When it comes to functional medicine, no other organ system exemplifies this patient-centered approach better than the gastrointestinal system. When I first started working as an internist, GI dysfunction perplexed me because the language (diagnosis and medications) to treat it felt limited. Intuitively, GI disorders seemed way more complex than the allopathic model accounted for, and at the same time, discordantly disconnected from diet patterns. For example, take irritable bowel syndrome (IBS), an umbrella diagnosis that fails to capture the intricacies of individual patients presenting with this symptom complex. Sure, you can divide it into IBS with diarrhea, constipation or both, but that does little to further delineate the true underlying root cause(s) for each patient. When you look at GI dysfunction from the lens of functional medicine, you can see that even within one subtype (e.g., diarrhea-predominant), there may be different combinations of underlying root causes. And diet is a major component of that!

The Root of the Matter

This is the key differentiator between the functional medicine approach and the disease-centered Western medicine approach: Rather than a top-down determination of disease treatments based on classifications, we turn the entire system upside down and search for hidden, underlying causes. In other words, if disease in the body were a tree, then traditional allopathic medicine is akin to identifying underlying issues by looking at the visible phenotype (the leaves and branches) but missing the buried clues within the root system. On the contrary, functional medicine turns the tree upside down and looks at the health of the roots first to understand why the leaves look diseased. Using this analogy, you can think of the gastrointestinal system as the body’s root system.

The “Sherlock Holmes” of Medicine

But, were we to leave it at that, we would be missing functional medicine’s greatest advantage when it comes to GI dysfunction. While it is not deceived by the trees when looking at the forest, functional medicine is true “Sherlock Holmes” medicine, because every detail counts. It is the stone unturned in a patient’s history or presentation that often holds the clue to their physiological disturbance(s). Nowhere is this more salient than when investigating gastrointestinal issues.

Where do we begin? We begin with a history of disease. But unlike a traditional incident-focused history, we crack open the barrel of patients’ experiences and look as far back as their birth and prenatal period, then move forward along the timeline of their health, excavating for every important detail. Were they breastfed? Did they suffer from colic or recurrent ear infections? Were they put on repeat courses of antibiotics as a child or later on as an adult? What is their diet? Is it a healthy, balanced diet (more often no, than yes)? Or do they think it’s healthy and balanced, but upon further investigation you find a lot of cheat moments? Do they eat too many sweets? Or are they filling themselves with hidden sugars in the foods they eat? Dig, dig, dig…because people don’t normally report their true diet in the first line of questions. When did their symptoms start? What was going on in their lives at the time? How does stress affect them? How much stress did they have at the onset of their symptoms? We look, look, look...turning over every stone that holds a previously overlooked detail of their histories.

Putting the Patient First

As an accidental functional GI specialist, who struggled with his own irritable bowel health issues until figuring out the underlying root causes, I can tell you that a detailed history of the illness is both diagnostic and critically important for a successful treatment plan. Within this patient-centered approach, you never deny the patient’s experience over test results. A structurally normal endoscopy in a symptomatic patient doesn’t mean the patient has psychological issues. Perhaps you didn’t run the right test to figure out the underlying reason for the patient’s complaints. Perhaps you didn’t know all the tests you could run. Food sensitivity testing, comprehensive stool analysis, stool PCR testing, urine organic acids, and even blood tests for celiac markers and genetics are all new, exciting windows by which to individualize the approach to GI dysfunction.

In addition, as patients tell you their histories, they reveal their level of awareness around the issues that have led them to you, with symptoms they don’t understand and hope you will solve. By understanding where patients are coming from, you can tailor a treatment program that accounts for their individuality. Can they follow your treatment protocol with five supplements, three food eliminations, home food prep, and daily lifestyle changes? Gastrointestinal care often requires significant dietary changes, and this may be too much for some people. When it comes to instituting complex treatments plans, as is often the case with GI dysfunction, the patient must come first.

Here are the three questions I ask my patients once I’ve done a thorough history, explained my first impressions, and instituted an action plan:

  1. Do you understand the plan I’ve detailed for you? It’s important to understand how much the patient captured of what you explained. Have them tell it back to you in their own words.
  2. If you could only do one of the things I asked you to do, which one is the easiest for you to implement? Can you do this right away? Get the patient to verbally commit to the one thing they can do right away! Keeping it simple in their minds increases their ability to follow a plan. You can stack action steps, like sequential dietary changes, over time to avoid overwhelming them.
  3. Do you face any challenges in your day-to-day life that would make it hard to implement the treatment plan? Are they always on the go? Do they work late hours? Don’t know how to cook? Help them strategize how they can follow the plan, while helping them fit it into their lifestyles. Food delivery plans for specific diets are widely available. This is a great solution for busy people.

If you can get a patient to walk out of your office with one clearly defined action step they have vocally affirmed they can do, you have succeeded in the first step in patient-centered medicine. Getting the patient on board, after gaining their confidence by asking all the detailed questions no other clinician did, is the key to success in treating GI dysfunction from the functional medicine perspective.

When all clinicians tackle complex GI issues from this patient-centered model, we will truly have advanced the disease treatment system into the disease resolution system of functional medicine.


Vincent Pedre, MD

Dr. Vincent M. Pedre is the medical director of Pedre Integrative Health and founder of Dr. Pedre Wellness, medical advisor to two health-tech start-ups (MBODY360 and Fullscript), and a functional medicine-certified practitioner in private practice in New York City since 2004. He is a clinical instructor at the Mount Sinai School of Medicine, and is certified in yoga and medical acupuncture. On faculty at The Institute for Functional Medicine, Dr. Pedre taught the first AFMCP in Lima, Peru in November 2017. Most recently, he joined the Lifestyle Matrix Resource Center as a Clinical Expert serving the Pillars of GI Health Program. He believes the gut is the gateway to excellent health. For this reason, he wrote the book, Happy Gut:The Cleansing Program To Help You Lose Weight, Gain Energy and Eliminate Pain, which helps people resolve digestive and gut-related health issues.