top of page

microbiome 101 (and why it matters)

Maybe it's because I'm in the nutrition world and participate in a social media microcosm where everyone is talking about the microbiome, but it seems that gut health is actually starting to become a more mainstream topic.

While there are a million trends in the health and wellness world, it turns out that the trillions of gut bacteria and other microbes that reside in our gastrointestinal tract are actually some of the most ancient forms of life on earth (1), and they're definitely not going anywhere anytime soon.

I became interested in learning more about the role of gut microbes about 8 years ago when, after learning I had developed several food allergies, I started to work with a variety of nutrition, allergy, and naturopathic practitioners. An allergy specialist (M.D.) gave me the initial diagnosis via bloodwork, then over the next couple of years I worked with a laundry list of folks, and eventually a common thread emerged: a likely imbalance of my microbiome likely due to overprescription of antibiotics (along with a few other factors). Thus, here I am, years later, with a rotating list of books about the microbiome on my nightstand and a much better quality of life. So here's the low-down on the gut bugs.


What makes up the microbiome and what does it actually do?

Scientists estimate that humans have at least 100 trillion microbes in and on our bodies, most of which are the bacteria that reside in your gut (most live in the large intestine/colon), but this also includes viruses, fungi, and other tiny organisms. The gut bacteria get most of the focus because they comprise the majority and they also have some of the most important roles to play in our body. We essentially have a nice little symbiotic relationship with the microbes, in that they use otherwise indigestible particles in our diet as fuel, and we use them for a variety of processes. Fun Fact: it's estimated that if we took all of the microbes in our gut and put them together, they would literally weigh as much or more than our brain (some practitioners are pushing for the microbiome to be considered its own organ!) (2).

So there's a whole colony of these things in our digestive system, but what do they actually do for us? Some of their main functions include:

  • Immunity: Did you know the vast majority of our immune system resides in our gut? Gut bacteria are crucial in maintaining a strong, healthy immune system. If we have a healthy immune system, our body is better able to fight pathogens that cause inflammation and disease. Imbalance in the microbiome has been linked to a number of chronic diseases and conditions such as inflammatory bowel diseases, obesity, diabetes, multiple sclerosis, cancer, allergies, eczema, asthma, and more (3).

  • Metabolism/Digestion: Gut microbes play a huge part in metabolizing the food we eat, how we use that food as energy, how we extract and absorb nutrients, even partially control our appetite. Imbalances in the microbiome have been directly associated with metabolic disorders such as diabetes, metabolic syndrome, and obesity (4).

  • Cognitive Function: It's now widely known that gut tissue (specifically what is called the Enteric Nervous System) has a very direct connection with our brain. Scientists have also concluded that 90-95% of the neurotransmitter serotonin (think: mood, sleep, sex drive) is produced in our gut. GABA (think: inhibitory or decreased anxiety) is another neurotransmitter affected by our gut bacteria. A decrease in "good" gut bacteria has been linked to depression, anxiety, IBS, and more recently it's been suggested that this may also play a role in autism spectrum disorders, dementia, and Parkinson's (5).

While there are a number of lifestyle and genetic factors that contribute to the development of disease states, it's becoming much more clear how our gut bacteria play a huge role in our overall health and presence or absence of disease. It's exciting to see the body of research that's finally getting the funding and recognition to confirm and expand upon this!


How to Support Your gut

So now that we know about the many vital functions of the gut microbiome, here are some things you can do to support it (1,2)!

Incorporate More:

  • Fermented, Probiotic-Rich Foods (sauerkraut, kimchi, other fermented vegetables, plain yogurt, kefir, kvass, low-sugar kombucha, etc. all contain naturally occurring "good" bacteria). Supplements have been studied marginally and some consider them useful in acute situations, although I'd prefer to get probiotics via naturally fermented foods, you can certainly work with your practitioner to find what's right for you.

  • Diverse Array of High-fiber Plant Foods (artichoke, avocado, brussels sprouts, green peas, onion, berries, apples, pears, lentils, beans, broccoli, bok choy, squash, zucchini, cauliflower, spinach, arugula, kale, etc.) This pillar is one of the biggest contributors to a diverse and healthy population of beneficial gut bacteria!

  • Prebiotics: Specifically feed the gut bacteria to help them reproduce (garlic, onion, Jerusalem artichoke, raw jicama, raw asparagus, and dandelion greens are all good sources along with the fibrous veggies mentioned above.)

  • Omega-3 Fatty Acid Sources (wild-caught salmon, mackerel, and sardines, flax seeds, hemp seeds, chia seeds, walnuts, pastured eggs, grass-fed and finished meats)

  • Other Healthy Fats (extra virgin olive oil, grass-fed butter/ghee, nuts and seeds and their oils - walnut, flax, etc.)

Try to Avoid:

  • Food Additives and Preservatives: (found in most packaged/processed foods)

  • Refined, Inflammatory Oils: (corn, vegetable, soybean, canola, and hydrogenated oils) - this of course, includes fried foods and most baked goods.

  • Refined Sugars and Flours: (added sugars in snacks, drinks, desserts, and even hiding in your "health foods", refined white flours, etc.)

  • Antibiotic Overuse: Talk to your practitioner to ensure antibiotics are your best course of treatment, as they kill the unwanted "bad" bacteria, but also kill off tons of the good bacteria in your gut as well.

  • Environmental Toxins: We can only do so much about air quality, but you can filter the air in your home (where we spend most of our time), and choose natural cleaning and beauty products over the traditional, chemical-laden ones.

  • Chronic Stress: Easier said than done, however chronic stress has also been linked to negative changes in the microbiome over time.


Want to Learn More?


  • Gut by Giulia Enders

  • Brain-Maker by Dr. Perlmutter

  • The Mind-Gut Connection by Dr. Mayer

  • Missing Microbes: How the Overuse of Antibiotics Is Fueling Our Modern Plagues by Martin Blaser

  • Follow Your Gut: How the Ecosystem in Your Gut Determines Your Health, Mood, and More by Rob Knight



1. Mayer, Emeran A. The Mind-Gut Connection: How the Hidden Conversation within Our Bodies Impacts Our Mood, Our Choices, and Our Overall Health. HarperWave, 2018.

2. Perlmutter, David. Brain Maker: the Power of Gut Microbes to Heal and Protect Your Brain - for Life. Yellow Kite, 2017.

3.  Lloyd-Price, Jason, et al. “The Healthy Human Microbiome.” Genome Medicine, BioMed Central, 27 Apr. 2016,

4. Festi, Davide, et al. “Gut Microbiota and Metabolic Syndrome.” World Journal of Gastroenterology, Baishideng Publishing Group Inc, 21 Nov. 2014,

5. Anadure, Ravi, and S. Shankhar. “The Gut-Brain Axis.” API Textbook of Medicine 2019, API, 2019, pp. 1–5.

*None of the information in this article is meant to take the place of the advice of your medical doctor, nor is it meant to diagnose or treat any disease state. Please consult your physician before implementing dietary interventions.*



bottom of page