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On Your Mark, Get Set, Gut Health!

If you’re here you’ve probably heard that “gut health” is important for your overall health and that it may be the reason you or a loved one is struggling with chronic symptoms. Let’s unpack what that means from a Functional Medicine perspective and several ways you can optimize your gut health.

Functional Medicine Defined

First, it’s important to define what Functional Medicine is. Functional Medicine is an approach to medicine that aims to investigate and address the root cause of illness, as opposed to managing a symptom or condition with a prescription. 

The Institute of Functional Medicine describes,

“Functional Medicine determines how and why illness occurs and restores health by addressing the root causes of disease for each individual.

The Functional Medicine model is an individualized, patient-centered, science-based approach that empowers patients and practitioners to work together to address the underlying causes of disease and promote optimal wellness. It requires a detailed understanding of each patient’s genetic, biochemical, and lifestyle factors and leverages that data to direct personalized treatment plans that lead to improved patient outcomes.

By addressing root causes, rather than symptoms, practitioners become oriented to identifying the complexity of disease. They may find one condition has many different causes and, likewise, one cause may result in many different conditions. As a result, Functional Medicine treatment targets the specific manifestations of disease in each individual.”

The Root Causes of Illness

Dr. Mark Hyman outlines the five root causes of illness that Functional Medicine practitioners and coaches are trained to investigate. I have reordered his original list for two reasons: 1) Stress deserves to be listed first as it almost always has some part to play and 2) I think it is easiest to remember the causes by the acronym STAMP. 

  1. Stress (physical or psychological)
  2. Toxins (biologic, elemental, synthetic)
  3. Allergens (food, mold, dust, animal products, pollens, chemicals) 
  4. Microbes (bacteria, yeast, parasites, worms, prions, etc) 
  5. Poor diet (standard American diet, or SAD) and poor movement*

*My own addition, although I think Dr. Hyman would agree.

These environmental and lifestyle triggers interact with genetics and can express different conditions in different people. Similarly, two people with the same condition may have developed it from different causes. Ultimately, the goal is to investigate an individual’s specific lifestyle and environmental factors in order to narrow in on the most likely cause of illness. 

How Gut Health is Connected to the 5 Root Causes

In this section, let’s explore how gut health is connected to the five root causes of illness. Each of these could be several articles on their own, but I hope this helps you get the idea: optimizing gut health requires a comprehensive approach and it can have a significant impact on total body wellness.


Stressors (both physical and psychological) impact GI function in several ways. Living in a state of chronic stress, or sympathetic nervous system activation (“fight or flight” mode), impairs digestion. Poorly digested food damages the intestinal lining and causes inflammation. Damage to the intestinal lining allows poorly digested food particles and toxins to cross the intestinal barrier into the bloodstream (this is called “leaky gut”). These escapees then activate immune cells right on the other side of the GI tract, leading to localized inflammation that moves throughout the blood and results in a systemic inflammatory effect. Approximately 60-80% of immune cells reside on the opposite side of the intestinal lining, so you can see how damage to that barrier can ensue a highly inflammatory reaction.


A poorly functioning GI tract leads to compromised detoxification processes in the body. This allows the body’s toxic burden to build and directly compromise other systems. Toxins are also a physical stressor on the body, which can trigger the aforementioned mechanisms. 


Allergens cause damage to the intestinal lining and promote GI inflammation, which activates the immune system and leads to systemic inflammation. They are also physical stressors on the body, exacerbating intestinal lining permeability and GI inflammation further. 


An overgrowth of bacteria and yeast can occur in the intestines due to stress, poor diet, toxins, food intolerances, some medications, and infections. An imbalance in the GI microbiome can lead to inflammation and leaky gut. Parasites and hidden infections can also reside in the gut, contributing to chronic immune system activation. 

Poor Diet and Movement 

Nutrient deficiencies from a poor diet can impair the function of the GI tract, as well as all other bodily functions. A poor diet may also contribute to stress on the body, toxin exposures, an imbalanced microbiome, and leaky gut. A sedentary lifestyle contributes to an imbalanced microbiome and promotes inflammatory pathways in the body.

Three Ways to Address the Root Cause(s) & Work on Your Gut

There are several ways to go about investigating the root causes of illness. While some Functional Medicine practitioners utilize a “test, don’t guess” approach and opt for comprehensive diagnostic testing upfront, Dr. Beard has found that many clients are able to achieve symptom resolution and/or reduction by first addressing the gut and working with a Functional Medicine Health Coach, without the need for expensive testing. Should issues persist after an initial gut health program, advanced testing can then be utilized.

1. Optimize Your Gut Health

There are several reasons starting in the gut can be advantageous:

  1. Gut health is intricately connected to all five root causes. It is the single most impactful area of the body you can focus on. For this reason, Functional Medicine practitioners like the motto, “When in doubt, start with the gut.”
  2. By addressing gut health first, you may find and fix the problem, negating the need for expensive testing.
  3. Addressing gut health “clears the smoke out of the room” by eliminating and/or deducing many of the common causes of chronic symptoms. Once you can check those off your list, you are better equipped to do further investigation into what else may be going on. 
  4. Optimizing gut health is often the first step, even if it isn’t the only step. Most Functional Medicine treatments and protocols require the client to have or be currently working on optimal gut health.

2. Work with a Functional Medicine Health Coach

A secondary approach to finding and addressing the root cause(s) is working with a Functional Medicine Health Coach. Properly trained coaches assist clients in addressing the causes which have the most potential for being the problem, based upon a thorough investigation of your health history, lifestyle, and environment. Clients often make much progress under the direction of a coach without the need for expensive testing. At the very least, you may be able to narrow down the potential causes by first addressing lifestyle and environment, and then considering additional testing if some symptoms continue to persist.

3. Complete Advanced Diagnostic Testing with a Functional Medicine Practitioner

The most aggressive approach to investigating the above root causes involves utilizing standard and/or advanced diagnostic testing. This is also the most expensive route, particularly if you choose to use several tests. The good news is that many Functional Medicine tests are now available for patients to order online themselves, without the referral of a physician. However, while some tests are straightforward and easy to understand, others may require interpretation by a trained Functional Medicine practitioner, adding to the expense of this option. Functional Medicine tests range in price from around $100-400.

How We Can Help You Get Started

At AmyBeardMD, each of us has had our lives dramatically impacted by Functional Medicine, and we want to make Functional Medicine affordable and accessible to anyone from anywhere. So whether you are a “do-it-yourself” type or you prefer expert guidance and accountability, our team has options for you!

Learn More About Healing the Gut

The Institute of Functional Medicine teaches the 5R Framework for Gut Health: Remove, Replace, Reinoculate, Repair, and Rebalance. This framework, along with years of clinical application and patient success stories, has guided Dr. Beard’s development of comprehensive protocols for gut health. Download our free ebook from our homepage to read about Dr. Beard’s application of the 5R approach and some of the nutraceuticals that can support gut health. 

Complete Amy’s Total Gut Job – A Diet & Supplement Program w/ an Online Course & Community

Dr. Beard has developed an online, self-guided, 8-week program to comprehensively optimize gut health and reduce inflammation by addressing the five root causes of illness as they relate to the GI tract. Amy’s Total Gut Job is based on the 5 R approach to healing the gut, taught by the Institute of Functional Medicine. Her program includes eliminating common problematic foods, supporting GI function with nutraceuticals, and strategically optimizing personal lifestyle and environmental factors. 

Work with Us

If there is anything in our wheelhouse, it’s optimizing gut health! We see clients from all over the United States (and the world!) via Zoom. You can learn more about our Functional Medicine services here.