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The Must-Have Digestive Tests of Functional Medicine

I hope you’ve been intrigued by the Health Tips on Functional Medicine we’ve written in the past month. It’s especially provocative that a growing number of physicians, as well as the Cleveland Clinic, are using functional medicine tests when challenged by a patient with longstanding, unexplained chronic symptoms whose conventional test results have been negative.

What exactly is a Functional Medicine test and how does it differ from the ones you’ve been getting all along from your family doctor?

Just as the word itself conveys, a functional test of one of your body’s systems (digestive, cardiac, hormonal, etc.) checks how efficiently that system is working. The single most common conventional test in gastroenterology checks your stools for the presence of blood. The result gives you exactly one piece of information: either you have some internal bleeding or you do not. It tells you absolutely nothing about how your GI system is functioning.

Here’s a simple comparison I hope will provide an “aha!” moment leading to all of functional medicine becoming clear to you.

Conventional medicine for GI symptoms
Let’s say you have chronic indigestion: bloating, gas, diarrhea, and/or constipation. Instead of feeling good and satisfied after eating, you feel crummy. You try eliminating certain foods and you’re not sure it makes a difference.

You go to your doctor, who prescribes Pepcid or Nexium (they’re all the same), but nothing changes.

She sends you to a gastroenterologist, who listens to your symptoms, says “seems like irritable bowel syndrome,” and instructs you to reduce stress and eat more fiber. You follow the guidelines and still nothing changes.

A month later you’re back again, and this time you get scheduled for a gastroscopy and colonoscopy. Both are singularly unpleasant experiences, and afterward your test results are completely normal. The gastroenterologist shrugs and stands by his diagnosis of IBS.

A friend recommends you see a functional medicine doctor. (If she’s a really good friend, she’ll insist you go to WholeHealth Chicago.)

Functional medicine for GI symptoms
After we listen carefully to you describe your symptoms and perform a physical examination, you’ll have some blood drawn and will leave the office with three functional medicine kits, instructions for specimen collection, and some FedEx envelopes for sending your specimens directly to the lab.

Likely you’ll receive:

Comprehensive Digestive Stool Analysis with screen for parasites and yeast (Candida)
This is the granddaddy of functional tests, used by thousands of practitioners (MDs, chiropractic physicians, naturopaths, osteopathic physicians, and clinical nutritionists) for more than 30 years. It’s not simply one test. Once you’ve sent in the vials containing your stool sample (you’re given a collection set to make it almost easy), the lab will perform up to 25 individual tests that will reveal how you’re digesting and absorbing your food, whether or not you have a healthy balance of bacteria, and if you have an infection with a parasite or candida.

If each test were run separately at a medical center like Northwestern, your bill would be well over $5,000 (I once calculated this), but using functional labs (like Genova, Doctor’s Data, and Great Plains) the price of this series is less than $500, with health insurance frequently offsetting some of the expense.

Test for hidden food sensitivities  This is a blood test that determines if your immune system is treating any of 96 commonly eaten foods as the enemy and creating antibodies in defense.  Unlike food allergies, which are immediate (lip swelling after eating strawberries, for example), sensitivity symptoms can occur one to three days after eating an offending food, usually manifesting as chronic indigestion. I urge you click the link above and spend a few minutes with the easy-to-understand report. At left the bars show foods to which the sample patient has no reaction. Bars extending to the right indicate foods that are causing an extremely high reaction. Look at the sample patient’s response to chicken and duck eggs, which is extremely high. Wheat, dairy, and tomatoes are also triggers.

Sometimes an irritating food will have already damaged your intestinal lining, producing a condition called leaky gut (also known as intestinal hyperpermeability). The presence of a leak can be revealed via a urine test (Genova) or a blood test (Cyrex Labs). As you might guess, eliminating irritating foods and healing leaky gut is a far better approach than “irritable bowel–reduce stress, eat fiber.”

If bloating is a major issue, testing for small intestinal bacterial overgrowth (SIBO) is a quick and easy take-home functional test. You begin by stimulating bacterial growth via drinking a pleasant-tasting liquid. Then every 30 minutes for three hours you blow into a balloon, snap on a vacuum tube, and send what looks like a box of empty tubes to the lab for gas analysis. Too much methane or hydrogen (or both) is likely responsible for your bloat. SIBO is surprisingly easy to treat with either antibiotics or more natural remedies.

