Your Gut Microbiome: 101

Your Gut Microbiome: 101

The gut microbiome: Both a rapidly expanding field that is racing to understand the broad health implications recently illuminated by research and the latest buzzword in health science. Studies are linking gut health to cognitive functioning, mental health, sleep, and chronic illnesses such as heart disease and type 2 diabetes.5, 7

As dizzying as the barrage of information on this topic can be at times, the fundamental concepts are simple and intuitive. Understanding these fundamentals is all that’s needed to begin an empowered undertaking of gut health optimization.

  1. Your gut microbiome consists of trillions of microorganisms (bacteria, fungi, viruses, etc.). Each person has a unique composition of these microorganisms. The composition is determined by a wide range of factors (such as where you grew up, what you ate as a child, your sleep habits, etc.).4, 5, 8
  2. There are two main factors that influence your microbiome on a daily basis: what and who you are cohabitating with, and your dietary habits.3, 8 
  3. Because the microbiome exists within the GI (gastrointestinal) tract, every time you eat you are selecting for what gut microbes should survive and which should die. A ham sandwich on a hard roll feeds one type of microbe, while a bean burrito feeds another, and a caesar salad feeds yet another.1, 3, 7
  4. Diversity is key. The more diverse your microbiome, the healthier and more resilient it will be. And, you guessed it, the key to a diverse microbiome is a diverse diet.1, 3, 5, 7
  5. Researchers often distinguish a “core microbiome.” This is like your microbiome's default setting. To have a lasting, unshakeable impact on the health of your gut, this is the aspect to focus on. Everything else will likely fall into step behind it.1, 3
  6. Long-term dietary habits are the most foolproof way to encourage the flourishing of your microbiome and the key to influencing your core microbiome.1, 3, 6
  7. Exposing yourself and your habitat to innocuous and diverse microbes is a great way to build resilience. When your immune system is consistently exposed to a diverse population of microbes, it is less likely to flare up (like an allergic reaction) when suddenly exposed to something foreign.3, 4

So, you want a thriving, diverse microbiome?
Here are three things you can do today, and two things to leave in the past.


  1. Eating lots of fruits, vegetables, high-fiber foods, and varying your diet.
    1. The bacteria that thrive in your gut are the ones that have the nutrients they need available to them. By eating a diet that encourages the right types of microbes, you can build a resilient and healthy microbiome.1, 3, 5, 7
  2. Spending time outdoors, petting a dog, or adding a plant to your home. Or better yet, do all three as often as possible. Well, don’t just keep buying plants, but maybe go stick your face in some and take a good sniff once a day.
    1. All of these habits are fantastic ways to increase your exposure to the healthy, diverse microbiology of the world around us. Dogs are a microbial treasure trove, since they go sniffing and rooting around in all sorts of places and then bring all of these microbes back into the house with them.3, 4, 8
  3. Eating more fermented foods
    Foods like sauerkraut, tempeh, miso, pickles, some yogurts (like plain greek yogurt), and sourdough are ancient and traditional foods that have seen a modern resurgence due to the countless anecdotes that attest to their many health benefits.3, 4

Leave behind:

  1. Highly processed foods
    1. Processed foods tend to feed the bacteria that promote inflammation and dysbiosis in the gut.1, 5, 6, 7
    2. If you slip up every now and then or if your lifestyle or location makes this difficult, the most important thing is to not beat yourself up about it. Make the choice that works for you, and the next time you are able, eat a meal full of veggies, whole grains, and protein. And make sure to drink lots of water and get a good night's sleep! In general, the gut is forgiving and resilient. Remember that both you and your microbiome can thrive at the same time.
  2. Sugary drinks
    1. One of the easiest ways to cut back on the amount of sugar in your diet is to cut out sugary drinks. Drinks like soda, sports drinks, sweet teas, and even fruit juices are extremely high in a form of sugar that is exceedingly accessible for your body. Sugar is a major contributor to inflammation in the gut,6 as well as to the malfunctioning of many other bodily processes.7
    2. Try replacing these drinks with flavored seltzers, lemon water, or unsweetened teas. Many herbal and green teas possess natural sweetness and actually positively contribute to your health.


  1. Bolte, L. A., Vich Vila, A., Imhann, F., Collij, V., Gacesa, R., Peters, V., Wijmenga, C., Kurilshikov, A., Campmans-Kuijpers, M. J., Fu, J., Dijkstra, G., Zhernakova, A., & Weersma, R. K. (2021). Long-term dietary patterns are associated with pro-inflammatory and anti-inflammatory features of the gut microbiome.
    Gut, 70(7), 1287-1298.
  2. Cleveland Clinic. (2020, February 5). 5 reasons you should add more fermented foods to your Diet. to-your-diet-infographic/
  3. Govender, K. (2019, November 3). Kiran Krishnan on How to Build a Resilient Microbiome. NourishMe Organics.
  4. Haahtela, T., Laatikainen, T., Alenius, H., Auvinen, P., Fyhrquist, N., Hanski, I., von
    Hertzen, L., Jousilahti, P., Kosunen, T. U., Markelova, O., Mäkelä, M. J., Pantelejev, V., Uhanov, M., Zilber, E., & Vartiainen, E. (2015). Hunt for the origin of allergy - comparing the Finnish and Russian Karelia. Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology, 45(5), 891–901.
  5. Hills, R. D., Jr, Pontefract, B. A., Mishcon, H. R., Black, C. A., Sutton, S. C., & Theberge, C. R. (2019). Gut Microbiome: Profound Implications for Diet and Disease. Nutrients, 11(7), 1613.
  6. Satokari R. (2020). High Intake of Sugar and the Balance between Pro- and Anti-Inflammatory Gut Bacteria. Nutrients, 12(5), 1348.
  7. Shi Z. (2019). Gut Microbiota: An Important Link between Western Diet and Chronic Diseases. , Nutrients, 11(10), 2287.
  8. Yong, E. (2016). I Contain Multitudes: The Microbes Within Us and a Grander View of Life.