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Jan 12, 2022

Microbiome Diagnostics: Three Stages of GI Dysfunction

by Dr. Dan Kalish

GI problems occur based on a predictable series of events, which means you can determine a successful plan for GI treatments based on lab data. By looking at the microbiome markers, the markers that reflect GI organ problems and the portions of the lab devoted to GI pathogens, you can come up with clinically impactful solutions for your patients.

The explosion of research in the area of the microbiome has led to an explosion of lab markers for clinicians to interpret. Unless you have a PhD in microbiology, most of the terms used and roles of these various organisms remain too difficult to unravel in such a way that you can explain the results to a patient, and design an impactful program. After several decades of study under two of the leaders in this field, Dr. Bill Timmins and Dr. Richard Lord, I’ve come to the conclusion that I would enjoy getting a degree in microbiology, and really understanding these labs in depth but that I would have to leave my patient practice to do that and it doesn’t seem realistic. 

So I have been confronted with this central problem: How to interpret complex labs and design simple programs for patients, and how to explain to patients what is wrong in a way that motivates them to make the diet and lifestyle changes that will impact their microbiome and GI health significantly. Just three or four days of eating healthy food can completely shift and improve the commensal bacteria, and getting patients to eat more vegetables, fruit and beans is critical to the microbiome re-establishing its normal balance of organisms.

I’ve broken this down into Three Stages of GI Dysfunction. Stage 1 is a microbiome disruption, meaning the commensal or normal bacteria can be seen out of balance on the lab report. Stage 2 means that one or more GI organs are involved, i.e. the pancreas isn’t making sufficient digestive enzymes or the stomach lacks HCl or the gallbladder isn’t releasing enough bile. Stage 2 can also involve the small intestine which can become inflamed or have its internal immune system in a state of disarray. Stage 3, the worst in many ways, is when GI pathogens have taken a foothold and there are actual low grade, chronic GI infections present, wearing away the gut lining and making the entire situation worse.

GI lab testing clearly reveals which of these three stages are present. Then, one can apply a consistent treatment model to address what the labs reveal. It sounds pretty easy because it is! The hard part is not knowing what to do, or how to prioritize your course of action.

Dr. Dan Kalish

Dr. Dan Kalish

Founder of the Kalish Institute
Dan Kalish, DC, IFMCP, is founder of the Kalish Institute, an online practice implementation training program dedicated to building Integrative and Functional Medicine practices through clinical and business courses.