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  • Writer's pictureErick Rivas

Antibiotics and the Microbiome

One of the areas of health in which we are seeing more and more research on is the microbiome and the role that the gut microbiome plays on our health. The microbiome is a colony of living bacteria that is found in our gut. What? Bacteria in our gut? Yup, we have trillions of microorganisms which are either of bacterial, viral, or fungal origin, which live in our gut. We have more bacteria in our gut than we do cells in our body. In recent years we have come to find out that the bacteria in our gut play an important role in keeping us healthy. Although this field of research seems to still be evolving, there is plenty of research to suggest that what we consume has a direct affect on our microbiome and in turn, our overall health.

One of the biggest contributors to dysregulation of the microbiome is the use of antibiotics. Penicillin, a popular antibiotic, was discovered in the late 1920's by research scientist Alexander Fleming. Ten years later we began to see the production of penicillin as a drug. Nowadays, the use of antibiotics is rampant with even the CDC acknowledging that antibiotics are being prescribed for illnesses that don’t require the use of antibiotics. So, let’s break this down because this is something that is very important. Antibiotics can be life saving and are an important part of medicine. However, when they are prescribed unnecessarily, it can lead to lasting damage to the microbiome. Let's break this down a bit more. Our gut consists of good bacteria and bad bacteria and the key is to have balance in order to maintain our overall health. Now, the purpose of antibiotics is to kill bacteria. Anti, meaning against, and biotic, meaning living organism. And antibiotics wont differentiate between the good bacteria in the gut and the bad, it will go after all bacteria. Like I said earlier, our gut is made up of trillions of these living organisms, so even one treatment of antibiotics can do damage to the microbiome.

You might be asking why this is important. Well, the health of our microbiome can impact our digestion, mood, metabolism, weight management, immune response, and much more. Therefore, it is important to know what you can do to restore your gut microbiome after going through a treatment of antibiotics so that you continue to function at an optimal level. For the purposes of this particular post, I will touch on two things which I believe will contribute in a positive way, not only to the health of the microbiome, but to your overall well being. The first is food, the second, and you may be surprised to hear this, is exercise.

The food we eat can have a profound effect on the way you feel, perform, and of course, on the microbiome. We have foods that are rich in probiotics as well as foods that are rich in prebiotics. So what are probiotics and prebiotics? To keep it simple, probiotics are bacteria which help support your gut health. Prebiotics are a food ingredient which ferment in the intestinal tract and stimulate the growth of the good bacteria or probiotics. Incorporating both probiotic and prebiotic rich foods as part of your diet will help restore and heal the gut. Below is a list of foods that can be incorporated into your diet to restore gut health.

Probiotic Rich Foods:










Raw Cheese

Sourdough Bread


Red Wine

Dark Chocolate

Green Tea

Pickled Vegetables

Prebiotic Rich Foods:








Jerusalem Artichoke





There are a variety of ways in which you could incorporate these foods. Here are a few examples: Kimchi can be eaten on its own but I like to have my kimchi as part of a salad. Yogurt, preferably grass fed and full fat, goes well with berries and some grain free granola, topped with a little bit of raw honey. Asparagus is always a delicious vegetable which can be grilled, baked, or sauteed and will complement many dishes. Onions and garlic can be incorporated into a variety of dishes. I find that onions and garlic give great flavor to food and I use them in anything from an egg scramble to sauteed green beans.

Just as important as the food that you consume, is the food which you need to eliminate in order to maintain a healthy gut. Namely, refined carbohydrates and sugars. Getting these out of the diet and adding more of the foods listed above, which are high in fiber, will help balance out the microbiome and help restore your gut health so that you can perform at your best.

In addition to the food you consume, exercise plays an important role in gut health. Studies have shown that there is a correlation between exercise and the health of the microbiome. A 2017 meta-analysis published in the journal Oxidative Medicine and Cellular Longevity, looking at the role of exercise and the microbiome concluded that “exercise appears to be an environmental factor that can determine changes in the qualitative and quantitative gut microbial composition with possible benefits for the host.” Essentially, exercise promotes a healthy and diverse microbiome which can have beneficial effects from improved immunity, to weight management and a reduction in metabolic dysfunction.

Now, there are other factors that can contribute to the health, or lack of health, in the gut. Sleep, stress, supplementation, alcohol consumption, and many more. However, the combination of food and exercise could be the key to restoring gut health and I believe is a great place to start. As I mentioned earlier, the health of the gut plays an important role in a variety of functions within our body and just one treatment of antibiotics can have profound affect on you gut health. Therefore, knowing what you can do and where you can start is important to your overall health and wellbeing.

Erick Rivas

Integrative Nutrition Health Coach



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