How to Test for Dysbiosis

Those 70 trillion to 100 trillion beneficial bacteria lining our digestive system are responsible for multiple physiological functions including:

  • Immunity: Our digestive tract is base camp for 70% of our immune system: a good relationship between the body and the beneficial bacteria is important to fight off colds and common infections.
  • Neurotransmitter production: Every class of brain neurotransmitter has been found in the gut, including about 80% to 90% of our serotonin.
  • Energy harvesting: Gut microbes extract energy from undigested food products as it passes through the digestive system.
  • Metabolic regulation: the microbiome plays a role in regulating everything from appetite and fat storage to sleep cycles.
  • Production of key vitamins & cofactors

A number of things can adversely affect microbiome composition, such as chronic stress, age, environmental toxins, food sensitivities, genetics, malnutrition, obesity, smoking, use of antibiotics, proton pump inhibitors and other medications, and most importantly, diet.

Some bacterial strains once present in the upper GI tract can cause gas, bloating, fat malabsorption diarrhea and constipation (or both). Ultimately, they damage the lining of the small intestine and prevent the body from absorbing essential nutrients.

Eluding the Radar

Dysbiosis is most prominent in the digestive tract and the skin, but really, it can be found on any exposed surface or mucous membrane, such as the vagina, lungs, mouth, nose, sinuses, ears, nails or eyes.

The only way to properly treat dysbiosis is to remove bad bacteria, yeast and parasites, all of which can be considered infections that elude the radar of conventional medical tests (Amit Dutta, et al. Gastroenterology & Endoscopy News. 2015; 66:4).

But that doesn’t mean we as clinicians must fly completely blind or rely totally on guesswork. There are a number of testing methods—some of which have been around for decades, others of which are very new—to help guide us. Just because they’re not (yet) part of the conventional gastroenterological toolkit doesn’t mean they should be ignored.

A Basic Approach

Dysbiosis testingThere are a number of effective ways to test for dysbiosis and a number of laboratories that test for it: Genova Diagnostics; Metametrix Laboratories; Doctors Data Laboratory; Enterolabs; QuinTron Breath Test; Commonwealth Laboratories and Cell Science Systems are among the top labs providing tests to evaluate potential dysbiosis.

It is also possible for patients to get genetic analysis of their gut microbiome for $89, from a company called uBiome.

Here’s a basic outline for how to approach patients whose symptoms fit the picture of dysbiosis.

  1. History: It’s important to listen to patients and their symptoms, diet, and past medical, family, and social history. This wealth of information can often give you a lot of diagnostic clues. It’s also the cheapest option and most patients prefer it.
  2. Comprehensive Stool Test: This non-invasive test gives you a picture of some of the organisms present in a patient’s GI tract, as well as some sense of bacterial balance and presence of yeast. This test is recommended for patients with diffuse and non-specific symptoms. Some clinicians question the value of stool testing because it does not give much information about organisms that may be deep in the mucosal walls or ensconced under biofilms. Likewise it may not tell much about bugs living upstream in the upper GI tract. But it can be a good place to start with many patients.
  3. Urine Test: This method looks for unique products of microbial metabolism in the urine. It can indicate presence of small bowel yeast, bacterial overgrowth, and unfriendly intestinal microorganisms that manufacture high quantities of compounds not normally produced by human cells, such as D-arabinitol. These compounds are absorbed into the blood from the intestines and eventually appear in the urine. The virtue of urine testing is that is very easy to do.
  4. Intestinal Permeability Assessment or Mannitol-Lactulose Intestinal Permeability Test: This test involves having the patient drink a premeasured amount of two sugars: lactulose and mannitol. The relative presence of these sugars in the urine will show how permeable the intestine is. An elevated ratio of lactulose to mannitol will indicate dysbiosis and leaky gut syndrome.
  5. Hydrogen or Methane Breath Test: This is the gold standard for assessing dysbiosis. Though fairly simple in principle, it can be cumbersome and time-consuming. It tests for Irritable Bowel Syndrome (IBS), Small Intestinal Bacterial Overgrowth (SIBO), and other digestive disturbances related to sugar or food intolerances.

a. After a baseline breath gas measurement, the patient ingests a standardized solution of lactulose or another substrate that is normally indigestible by humans but highly digestible by bacteria.

b. Measurement of hydrogen and methane in the breath at regular intervals—typically every 20 minutes—will indicate the degree of microbial fermentation of the lactulose within the upper GI tract.

c. Rapid and steady rises in hydrogen and methane are proof-positive of dysbiosis.

These tests can be repeated as needed to gauge progress with treatment of leaky gut.

It’s important to note that dysbiosis cannot be found through an endoscopy or colonoscopy, nor does it show up definitively on standard blood work, so many practitioners miss it.

Watch the B Vitamins

That said, according to Raphael Kellman, MD, a functional medicine physician in New York City, there are a few major clues to be found among measurements of basic blood nutrient levels.

“If B vitamins are low, and zinc is low, the patient’s microbiome is unhealthy,” says Dr. Kellman, MD. “There are many other things you can measure—butyrate, short chain fatty acids, the microbiome composition itself. But start with the B’s. If they’re low, the microbiome is not healthy.”

There are additional tests that can be useful in evaluating someone’s gut health.

  1. Food sensitivity tests: These tests involve measuring IgG and IgE levels to various food antigens, along with celiac panels.
  2. Genetic Tests: It’s now possible to measure how effectively patients’ enzymes are functioning, especially the enzymes involved in liver detoxification pathways and those that regulate brain neurotransmitters.
  3. Toxin Load Assessment: This looks for heavy metals, solvents or pesticides. If a patient has a high toxin load, the next step is to discuss detoxification interventions.
  4. The Pulse Test: A change in the pulse and/or heart rate greater than 10 beats per minute will often follow exposure to a problematic food or toxin. Though not a definitive testing method by any means, this is certainly an inexpensive tool, and it can add information when it’s correlated with symptoms and data from other tests.
  5. Antigen tests for H. pylori, C. difficile and other bacteria: These tests can help you get a better sense of who’s living in the neighborhood, so to speak, and what may be contributing to the symptom patterns.

Identifying and reversing dysbiosis can be life-changing for many patients. It’s a condition that can be effectively addressed by targeting and eliminating pernicious bugs or those that are not where they should be in the GI tract, by removing processed bad foods, adding back healing good foods and probiotic flora, and by helping to restore the damaged intestinal lining with specifically targeted herbs, nutrients and foods (like bone broth).

It’s exciting to see new research showing that dysbiosis plays a role in metabolic pathways that lead to obesity, diabetes, cardiovascular disease, gastrointestinal conditions, autoimmune disease and cancer. More study in this field can help reduce the burden of disease in society. In the meantime, trust thy gut—it may already know what thy head hasn’t yet figured out.

Madiha Saeed, MD, is a holistic family medicine physician in Aurora, IL. She received her MD from National University of Science and Technology and completed her residency in 2010 at St. Joseph Regional Medical Center. She is currently board certified in Family Medicine and is board certified in Integrative Holistic Medicine.
The Society of Teachers of Family Medicine awarded her the Resident Teacher Award in June, 2010. Dr. Saeed also has a diploma in clinical homeopathy.

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