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The Wonders of the Microbiome Revealed


Written by: Cheyenne Lockwood, BSc Biochemistry and Molecular Biology

Reviewed by: James Simony, MD



Did you know that your body is home to over 100 trillion microbes? There are more microbial cells on your body than your human cells! The normal microbiota or “flora” of the human body are microscopic organisms that live on the skin, mucus membranes, and intestinal tract (1). These microorganisms include bacteria, fungi, and archaea. We serve as a host to these tiny organisms, and many are beneficial and essential to our health.


The large intestine houses a majority of the microorganisms in our body. Bacteria in our gut help us by breaking down and fermenting our food, which can have major impacts on digestive health. Additionally, bacteria in our gut produce some B vitamins and vitamin K which play major roles in metabolism and blood clotting, respectively. Moreover, the bacteria in our gut help to keep bowel movements regular (2). The microorganisms that live on and in our body also helps shape our immunity. Bacteria protect us from infections by occupying a “niche”. What this means is that the good bacteria occupy space and resources, so when a pathogenic bacterium invades, they must fight for resources. If the good bacteria overpower the bad bacteria, the bad bacteria will die off, and no infection will occur (3).


The two most common ways your microbiome can be harmed is from diet and antibiotic usage. The food you eat also feeds the bacteria in the gut. If your diet is high in sugar, artificial sweeteners, and processed foods, your microbiome may be impacted (4). Additionally, antibiotics are not entirely selective on what bacteria they kill. This means that when you take antibiotics, some of the good bacteria will likely be killed off too. Oral or intravenous antibiotics are considered systemic and will impact the entire body, including the gut. However, systemic antibiotics are sometimes necessary when you have an infection.


Since we can’t always avoid the usage of antibiotics, the best way to support your microbiome is through diet and supplementation. Prebiotic foods are foods that feed the bacteria in your gut. These foods have specific fibers such as fructans, inulin, fructooligosaccharides, galactooligosaccharides. These foods include oats, garlic, apples, and beans. The fiber from these foods does not get broken down in the small intestine. Instead, it makes its way to the large intestine, where the bacteria is housed in our gut (5). The bacteria then feed off the fermented fiber. To repopulate your microbiome, you can eat probiotic foods. These foods contain beneficial bacteria. These foods include kefir, yogurt, aged cheese, tempeh, kombucha, and fermented vegetables (pickles, olives, etc.)(6). Even baby formula is fortified with probiotics and breastmilk naturally contains probiotics (7).


If you want to take it one step further, you can also try probiotic supplements. These types of supplements can be found in almost any drug or health food store. They typically come in a capsule but can also come in a gummy or liquid form. When choosing a probiotic, it is important to know some key terms. The number of strains indicates how many different types of bacteria there are. The CFU or colony-forming units indicate the approximate total number of bacteria. While there isn’t a specific dosage required, it is important to note the initial side effects of probiotics. When you first start taking probiotics, especially one high in strain number and CFUs, you may have some bloating, gas, and change in bowel movements for the first weeks of usage. This occurs because your microbiome is changing, and the bacteria may produce more gas than usual. Because of this, it may be helpful to take your probiotics before bed. Additionally, it is important to follow the product’s instructions regarding storage. The probiotics may not be stable in certain conditions. For example, some products may require refrigeration (8).


If your doctor has prescribed you an antibiotic you must complete the full course of medicine. If you stop prematurely, you could develop antibiotic resistance. This happens because when the antibiotic is stopped too early, some of the bad bacteria remain. The remaining bacteria are resistant to the antibiotic and repopulate. This will cause the infection to grow once again, only this time, a stronger antibiotic will be required (9). Since taking the antibiotic will kill off some good bacteria, you can rebuild your microbiome after you finish your medication. This can be done by including the prebiotic and probiotic foods discussed above. You can also add a supplement if you wish.




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Steel City Pediatrics

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Pueblo, CO 81005

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