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What Is a Microbiome and Why Is It Important?

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In the great words of Hippocrates, "All disease begins in the gut."  The digestive tract is not just for digesting and absorbing nutrients. A well-functioning digestive system will maximally absorb nutrients from our food to provide the energy and the building blocks for maintaining health, healing, and repair. Healthy digestion is not only the processing and assimilation of nutrients, it also involves regular elimination through healthy bowel movements, a balanced immune system, and mucosal barrier function. It is also involved in the proper function of our immune function. In fact, approximately 70% of the immune system resides in the gut!

Good gut health has also been shown to positively influence brain health and research reveals that there is a strong gut-brain connection. Good gut health will positively influence metabolic, hormonal, immune, and neurological health.

What is the Microbiome?

Humankind has co-evolved with its microbiome. Consider that if our bodies are our temple then our microbiota is its loyal attendants. We have lived in symbiosis since the beginning of time. These microorganisms are made up of "friendly" bacteria, viruses, protozoa, archaea, and fungi. When microorganisms behave synergistically to further the wellbeing of their host, they are called a commensal. Understand that the microbiome is a delicate ecosystem in the same way that the earth, its Amazon rainforest, and Great Barrier Reef are each an ecosystem. Like other ecosystems, our microbiome thrives on the diversity, harmony, and cooperation of its species. This causes physiological homeostasis (balance) that sustains the wellness and vitality of the host.  Science reveals that the more diverse the gastrointestinal microbiome is, the more it will positively influence every aspect of our physiological and psychological wellbeing. Our physiology has evolved with and trusts and relies on microbiota to regulate our genetic expressions, hormones, immune response, metabolism, mood, cognition, the assimilation of nutrients, and neurology.

However, a damaged microbiome is not commensal in that it does not promote the wellbeing of the host. This is often called dysbiosis and leads to digestive imbalances that could lead to more serious digestive issues. This imbalance can turn on the switch for those genes that code for unhealthy aging and inflammation. 

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The Importance of a Healthy Gut Lining

A healthy gut requires an intact mucosal barrier function. Central to the intestinal lining and part of the mucosa is a gel-like layer of mucous. It is 90% water and 10% glycosylated proteins. Mucous hydrates and protects the epithelial layer of gut mucosa while being permeable to transfer nutrients. A healthy mucous layer is nutrient-dense and is both food and home to a commensal microbiome. The intestinal mucosal barrier forms part of our defense mechanism in the immune system. The mucosal cells are strongly attached to each other through tight junction proteins called occludin and zonulin. The tight junction forms a semi-permeable protective barrier so undigested proteins and toxins do not readily cross the mucosal barrier.

What Has Damaged our Microbiome?

After World War II, there was a shift towards a western-style diet of increasingly processed foods that were low in fiber and high in salt, saturated fats, and refined carbohydrates. 

This shift away from whole foods, high fiber, and a plant-based diet is associated with a dysbiotic microbiome that tips the scales towards the genetic switches that cause unhealthy aging and dis-ease  With the dietary shift towards processed foods, we see an increase in autoimmune disorders, mood disorders, neurodegenerative conditions,  metabolic diseases, and accelerated aging.

The Standard Western Diet leads to a damaged microbiome that contributes to some of these common health challenges:

  • Mood, cognition, and neurological imbalances
  • Metabolic condition
  • Digestive irregularities
  • Unhealthy gut lining
  • Hormonal imbalances

A healthy microbiome will promote the maintenance of health and reverse the symptoms of chronic dis-ease.

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The 5 R’s to Cultivate A Beneficial Microbiome


  • Processed foods (anything with more than five ingredients on its label) 
  • Foods with additives, dyes, emulsifiers, preservatives, flavorings, and anything in them that you can't pronounce or don't know what it is 
  • Refined sugar, fructose, corn syrup, high-fructose corn syrup, sucrose, or candy
  • Refined grains
  • Saturated fats
  • Exposure to environmental toxins
  • Energy drinks, high-sugar sports drinks, soda (regular or diet)
  • Fruit juice where pulp (fiber) has been removed 
  • Coffee (Caffeine is a central nervous system stimulant and may fatigue your adrenals with habitual use. Even decaf has up to 50% caffeine, and the chemicals used to decaffeinate are worse than the caffeine itself.)

