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Microbiome Testing & The Importance of Gut Microbes

Posted by Dr. Barry Taylor on Jan 25, 2019 3:03:24 PM


Barry Taylor, ND

A comprehensive stool analysis has been the standard test for large intestine microbiome health in functional medicine for decades.

In most cases, a stool analysis will show you whether or not the patient has a healthy flora population, and if there are any infectious agents interfering with the overall gastrointestinal health. This test is a great starting point, but it provides a rather narrow view of the exceedingly complex gut microbiome. With a more robust knowledge of the small intestine microbiome, the standard comprehensive stool analysis by itself might not be enough to determine a patient’s microbiome problem. Additional documented information is needed for viewing a patient’s microbiome through a more comprehensive lens.

Microbiomes and Their Impact on the Brain

The gut microbiome has been found to have various effects on the human brain. Lipopolysaccharides and other structural bacterial components communicate with the innate immune system through tonic stimulation. Too little stimulation can result in a weak innate immune system, and conversely, excessive stimulation may lead to systemic central nervous system inflammation and in some cases affect the central nervous system as well.

Gut microbes have been found to influence:

  • Sleeping patterns.

  • Stress reactivity of the HPA axis.

  • Moods.

  • Memory and cognitive values.

  • The immune system.

Overstimulation and inflammation of various nerves can occur due to many factors. Symptoms include bloating, occasional diarrhea, gas (frequent belching or flatulence), abdominal discomfort, food intolerance, vitamin deficiency, and more.



Going Upstream

When you visit the hospital or make a doctor’s appointment with a traditional medicine practitioner, chances are they’re going to treat the symptoms downstream of the real problem.

Sometimes, the healthcare professional may be keyed in and have the patient on the right track, but they missed something somewhere. An example of this is someone who has been dealing with Candida for an extended period of time while on a Candida diet and anti-yeast formulas. The physician may miss that their flora is off by a substantial amount, or they may miss another factor such as a parasite or toxins that are interfering with progress. Thus, the treatment is still downstream of the overlying issue which is causing the symptoms.

Functional medical practitioners take a different approach. Identifying how to treat the problem upstream of the source is imperative. Along with basic tests, like a comprehensive stool analysis, the patient should also be clued into how to monitor their own vitality. This way, as treatment progresses, the doctor or naturopath can evaluate improvement or regression. Is the patient sleeping better? Are they waking up with more pep in their step? Are they less tired in the afternoons? Does a particular type of food seem to cause a reaction?

If the patient can accurately report key aspects of their overall vitality, a functional medical practitioner will better understand if and when additional is necessary.

Probiotics, Prebiotics, Synbiotics

Probiotics is a catchall term that includes both prebiotics and probiotics. Synbiotics are the synergistic combination of both. Treating GI-related issues upstream starts at the gut. Returning the gut microbiome to a balanced state through the use of probiotics will help.*

But not all probiotics and prebiotics are created equally. Strain varieties, number of live microorganisms, and the shelf life of the supplement’s potency are all major factors in quality and effectiveness. Some probiotics and prebiotics are ideal for general long-term use, while other may be better suited to short-term, targeted needs.

If you or your patient are taking a suitable high-quality probiotic, but you’re seeing limited results, check whether they’re being taken with food or not. The stomach’s hydrochloric acid is a known probiotic killer. Even though some probiotics and other microbiome regulators are marketed as ‘enteric-coated’ to survive sitting in an acid-filled stomach (like after a meal or with food), it is best to take any probiotics completely separately from meals to ensure that they do their job in fully recovering your microbiome integrity.


In some cases, additional tests may be needed to identify exactly where the problem lies. But with a properly interpreted stool analysis and a well-monitored patient, a good functional medical practitioner should be able to determine the correct course of action to correct an unbalanced microbiome and get it working with the body and mind in a healthy and harmonious manner once again.


*These statements have not been evaluated by the Food and Drug Administration. This product is not intended to diagnose, treat, cure or prevent any disease.

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