Dr. B’s Microbiome Omelet

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Hi, I’m Dr. B, practicing functional dentist for 35 years. I graduated from the Dugoni School of Dentistry in San Francisco, CA in 1987 and am a member of the American Academy of Dental Sleep Medicine (AADSM), Academy of General Dentistry (Chicago, IL), American Academy for Oral Systemic Health (AAOSH), and Dental Board of California. I'm on a mission to empower people everywhere with the same evidence-based, easy-to-understand dental health advice that my patients get. Learn more about Dr. B

We often hear about the gut and brain connection, but we tend to forget that the microbiota of the human gastrointestinal tract actually starts in the mouth. (1) The mouth is the gateway to the body, and everything you eat and drink directly impacts the oral microbiome—even before it affects the gut.

When the oral microbiome is unbalanced, harmful bacteria are allowed to proliferate and potentially cause cavities, bad breath, and gingivitis. And this is before the oral bacteria travels to the rest of the body, where it can negatively impact overall health.  In fact, research shows that there’s a 45% overlap of bacteria between the mouth and the colon.

Now that we know the oral microbiome plays a huge role in our overall health, why not fuel it with the right foods? Insert my Microbiome Omelet, which I developed to feed the good oral bacteria and prevent dysbiosis, or imbalance.

Even better, this omelet recipe is completely free of any ingredients that would feed bad bacteria.

Let’s take a closer look at what’s included in this recipe, and the benefits they offer:

Serrano peppers: Serranos contain capsaicin, the compound that gives the peppers their spice factor and anti-inflammatory properties. (2) And in relation to the microbiome, a recent study found that capsaicin can prevent microbial dysbiosis. (3)

Shiitake mushrooms: Shiitakes are rich in vitamins and minerals, including niacin, vitamin B6, and pantothenic acid. Additionally, research has shown that shiitake mushrooms have antimicrobial effects that can lower the amount of gingivitis-causing bacteria in the oral microbiome, while still protecting beneficial bacteria. (4)

Leeks: Leeks help fight inflammation and infection and are a great source of vitamins K and A. They also contain prebiotics that feed beneficial bacteria and help to balance the microbiome. (5)

Cilantro: Cilantro has detoxifying and antibacterial compounds that can help balance the oral microbiome. (6)

Ghee: Packed with fat-soluble vitamins, such as A, E and K, ghee can help reduce leaky gut (which is often related to an imbalance in the oral microbiome) and IBS symptoms.

Hungry yet? Let’s get to the recipe!

Learn More: The Mouth-Body Connection: 6 Ways Oral Health Impacts Overall Health Print

Dr. B’s Microbiome Omelet

What could possibly be better than a delicious and completely satiating, nutrient-dense breakfast that includes the proper ingredients to balance your microbiome? Nothing. That’s why I’ve created this Microbiome Omelet so that you can reap the benefits by fueling your body with the right foods to keep you healthy, happy, and thriving!

  • Author: Dr. Burhenne
  • Prep Time: 5 minutes
  • Cook Time: 8 minutes
  • Total Time: 13 minutes
  • Yield: 1-2 1x


  • 1 medium serrano pepper ((if too spicy substitute with a green pepper), seeds removed and chopped)
  • 3 medium shiitake mushrooms ((chopped))
  • 1 small leek ((chopped))
  • 2 pasture raised organic eggs
  • 1/4 cup ground pork (grass fed if possible) ((cooked))
  • 1/4 cup cilantro ((chopped))
  • 1/2 tablespoon Extra Virgin Olive Oil
  • 2 tablespoons basil pesto ((made with olive oil not hydrogenated oils))
  • 1 teaspoon ghee
  • 4 slices sheep pecorino fresco -semi firm ((optional*))
  • 2 teaspoons liquid or coconut aminos
  • Sea salt and pepper to taste


  1. Saute the vegetables in olive oil until slightly brown and add liquid or coconut aminos and set aside.microbiome omelet
  2. Thoroughly wash fry pan used for cooking vegetables. Put fry pan back on stove and add ghee.
  3. In a small bowl, lightly stir eggs (do not mix yolk and egg white completely). Pour in egg mixture. Add 4 slices of cheese onto eggs, if desired.microbiome omelet
  4. Add veggies and cooked pork on top when eggs are almost fully cooked and fold over omelet.
  5. Top with basil pesto and cilantro and add sea salt and pepper to taste!microbiome omelet