Replace with

  • Water and herbal tea
  • Organic whole, plant-based foods
  • Organic meat, fish, eggs to 2-3 servings/week grass-fed, hormone-free, antibiotic-free  
  • Healthy fats coconut oil (high heat), butter, ghee, olive oil (low heat or salad), avocado oil, nuts, seeds
  • Organic vegetables unlimited each day 
  • Fruit up to three servings per day, preferably low glycemic fruits like berries, apple, grapefruit, lemon, and pitted fruits like cherries, apricot, plums, peaches, or avocado.
  • Organic whole grains (gluten-free if gluten sensitive)
  • Herbal coffee or chai


  • Attract and nourish a healthy microbiome with a whole foods, plant-based diet.
  • Fiber is a prebiotic. Eat at least 40grams of fiber per day.
  • Probiotic-rich foods with every meal from a variety of sources. (Kimchi, coconut kefir, sauerkraut, kombucha, miso, yogurt, pickles, or tempeh.)


  • Herbs as spices or teas and either fresh or dried are our secret weapon and create agents in the body help fend off undesirable effects. 
  • Try to eat at least 30 different plants each week
  • Consider fresh or dried infusions of plentiful but nutritive spring tonic herbs of nettle, dandelion, etc. 


  • Adaptogens 
  • Sleep 
  • Exercise 
  • Meditate 
  • Sunshine

Where we put our fork affects everything that we are, and 90% of who we are is our microbiome. Through food and lifestyle choices we can attract those commensal microflorae that will turn on the genetic switches that maintain wellbeing. Understand that what we feed our microbiome is pivotal. Every meal tips the scales towards wellbeing or dis-ease. A commensal or dysbiotic microbiome is dependent upon us. We give them food and a home. What we eat, they also eat. They in turn switch on and off the genes that regulate many processes throughout the human body.

*This post is part of a series.  Please continue to tune in to learn more about ways to support your microbiome through healthy life choices. 


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Topics: Herbalism

Crystal Dawn Silas, MD- Guest Writer

Written by Crystal Dawn Silas, MD- Guest Writer on April 26, 2021

Crystal Dawn Silas, MD is an herbalist, emergency room physician, blog writer, speaker, and world traveler who informs and empowers people towards a more happy, healthy, and wholesome life. Dr. Crystal Dawn was born in Queens, NY, and graduated from Wright State University in Dayton, Ohio. She completed her family medicine residency in San Bernardino, California, and then joyfully found her path into the herbal community. Dr. Crystal Dawn has participated in two herbal apprenticeships. Her first herbal teacher was Shatoiya De La Tour at Dry Creek Herb Farm in Auburn, CA. She then participated in Advanced Herbal Study with Rosemary Gladstar on Sage Mountain in Vermont. Dr. Crystal Dawn has also been initiated onto The Priestess Path with Alisa Starkweather in the New England area. She is currently serving as an adjunct faculty member for the Association Advancement of Restorative Medicine (AARM) and has been enjoying her boutique medical practice where she infuses medicinal botanicals, and other integrative approaches, into her wellness modalities. She nurtures neuroplasticity (a growth mindset) towards the cultivation of the daily lifestyle choices that enhance the body, mind, heart, and spirit's innate abilities to balance and heal. Dr. Crystal Dawn’s favorite holistic tools include medicinal botanicals, food as medicine, breathwork, meditation, epigenetics, microbiome enhancement, Ayurveda, exercise, yoga, guided imagery, forest bathing, nutraceuticals, plant medicines, and immersion retreats. Find Dr. Crystal Dawn via Facebook or Instagram! (@Drcrystaldawn)

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