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4 Herbs to Boost Your Microbiome

Updated: Jan 22, 2020

What is a microbiome?

In biological terms, we're comprised of more microbes than cells. Microbes (bacteria, viruses, fungi, and protozoa) are the genetic material that thrives on and within us. Over 100 trillion of these microbes are responsible for the synthesis and clotting of essential vitamins and minerals, protecting the body from illness, and assisting with bodily functions such as digesting food. This fascinating system wasn't discovered until the late 1900s, and ever since scientists have been working to understand this system as a whole (1).

Functionality of the Microbiome

Just like the human genome, genetics and environmental factors affect the microbiome. Thanks to the knowledge of epigenetics, we now know that we can control both of those factors, thus not being bound to an illness. The majority of microbiomes exist within the gut, specifically in the large intestine.

90 percent of the body's serotonin is produced in the gut.

The gastrointestinal system directly correlates to our mental wellness and overall wellness. In historical texts and teachings, the kidneys were once thought to be the seat of the soul, where our emotions and multidimensional self reside. Our predecessors had an innate knowing of the importance of the digestive system long before the term microbiome was created.

In addition to the two factors that affect the microbiome, lifestyle choices are the common denominator between genetics and the environment. Of those lifestyle choices, herbs may be utilized to further understand and heal one's microbiome. These herbs will vary from person to person, as microbiomes differ already without factoring in hindered metabolic processes that result in issues such as diabetes and autoimmune illnesses.

Optimal Herbal Choices for the Microbiome

Scientists have published studies about certain herbs that directly affect the microbiome. My findings are listed below, in addition to a thorough explanation as to their components and energetics.


Derived from the inner bark of the tree, the mucilage nature of slippery elm caters to the gastrointestinal tract, from the airways (larynx, esophagus, etc) to the lower digestive tract (stomach, intestines).

According to the Natural Medicines Comprehensive Database, slippery elm is used for the treatment of coughs, sore throat, colic, diarrhea, constipation, hemorrhoids, irritable bowel syndrome (IBS), cystitis, urinary inflammation, urinary tract infections, syphilis, herpes, expelling tapeworms, protecting against stomach and duodenal ulcers, for colitis, diverticulitis, GI inflammation, and acidity (2).

As the vicious, mucilage-rich liquid of slippery elm enters the body and trails down the gastrointestinal tract, it facilitates the union of unlike compounds whilst temporarily confining large polymers over the mucosal surfaces of the tract. This action attributes to the soothing property of slippery elm as it coats the irritated areas (3).

Studies have shown slippery elm has systemic anti-inflammatory effects in the stomach and intestines, as well as increases the production of cytokines in the immune system (4).


The leaves, roots, and seeds of Burdock are cultivated medicinally for its gastroprotective and hepatoprotective properties. Traditionally, burdock used to treat diseases such as sore throat and infections such as rashes, boils, and various skin problems (5).

One of the most rich sources of prebiotics and inulin, the nutritious burdock root can be steeped in a tea or eaten as a root vegetable.


Its cooling nature disperses accumulated heat within the liver, stomach, and small intestines, which restores energy flow within those organs, avoiding discomfort such as gas, bloating, and constipation.

The gelatinous nature of this plant holds potent healing properties for the gut.

Known for its soothing action, aloe vera is rich in prebiotic compounds, thus assisting with restoring a healthy gut microbiota. Need a combination of prebiotics and probiotics? Naturally, fermented aloe vera contains both nutrients, which further enhance microbiome health (6).


This classic digestive tonic grows readily just about anywhere, yet it's best to pick in the cooler months as its medicinal properties are most concentrated in the root at this time.

It's subtle and effective in nature (dosage depending) and pairs well with probiotics, as it's rich in prebiotics.

Harvest and preserve in the cool months to utilize as a tea as the digestive system tends to be sluggish during this time (7).

Additional Lifestyle Integrations for Microbiome Health

Before you dive into herbs, I want you to know there are things you can do outside of plant medicine that can improve your microbiome health.

According to my health coaching plan, there are six pillars of health: nutrition, sleep, physical movement, stress management, sunshine, and breath.

Incorporating these pillars into your life in a conscious manner will deliver a prominent change to your well-being. Of course, the herbal aspect of healing can be intertwined with the nutrition pillar, further propelling healing.

Consult with a gastroenterologist, a holistic nutritionist, dietician, an herbalist, or a combination of health professionals to assist in your microbiome wellness. There are at-home kits, but I would caution as they are still in the beta phase and your results are based on comparison and the culture taken at a certain time and place.



1. Hair, M., Sharpe, J. (January 2014) Fast Facts About the Human Microbiome. The Center for Ecogenetics and Environmental Health, University of Washington.

2. Jellin JM, Gregory P, Batz F, Hitchen K, Burson S, Shaver K, Palacioz K (eds). Natural Medicines Comprehensive Database. Therapeutic Research, Stockton, 2000.

3. Watts, Christopher & Rousseau, Bernard. (2012). Slippery Elm, its Biochemistry, and use as a Complementary and Alternative Treatment for Laryngeal Irritation. Journal of Investigational Biochemistry. 1. 17-23. 10.5455/jib.20120417052415.

4. Yousuk L, Hyunjin P, Ryu H, Chun M, Kang S, Kim HS. Effects of elm bark (Ulmusdavidiana var. japonica) extracts on the modulation of immunocompetence in mice. Journal of Medicinal Food, 2007: 10:118-125

5. Yuk-Shing Chan, Long-Ni Cheng, Jian-Hong Wu, Enoch Chan, Yiu-Wa Kwan, Simon Ming-Yuen Lee, George Pak-Heng Leung, Peter Hoi-Fu Yu, Shun-Wan Chan. A review of the pharmacological effects of Arctium lappa (burdock). Inflammopharmacology. 2011 Oct; 19(5): 245–254. Published online 2010 Oct 28. doi: 10.1007/s10787-010-0062-4

6. Catinean, A., Neag, M. A., Muntean, D. M., Bocsan, I. C., & Buzoianu, A. D. (2018). An overview on the interplay between nutraceuticals and gut microbiota. PeerJ, 6, e4465. doi:10.7717/peerj.4465

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The herbalist, chemist, and medicine maker at Asili Apothecary, Gloria created this space to facilitate healing and learning for yourself and those around you. The apothecary and homestead is based in Fayetteville, NC. Gloria enjoys time with her family and Mother Nature.

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