of the gut, which is similar to a cheesecloth, has holes in it. When this happens, our gut allows particles that are too big to go through it, or it allows in things our body really wants to keep out. So our gut can’t perform its protection feature. We think that it can be an underlying cause of inflammation that can cause a wide variety of symptoms.

Most of us have it to some degree, because of what we are exposed to in our culture.

Symptoms: bloating, gas, cramps, food sensitivities, and aches and pains.

Causes: many, including diet (especially wheat - see the handout showing the junctions between the cells), low stomach acid, yeast overgrowth, bacterial overgrowth, alcohol, stress, food sensitivities, celiac disease, bowel infections and medications (esp NSAIDs). Our stool test is looking for most of the underlying causes. The rest we are treating naturally with our program by removing common triggers that irritate our gut.

SIBO  - small intestinal bacterial overgrowth

Also very common and often combined with leaky gut because SIBO can cause leaky gut. Because this is an overgrowth of bacteria much higher up in the gut in the small intestine it is not tested for with the GI Effects Stool test, but usually we figure this out based on your symptoms.

10 symptoms of SIBO: gas, bloating after eating, diarrhea, abdominal pain or cramping, constipation (less often)

Associated diseases - multiple food intolerances, fibromyalgia, chronic fatigue syndrome, diabetes, neuromuscular disorders, autoimmune diseases, interstitial cystitis.

B12 deficiency and fat malabsorption can be caused by SIBO -- prevents you from absorbing your nutrients. So, this can be a cause of nutrient deficiencies.

The Microbiome

Good bacteria are affecting every aspect of our health - it’s a rising field with so much information yet to be learned. For example, we can’t even test for many of the species we expect are in our gut.

We have microbiomes everywhere on our body and they are all different.  Even 1cm apart in our ear or nose has a different microbiome than the next space in our body. e.g. oral, skin, vaginal,gut, and nasal/lung.

Obesity - we know that a high firmicutes : bacteroidites ratio increases obesity and that when you change that flora, obesity gets better. Probiotics can’t quite fix this, but they’ve looked at fecal transplants in mice, and as we work on getting our healthy bacteria fertilized, this will improve our chances.

Other diseases where we’ve seen an association: Crohn’s, Alzheimer and other brain issues, psoriasis and other autoimmune disease, acne and other skin issues, undiagnosed abdominal issues, and many others.

So, because our nutrition changes are designed to heal our microbiome, it also should help reduce symptoms and reduce risk for all of these other diseases.

Remember these ways we can grow our microbiome gardens:

  • Eat Real Food - most importantly vegetables!

  • Decrease stress.

  • Get outside in the sunshine and garden ... embrace those soil organisms!

  • Do not use antibacterial soaps ...or be excessively clean.

  • Do not eat processed foods.

  • Avoid pesticides.

  • Eat organic meat so you avoid the antibiotic and toxin laden regular stuff.

  • Avoid antibiotics if possible.



When you get your stool test off in the mail please call us and set up an appointment for feedback on your test (30 days +).

If you get a bill from a lab please do not pay.  Feel free to bring it in and we'll check it out for you.