Optimizing Digestive Health Part II – Creating a Diverse, Robust Microbiome.

Welcome back for part II of Optimizing Digestive Health. Today we are talking about the microbiome which fascinates me beyond nearly any other topic in health!

Why is it so fascinating? For me, it is the incredible research that has emerged over the last 20+ years uncovering the immense complexity and integratedness of the human body and our health with the trillions of microbes that call the inside of our GI tract home. The other aspect of this story that I love is that Ayurvedic Medicine said over 5,000 years ago that gastrointestinal health is the foundation of our health, then Hippocrates said it, and today science is finally investigating and confirming this foundational principle.


What is the microbiome and what makes a healthy one?

Your gastrointestinal microbiome is composed of trillions of microbes (bacteria, fungi and viruses) that live in your large intestine (colon) and the composition of all those microbes are specific to YOU!  This ecosystem of microbes does a whole lot more than we ever imagined, with massive contributions toward influencing inflammation, immune system balance, neurotransmitter (i.e. serotonin) production, hormonal function, gene expression, nutrient metabolism and detoxification. 

Microbiome diversity, which means LOTS of different types of bacteria, is one of the most important factors not only for gut health, but also for the balance and health of our entire body. There is still much research to be done on the interaction between each microbial species and the human organ systems but what is clear is that when those little critters interact and compete, something magical happens that keeps us healthy. 

How do those critters come to live inside of us? 

Microbes have gotten a bad rap and been seen as the enemy as far as health goes. While certain antiseptic practices have most certainly contributed to a decrease in some health concerns, there is an important balance between microbial exposure and antiseptic practices that is vital to our health. Our culture tends to be germophobic, working to create as close to a sterile environment as possible and with a plethora of anti-microbial products to choose from to make this happen. 

In an attempt to eradicate microbes from our environment in the name of hygiene and health have we compromised our health? What the research is saying is YES! Some researchers are correlating the increase in chronic health conditions to a decrease in exposure to a diversity of microbes from childhood. The presence of antiseptic practices in our daily lives ranging from anti-bacterial soaps to antibiotics have altered our microbiome and this affects the functioning of every cell in our body.  

Our first big exposure to diverse microbes, and really the beginning of our GI microbiome, is when we emerge into this world from our mother’s womb. Whether a child is born vaginally or by C-section has impacts on the health of that child as they continue to grow. For example, children delivered via C-section have increased risk of metabolic and immunologic diseases such as allergies, asthma, diabetes and obesity. New research shows that by swabbing the mouth of newborns, delivered by cesarean, with microbes from their mother’s vaginal tract, it increases their GI microbiome diversity and is a promising treatment to decrease health risks for those delivered by cesarean birth. Are you seeing the connection between our microbiome and our health?

The greatest early contributions to growing a diverse microbiome are the birth process and breastfeeding. We know that breastfed babies tend to have a greater microbiome diversity. 

As babies come into contact with the microbial world through humans, different environments, food, etc. the microbial diversity in their gut increases through these interactions. 

Don’t worry if you were born cesarean and were not breastfed, there is LOTS you can do to increase your microbiome diversity starting now. 

How do the bad guys get there? How do the good guys stay there? How does balance become disrupted within our Microbiome?

There are several ways in which our microbiome becomes out of balance, below are a list of common reasons: 

    • Poor diet- these are foods that create inflammation for you 
    • Decreased ability to digest food
    • Chronic stress
    • Age
    • Disease 
    • Antibiotic use
    • Environmental toxins such as glyphosate 



How do we get more good guys than bad guys? 

Things you can do to increase our Microbiome Diversity (this is NOT a comprehensive list): 


  • Exercise:  increases microbiome diversity, especially beneficial bacteria (ones that increase our health)- Particularly exercise increases good bacteria that produce MORE butyrate which is a SCFA(Short Chain Fatty Acid). SCFA in general are one of those messengers that set our circadian clocks in the liver. They are vital to setting circadian health throughout the body. Butyrate is the primary fuel source for our intestinal cells, which means it protects us from leaky gut! Butyrate also reduces inflammation, and people who have increased levels of butyrate have less inflammatory disease and are less likely to suffer from allergies. 
  • Get out in Nature: Spending more time outdoors is correlated with a healthier GI tract and immune system! 
  • Know your Food Intolerance: Ask your doctor to test which foods you specifically don’t break down well. 
  • Appropriate Antibiotic use: A review done by the CDC in 2014 reported nearly 60% of all antibiotics prescribed in the urgent care were unnecessary. Seeing your Primary care doctor regularly or establishing a relationship with your integrative medicine doctor helps to reduce the inappropriate use of antibiotics which saves your gut and saves lives (23,000 people die per year due to antibiotic resistant infections). 
  • Avoid inflammatory foods: These are processed sugar, gluten, bad fats such as processed vegetable oils (canola, soy, safflower, sunflower, etc.), margarine. This list is not exhaustive. 
  • Eat pre-biotic foods to feed the good bacteria– if you don’t feed them, they won’t want to stay! Foods such as root vegetables (carrot, radish, turnip, parsnip, sweet potato, jicama, garlic, onion, etc.) and 100% whole gluten free whole grains such as quinoa, buckwheat, amaranth, millet, rice, oats. Start eating a little bit of these with each meal. 


I hope you all enjoyed talking about the microbiome! In the New year, look out for part III of Optimizing Digestive Health as we dive into digestive functionality. 

Have a beautiful holiday season. 

With much care, 

Dr. Sara Koorjee