Herbs and the Microbiome

Dr. Natalie MacIsaac, ND

The microbiome in our gut is a dynamic environment that shifts in response to our diet, our hormones, and our stress levels. Studies have linked the microbiome to mood and behavior, gut disorders, eczema, asthma, chronic sinusitis, and obesity. The most popular and well known treatment to support gut and immune health is probiotics. These friendly bacteria make their way to the large intestine where they bring balance by displacing or destroying harmful bugs and yeast. Unfortunately, it doesn’t always work well for everyone. If you’ve ever taken a probiotic and felt worse then you may be adding to the problem instead of treating it. For people who have not had success with probiotics, anti-bacterial and gut healing herbs like Berberis and Dandelion may help to improve your micro biome and boost your immune health.


To maintain a healthy micro biome the beneficial bacteria in your gut need to be in the correct amounts and proportions to other bacterias. Berberine is known to restore normal bowel flora by acting as an anti-bacterial to an overgrowth of harmful bacteria.  There are many species of this wonderful genus of plant including the commonly used goldenseal and barberry root.  Both of these herbs contain the active ingredient berberine.


Having regular bowel movements is essential to maintaining a healthy micro biome. Constipation can upset the healthy balance of bacteria by allowing them to proliferate and spread to the small intestine. Our primary natural laxative is bile, so in addition to fruits, vegetables, and fiber, herbs that stimulate bile production can ensure regular bowel movements. Dandelion greens and herbs are an excellent option to support this process. You can add the fresh greens to a shake, stir-fry them with other greens or vegetables, or add them to a salad. If the bitter taste is too much for you, you can also take it as a liquid herb or pill.

If you continue to have issues with your digestion despite taking probiotics, please talk to your naturopath at Sage Clinic.  A worsening of symptoms with probiotic use may indicate the presence of a condition known as small intestinal bacterial overgrowth or SIBO.  Your Sage Clinic naturopath is able to offer you state of the art testing to confirm this diagnosis.