Nourishing Your Microbiome - Lakeside Natural Medicine

Natural Health and Wellness for the Whole Family

Nourishing Your Microbiome

BySarah Axtell, ND September 14, 2016

gut-diagramIN THE PRESS: This article was featured in Natural Awakenings Magazine in 2016.

We have ten times more bacterial cells in our body than we do human cells. These microorganisms cover us head to toe and are major players in our current and future state of health. Many people fear bacteria thus resulting in the overuse of oral antibiotics, antibiotic soaps and salves, and hand sanitizers. But we must consider how some of these bugs are not detrimental but rather fundamental to life.

We have a complex internal ecology composed of microorganisms and their genetic code that thrives within us. This is termed the microbiome. We are finding that the DNA of our gut bacteria may have a much greater impact on our health than our own DNA. This natural occurring community of flora is the foundation of all life on earth.

Oftentimes there is an imbalance of bacteria as more people have pathogenic, or bad, bacteria and not enough of the good bugs. The good news is we can change, heal and nourish our microbiome through what we eat and through our environment. Let’s first consider risk factors that can lead to a dysfunctional microbiome, thus increasing your risk for disease.

Risk Factors for a Dysfunctional Microbiome

  • C-section birth (we first get inoculated with good bacteria as we pass through the vaginal canal during the birthing process; however, babies born via c-section miss out on this good flora)
  • Formula fed
  • Frequent antibiotic use throughout childhood and adulthood (at least once every two to three years)
  • Medications- antacids, steroids (prednisone), NSAIDs and antibiotics
  • Excessive consumption of sugar, gluten, and artificial sweeteners
  • Drinking tap water (chlorine)
  • Hormone therapies, such as oral contraceptives, hormone replacement therapy
  • Eating GMO foods, thus exposing you to glyphosate- a harmful herbicide that kills beneficial bacteria
  • Stress
  • Low fiber diet

Roles of our Microbiome:

  • Digestion and absorption of nutrients
  • Physical barrier to the outside world, protecting us from harmful invaders, such as pathogenic bacteria, viruses and parasites. When this is out of balance, we get a “leaky gut.”
  • Detoxification– the gut bugs neutralize many toxins in your food. When you decrease the good bacteria in your gut, you increase the workload on your primary detoxification organ, the liver.
  • Immune support- Approximately 80% of your immune system is located in your gut. When there is an imbalance in gut flora, there is an increased risk of autoimmune diseases, such as Rheumatoid arthritis and Multiple Sclerosis.
  • Mood– 90% of your serotonin (“happy” neurotransmitter) is produced and stored in your gut. Anxiety, autism, and depression have been linked to a dysfunctional microbiome.
  • Weight management- The “Western” microbiome, as compared to the microbiome of individuals from Africa, significantly lacks diversity and has more bacteria from the group Firmicutes than the group Bacteroidetes. Firmicutes can harvest more energy from food, hence their association with weight gain when they dominate in the gut.
  • Stress management– Gut flora has a profound effect on your endocrine system.
  • Controlling whole-body inflammation– When inflammation persists, we are at increased risk for obesity, diabetes, cancer, asthma, arthritis, heart disease, Parkinson’s and Alzheimer’s disease.

Nourishing Your Microbiome


Eat a diet rich in fiber, particularly vegetables rich in prebiotics, a nondigestible food ingredient that promotes the growth of beneficial bacteria. This includes chicory, Jerusalem artichoke, garlic, onions, leeks, and jicama. While these foods can be beneficial for most, individuals with Small Intestinal Bacterial Overgrowth (SIBO) will need to avoid these foods until their small intestinal bacterial overgrowth has been addressed.

Avoid excess sugar and artificial sweeteners. Studies show that gut bacteria of people who regularly consume artificial sweeteners look different from gut bacteria who do not.

Avoid gluten. This protein found in wheat, barley and rye is inflammatory to the gut lining, thus contributing to a dysfunctional microbiome.

Eat fermented foods that contain live cultures, such as live-cultured yogurt, kefir, kimchi, sauerkraut, kombucha, tempeh, and pickled vegetables.

Eat organic, non-GMO foods to avoid glyphosate exposure.


Avoid hand sanitizers and antibacterial soaps.

Avoid unnecessary courses of antibiotics.

Drink filtered water to avoid chlorine consumption.


Not all probiotic supplements are created equally. Always look for a probiotic that requires refrigeration and has at least 10 billion organisms per capsule. Probiotics with a diverse array of strains are best, such as Lactobacillus acidophilus, Lactobacillus brevis, Lacobacilus rhamnosus, Bifidobacteium lactis, and Bifidobacterium bifidum.


To help determine the state of your microbiome (ie. Types of bacteria, presences of parasites, level of inflammation in your gut), a comprehensive stool analysis can be helpful. Most functional doctors, such as naturopathic doctors, routinely order these tests and can help you interpret them and address any imbalances.

Related posts – probiotics

Overview of most beneficial strains of probiotics.

Good bugs: Top reasons why you need to take a probiotic?

Guide to Choosing High A Quality Probiotic 

Editor’s Note: The information in this article is intended for your educational use only. Always seek the advice of your physician or other qualified health practitioners with any questions you may have regarding a medical condition and before undertaking any diet, supplement, fitness, or other health program.

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