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What is Dysbiosis? Imbalanced Intestinal Flora

Dysbiosis is a term used in naturopathic medicine to describe an imbalance in the normal mix of microorganisms (called “flora”) in the intestinal tract. Alterations in the intestinal flora include overgrowths of harmful yeast, parasites and bacteria or deficiencies of healthy bacteria. Many patients suffering from chronic digestive symptoms who have been labelled with irritable bowel syndrome (IBS) actually have dysbiosis as the undiagnosed root cause.

Yeast, Bacteria and Parasites

There are three main types of harmful organisms that can overgrow in our intestinal tract. Yeast overgrowth is the most common and can be caused by a high-sugar diet or even a single course of antibiotics. Candida albicans is the most common yeast strain to overgrow and can cause symptoms including constipation, gas, bloating, skin infections and yeast infections in women. Harmful bacteria can become dominant, causing a condition called small intestine bacterial overgrowth (SIBO). SIBO is very often misdiagnosed as irritable bowel syndrome. Parasites can also be picked up from our food and water consumption, especially when travelling internationally.

Diagnosing Dybiosis

A detailed diet, medication and travel history along with specialized stool testing can help naturopathic physicians identify the exact type of intestinal imbalance that is present. Conventional stool testing often misses cases of chronic intestinal infections. Many naturopaths use alternative labs for stool testing called Comprehensive Parasitology that is more thorough and focuses on detecting all types of intestinal infections, both acute and chronic. When a bacterial or yeast strain is detected with this test, the lab cultures the organism from the patient’s sample and applies various drugs and herbs to the organism. A chart is provided with each lab result that shows which treatment the organism is sensitive to and which it is resistant to. This can allow the doctor to prescribe a targeted treatment protocol based on the objective information the test provides.

Dysbiosis Treatment

Treatment of dysbiosis includes antimicrobial herbal remedies to eradicate harmful microorganisms and probiotic supplements to replenish beneficial bacteria. Probiotics contain billions of health-promoting bacteria in each capsule and help us re-establish a healthy intestinal flora. Without them an intestinal infection will often recur shortly after treatment.

Before concluding that a patient has irritable bowel syndrome, the possibility of a chronic intestinal overgrowth should be thoroughly evaluated. In my practice I have seen some patients who have suffered from what were considered IBS symptoms for over 20 years, only to realize with appropriate testing that they were dealing with dysbiosis. Some actually remember the symptoms beginning with an acute illness picked up while travelling decades earlier. Treatment can be simple and short term and may potentially cure chronic digestive symptoms.

Dr. Arjuna Veeravagu is a naturopathic physician, registered acupuncturist and founder of Sage Clinic in Yaletown. To schedule a consultation with Dr. Veeravagu please email or call 604-697-0397.


To learn what foods can help reduce gut inflammation, see our article “How to Reduce Gut Inflammation“, and find out what natural remedies are good for digestion in this article written by Katolen Yardley, a Medical Herbalist.