I hope you’re now appreciating the difference between a single digestive test (like a stool culture or a colonoscopy) and a functional analysis of your entire gastrointestinal system.

Over the years I’ve taken care of numerous patients with chronic symptoms who underwent multiple (and completely normal) colonoscopies when all they needed was to take some digestive enzymes (as they learned from their Comprehensive Digestive Stool Analysis) or to eliminate dairy (as revealed by their food sensitivity profile).

Future of functional testing
Functional testing has now expanded to check your hormones; the state of your nutrition (vitamins, minerals, amino acids, fatty acids, neurotransmitters); your risks for cancer, osteoporosis, and heart disease; how efficiently you eliminate toxins; and how you handle oxidative stress.

One of the most exciting areas of functional medicine uses a quick scraping of the inside of your cheek (like 23andMe) to look at your genetic susceptibility to long-term health risks, what type of diet is best for you, what supplements are useful (and which you don’t need), and even what physical activities will be most helpful to your body.

In order to keep up with our patients’ demand for functional medicine physicians, later this month WholeHealth Chicago will welcome to its staff Neeti Sharma, MD, a board-certified internist like me, but who also has postgrad training at the Institute of Functional Medicine. We’re all looking forward to working with her.

More later and…

Be well,
David Edelberg, MD

PS: If easy digestion is an issue for you, take a look at our WholeHealth for Winter Digestion seminar Jan 19, 2019.

Leave a Comment

  1. Vivian says:

    What do you think of Dr. Gundry’s work, especially his recommendation of prebiotics and probiotics? Thank you.

  2. Dr E says:

    The suggestions are reasonable and very safe. His nutritional suggestions are all quite sound

  3. Kevin Muellner says:

    I’ve been diagnosed with Chrone’s disease and am seeking treatment options that do not involve biologics drugs since these are have dangerous side effects. Please contact me if you can provide the type of treatment I’m seeking.

    • cliffmaurer says:

      Hi Kevin –
      Our practitioners use a number of approaches to help patients diagnosed with Crohn’s disease. It’s such a commonly treated condition at WholeHealth Chicago that you could begin treatment with any of our physicians or nurse practitioners, then from there – depending of course on your particular case – recommendations to work with our nutritionist and/or one of our acupuncturists might be given and a treatment plan can begin. If you call our Patient Services staff at 773.296.6700, someone can get you in with one of our providers soon so that you can discuss treatment options and get started.

      I hope this helps, and we all wish you the very best in starting to feel well again.
      -Dr M

  4. Tess says:

    This article is fantastic! I have been through all of the things described in the traditional realm of medicine. I found Whole Health Chicago researching natural ways to combat gastric issues. I want to join your practice—I totally believe functional medicine is the path to superior healthcare!!! AND I live in California. AND, I have HMO insurance. Is there an AFFORDABLE way to work with one of your doctors and obtain the comprehensive testing you describe? Thank you for the great work and very clear explanations!

    • cliffmaurer says:

      Hi Tess,
      If you give our Patient Services representatives a call, they can discuss fees for telemedicine visits, and hopefully this will work out. They can be reached at 773-296-6700. We’d love to help you figure all of this out!

      My best,
      Dr. M

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Far and away, the commonest phone call/e mail I receive asks about COVID-19 diagnosis.
Just print this out, tape it on your refrigerator door, and stay calm.


• Runny nose
• Sneezing
• Red, swollen eyes
• Itchy eyes and nose
• Tickly throat
• No fever

• Runny nose
• Sneezing
• Sore throat
• Mild muscle aches
• Mild dry cough
• Rarely a low fever

• Painful sore throat
• Hurts to swallow
• Swollen glands in neck
• Fever

FLU (Standard seasonal flu)
• Fever
• Dry cough (no mucus)
• Sudden onset over few hours
• Headache
• Sore throat
• Fatigue, sometimes quite severe
• Muscle aches, sometimes quite severe
• Rarely, diarrhea

• Shortness of breath
• Fever (usually above 100 degrees)
• Dry cough (no mucus)
• Slow onset (2-14 days)
• Mild muscle aches
• Mild fatigue
• Mild sneezing

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