Managing the Microbiome

Deep within the body lives trillions of microscopic beings, protecting and serving your health daily, referred to as the microbiome. The microbiome is the healthy bacteria, fungi, and viruses that inhabit the gut. Don’t let those words scare you, their primary purpose is positive for health. The gut, while you may think of a protruding belly, is the term used to describe three main organs; the stomach, small intestine and large intestine. This is where we digest food, absorbs nutrients and produce waste. These three organs have a major role in our overall well-being, being the host this expansive microbiome.
By maintaining these microorganisms in balance, we can positively affect our health. This includes prevention of infectious diseases, metabolic issues, immune and neurological disorders as well as mental health (2). There is a strong line communication between the microbiome and our immune, metabolic and cognitive/emotional functions (1). Centering in the gut, the most influential factor on the microbiome is our diet, accounting for 57% of changes (3). The impact of diet on the microbiome and health share a close relationship. In a review study conducted by Singh et al (2017), the impact of different diet patterns on the microbiome provides insight on how to nurture a healthy gut.
When examining protein, high animal meat diets are correlated with an increase in bacteria associated with inflammation, cardiovascular disease and inflammatory bowel disease (4). The popularity of high protein/low carbohydrate diets for weight loss, while it results in weight loss, can be detrimental to health and the microbiome, including increased bacteria associated with inflammatory bowel disease (4). On the other hand, a diet high in plant-based protein, such as soy, beans, and legumes, exhibit positive effects on the microbiome and health. Pea protein specifically may increase health-promoting bacteria and decrease pathogenic bacteria, having an anti-inflammatory effect (4). Although it is derived from an animal-based source, whey protein has similar effects (4).
Fibrous carbohydrates are non-digestible but are essential to provide nutrients for the microbiome (4). These include foods like whole grains, vegetables and legumes and can be commonly referred to as prebiotics. Consumption of prebiotic foods is associated with a positive shift in the microbiome (4). These foods are considered heart health and can also aid in decreased inflammation, cholesterol, triglycerides and blood glucose (4). The popular probiotics are another set of foods that influence the microbiome. These foods contain health-promoting bacteria that manage intestinal health and aid in decreasing inflammation (4). These foods include fermented foods such as yogurt, kefir, sauerkraut, kimchi, green olives, pickled ginger and vegetables, natto, and sourdough bread (2). Each food contains different strains of bacteria, therefore eating a variety of probiotic-rich foods is key. Diets high in these foods are associated with improved gastrointestinal health as well as markers of cardiovascular health such as cholesterol and triglycerides (4).
Without doing a complete diet overhaul, some small changes can make an impact on improving your microbiome and overall gut health. Modifications to existing meals with some simple swaps can bring on some benefits.
1) Go meatless once a week. A big meat eater? That’s okay, we know there are plenty of benefits to eating animal-based proteins, but cutting back can help your gut and health. A great way to accomplish this is by designating a day of the week to cut out meat. This is a great time to add in prebiotic foods like legumes, such as beans and lentils, or probiotic foods, like yogurt and tempeh, to get in needed protein. Fish is okay!
2) Change up your bread game. This one comes with two options: whole grain bread for increase fiber or sourdough bread for probiotic goodness. Either way, it’s a gut-healthy win.
3) Try something new. Unsure what kimchi is? Kimchi is a staple Korean food of fermented vegetables like, cabbage and radishes, and flavored with spices. You can find it in most grocery stores and can be enjoyed as a snack, with eggs, in tacos, or mixed into a stir fry for started.
4) Go for sushi. Make sure you start with a miso soup and eat the ginger. Miso and pickled ginger two of the probiotic-rich foods.  The ginger is also a delicious and a way to cleanse the palate between bites.

5) Throw some sauerkraut on it.  It isn’t just for hot dogs and sausages.  Sauerkraut can be tossed into salads, layered into a wrap or sandwich, the topping on your eggs or on your next avocado toast.

With the gut in the center of the body, it is an essential part of our overall health. By feeding our microbiome these essential foods, we can aid in a variety of health outcomes including gastrointestinal health, inflammation, cardiovascular health and managed blood glucose. Experiment with a variety of prebiotic and probiotic foods to get started on the path to a healthier gut, body, and mind.


(1) Quigley, E. M. M. (2013). Gut Bacteria in Health and Disease. Gastroenterology & Hepatology9(9), 560–569.

(2) Ellis, E. L. (2018, March). The Potential of Probiotics. Food and Nutrition, 19-21.

(3)Clark, Allison, and Núria Mach. “Exercise-Induced stress behavior, gut-Microbiota-Brain axis and diet: a systematic review for athletes.” Journal of the International Society of Sports Nutrition, vol. 13, no. 1, 2016, doi:10.1186/s12970-016-0155-6.

(4) Singh, R. K., Chang, H.-W., Yan, D., Lee, K. M., Ucmak, D., Wong, K., … Liao, W. (2017). Influence of diet on the gut microbiome and implications for human health. Journal of Translational Medicine15, 73. http://doi.org/10.1186/s12967-017-1175-y

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