Should You Get a Stool Test?

Friday Aug 2 | BY |
| No Comments

Stool Test

With all the research on gut health, should you submit to a stool test to see how you’re doing?

What’s the next best step toward optimal wellness after you’ve made positive changes to your diet, added super foods, started a nutritional supplement plan, and taken blood tests to assure that your food and supplements are working?

If you guessed gut health, you’re right.

For decades, naturopaths have emphasized the importance of a healthy colon, also called the human gut. Whether it’s with colonic irrigation, Dr. Jensen’s colema boards, herbal laxatives, probiotics, and coffee enemas—you name it—people have been trying to fix their guts forever.

Now doctors have gotten in to the act by performing fecal implants. During the procedure, stool from healthy young person is injected into the rectum of an older, sick person. Guess what? It cures antibiotic resistant bacterial infections, including the toxin-producing bacterium known as Clostridium difficile that takes over the gut and eats away at the lining. C. diff is a nasty bug that causes severe diarrhea and infects more than three million people in America each year.

With a mortality rate as high as pandemic influenza and an annual cost of $1.6 billion in the United States, C. diff is a serious health problem. Fecal implants have a 95% success rate, and cost very little. Not as glamorous as brain surgery, but fecal implants work!

Should You Get a Stool Test?

The gut is so important that scientists are leap-frogging ahead of doctors. I wrote about the gut genome project in a previous blog. But mapping bugs in the gut is just the beginning.

Scientists have found that gut ecology and immune activity have powerful influences on mood and inflammation. Gut microbiota influence glucose metabolism, weight, and acne breakouts. Irritable bowel syndrome is essentially a disease of imbalanced gut ecology.

If the gut is so important, is stool testing useful as part of your overall wellness plan?

In naturopathic medicine, we’ve been utilizing stool testing for some time. However, even though doctors recognize the importance of gut health on overall wellness, as well as disease prevention, the laboratory science of stool testing is in its infancy.

Companies In the Stool Testing Game

Specialty labs like Genova Diagnostics and Metamatrix Clinical Laboratories (recently joined up with Genova) have led the way in clinical testing for gastrointestinal health for more than two decades. DiagnosTechs provides a gastrointestinal panel that uses stool and saliva samples, and gives a glimpse of common food allergies.

There’s a major difficulty, however. Gut ecology is so vast and complex that it’s hard to get an idea of gastrointestinal health from a single test.

Partial Lists of Genova Diagnostics’ Tests in a Stool Sample

  • Bacteriology Culture, aerobic
  • Bacteriology Culture, aerobic x 3
  • Bacteriology Culture, anaerobic
  • Beneficial SCFAs
  • Beta-Glucuronidase
  • Bile Acids
  • Calprotectin
  • Cryptosporidium EIA
  • Deoxycholic Acid
  • Entamoeba histolytica
  • Eosinophil Protein X (EPX)
  • Giardia lamblia EIA
  • LithoCholic Acid
  • Pancreatic Elastase
  • Parasite Identification, Concentrate Prep
  • Parasite Identification, Trichrome Stain
  • Putrefactive SCFAs
  • Yeast Culture
  • n-Butyrate %
  • pH

When diagnosing gut issues, conventional doctors know that it’s best to focus on a single problem, like parasites, bacteria, yeast (like Candida albicans), or bleeding. But for use in wellness medicine, that’s clinically myopic. The standard ova and parasite stool tests done by conventional doctors are insufficient to determine what’s going on in your gut.

Tests from Genova/Metametrix evaluate digestion and absorption, bacterial balance and metabolism, yeast and immune status for patients with irritable bowel syndrome, indigestion, malabsorption, and other GI-related problems like fatty liver disease and gallstones. Additionally, they look for parasites using microscopic examination and EIA testing. Sounds great, but are all test analyses useful?

Most People Can Hold Off for Now

Functional medicine tests look at so many things that it’s overwhelmingly challenging for the doctor to get an idea of a person’s gut health from a single stool sample. And those things change because the gut environment is dynamic. A patient would have do serial testing over time to get any real idea of what is going on.

Even with these inherent drawbacks, comprehensive stool testing has clinical value. I’ve been ordering stool testing since 1985, but now only use them for patients who have gastrointestinal conditions. I’ve found that generally healthy people have normal stool test results. It seems that the human gut has remarkable ways to maintain its own equilibrium.

Based on my experience, routine stool sample screening for all patients or for younger healthy patients is not warranted. I regularly use these tests for patients with chronic disease, autoimmune diseases, and gastrointestinal conditions. I have no doubt that labs will come up with a simplified version that’s easy to interpret for people to order their own stool tests—but that hasn’t happened yet. For now, you’ll have to find a doctor knowledgeable in stool test interpretation to help you discover what’s going on inside your gut.

Dr. J. E. Williams


Dr. Williams is a pioneer in integrative and functional medicine, the author of six books, and a practicing clinician with over 100,000 patient visits. His areas of interest include longevity and viral immunity. Formerly from San Diego, he now resides in Sarasota, Florida and practices at the Florida Integrative Medical Center. He teaches at NOVA Southeastern University and Emperor’s College of Oriental Medicine.

Visit Dr. Williams’ Website:

And Follow on Facebook:


Comments are closed.