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Let's Talk About Stools!

Updated: Sep 17, 2023

Hello everyone! Of course I'm not talking about bar stools. Part of my own Functional Medicine journey has been to investigate what is happening in my gut and fix it so my body can heal itself. We can talk about the gut in abstract terms of our microbiota, but how do you really know what’s going on in there? One of the labs that can be performed is called the GI-MAP. It gives a good picture of what is happening in your gut on a microscopic level. Imbalances that appear in the gut microbiota can be indicators of other chronic conditions.

The GI-MAP looks for pathogens, like C. difficile, certain strains of E. coli, and other pathogenetic bacteria, as well as parasites or pathogenic viruses. The GI-MAP also checks for H. pylori, which is the usual suspect for stomach ulcers. Many carriers of H. pylori do not show symptoms, and it is estimated that 50% of the world’s population may have a colony of H. pylori residing in their gut. It’s better to take care of H. pylori before an ulcer appears. Traditional treatments include acid-blocking medications as well as antibiotics. Both of these can cause other disruptions of the microbiome.

The lab test also checks for normal gut bacteria that is supposed to be there. If the normal flora is showing abnormalities, it may show up as constipation or diarrhea or inflammatory responses (including eczema/psoriatic-like rashes, joint pain, etc.). One of these guys is becoming a superstar of gut flora. It is called Akkermansia municiphila. There are many new studies about these bacteria because it has been shown to be low in patients who are obese or have metabolic disorder. However, higher levels of this bacteria are linked with better gut function, improved immune health, and better metabolic health. If the normal flora is low, or imbalanced, a good broad-spectrum pro-biotic may be beneficial. It is also recommended to increase vegetables (up to ¾ of your plate should be dedicated to the rainbow of veggies), decrease sugar and refined carbohydrates, eat/drink fermented foods (if tolerated), and consider pre-biotic supplements.

Then there are the opportunistic bacteria. When other beneficial microbiota become dysfunctional or imbalanced, these guys are no longer kept in check. They take advantage of the situation and can cause some real havoc on the system. Certain opportunistic bacteria are linked to autoimmune responses in the body, like Rheumatoid Arthritis, Crohn’s Disease, Lupus, Type 1 Diabetes, or Thyroid Disorders.

So, once we figure out what is happening in the gut, how do we treat it? The most common approach is called the 5 “R” Protocol.

1) REMOVE: using antibiotics, antifungals, antivirals, etc. to remove the offending agent (which could also be offending foods, gluten or medications that are causing the dysfunction). 2) REPLACE: Provide digestive support if there is evidence that the body is not absorbing or digesting properly. 3) REINOCULATE: Bring in the good bacteria with probiotics and prebiotics. Prebiotics could include fiber, pectin and oligosaccharides that are found in healthy foods (like the rainbow of fruits and vegetables). 4) REPAIR: Support a healthy gut by providing immune support and using supplements to improve the intestinal barrier and mucosal cells. 5) REBALANCE: Look at the whole-body health and lifestyle factors to prevent future issues. This can include sleep, diet, exercise, and stress management.

The 5 “R” Protocol is best performed under the guidance of a primary care practitioner and functional medicine practitioner working together to help you achieve your health goals and heal your gut. You can start with a Lab Consultation with PIVOT Integrative Consulting, LLC to find out what your gut health looks like microscopically. Just contact me at for a free introductory call! Are you ready to start your journey to a healthier, more balanced life?

Cheers to your gut health!

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