Mapping the Microbiome: Lab Testing for Dysbiosis 

Dr. Leah Hassall, ND

As the interest in the human microbiome grows, the complexities of the microbiome and the link between a dysfunctional microbiome and chronic conditions such as fibromyalgia, acne, diabetes, eczema, allergies, IBS, inflammatory bowel disease, obesity, depression and anxiety, cancer and many autoimmune conditions continues to unfold. When we refer to the microbiome, we are talking about all of the microbes (bacteria, parasites and fungi) that live in and on our bodies. They are found in our mouths, guts, skin, urinary tract system…in fact, their combined amount of DNA far exceed our own making us more “microbe” than human! When we refer to dysbiosis, we are talking about an imbalance in the relative amounts of “helpful” microbes compared to “disease-causing or harmful” microbes in healthy person. A well-known example is a yeast infection, which can happen in the vagina, but also in skin folds and in the mouth. Yeast is a microbe that we normally live with without much issue. When the environment becomes more favourable to its growth (i.e. increased pH, increased stress, poor diet), then the microbes that normally keep it in check are no longer able to prevent its overgrowth.

How Do We Know if Someone Has Dysbiosis? 

In the small intestine: The small intestine should have relatively few microbes living in it when compared to the large intestine. During times of fasting (i.e. overnight or between meals), the small intestine does its housekeeping duties by sweeping bacteria and food into the large intestine where it belongs. In some people, this mechanism is not working optimally, or is totally absent. This allows bacteria to overgrow in the small intestine where they ferment gases and produce bloating, diarrhea and/or constipation. It is thought that 60% of IBS cases are caused by this overgrowth, known as SIBO (small intestinal bacterial overgrowth). It is associated with conditions such as IBD (Crohn’s and colitis), fibromyalgia, fatty liver disease and many others. Testing for SIBO involves a 3 hour lactulose breath test that people can do at home. To learn more about SIBO testing and treatment, please watch this video.

In the large intestine: the small intestine and the large intestine (colon) are totally different habitats for microbes. Billions of microbes co-habit this zoo and have important roles in fermentation of fiber, production of vitamin (B vitamins and vitamin K) and development of the immune system. Because of this, we need totally different testing. Stool sample testing can offer a non-invasive, relatively simple way to detect a wide range of harmful and beneficial bacteria, parasites and yeast/fungi. They can also tell us which herbal and pharmaceutical agents will be most effective against them so we can better target and treat them.

In the vagina: There are many different organisms that can cause vaginal discharge. One of the most common reasons for vaginal discharge is a yeast overgrowth, but others include sexually transmitted organisms (Gonorrhea, Chlamydia and Trichomonas) and bacterial vaginosis (BV). BV is an overgrowth of the bacteria that are normally found in the vagina. Gonorrhea, Chlamydia and Trichomonas are not present in a healthy person. The only way that we can determine what is causing the problem with 100% certainty is by doing a swab (on the skin or in the vagina) and culturing it in the lab and/or viewing it under the microscope. By correctly identifying the microbe, we can better treat it! Gonorrhea, Chlamydia, Trichomonas and other sexually transmitted infections are not the result of dysbiosis (even someone with great vaginal flora can get these!), but sometimes the treatment can lead to dysbiosis as the antibiotics used may also destroy healthy Lactobacilli and Bifidobacteria. Here is where probiotic therapy (rich in L.rheuteri and L.rhamnosus) can be helpful. Chronic BV is more of an issue with dysbiosis. This is where hormone balancing, lowering vaginal pH and probiotic therapy can be used.

Looking to the Future

An exciting way to determine if someone has dysbiosis and know exactly who is living in our digestive tracts would be to map the entire genome of all of the microorganisms. What seems like science fiction is now available in some countries. uBiome is a biotechnology company in the United States that is doing just that. Smart Gut testing is not currently available in Canada (at the time I am writing this article), but when it does become available, it could be a fascinating and useful tool in understanding the microbiome and dysbiosis in humans. Perhaps one day we will be able to tweak the microbiome in a more targeted way in addition to improving the overall microbiome through diet, exercise, sleep and reduction of stress.

If you are interested in seeing if dysbiosis is at the root cause of your health concerns, naturopathic physicians are experts in microbiome testing and treatment.


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