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A Healthy Gut Microbiome Will Boost Your Immune System

We are all a bit conscientious of our immune systems right now. So, I thought I would take a moment to talk about our microbiome of our gut. What is a microbiome exactly? We are host to over 100 trillion microbes!! We’ve all heard of it before, but what does it really mean? Your gastrointestinal microbiome is a composition of bacteria, fungi, protozoans, and viruses within the intestinal tract. Everyone has a unique microbiome. They are  influenced by food intake, age, gender, geographical location, environmental factors and lifestyle. Some can be bad and create disease or illness, while the “healthy bacteria” create homeostasis in the gut. We have a symbiotic relationship with our microflora. We provide a home, food and breeding ground for the bacteria and in return they synthesize vitamins (Vitamin B1, B2, B5, B6, B12, Vitamin K, biotin and folic acid are some examples) and break down nutrients for our benefit. In addition, our bacteria microbiome plays an intricate part in our immune function and response.

So how do they protect us in regards to our immune system?

1. There are some studies that suggest we start developing our microbiome in the womb, but essentially from the time of birth we inoculate our gut with a microbiome, either from the vaginal canal or if the baby was born from a c-section it usually has a inoculation from skin flora. Breast milk too helps with inoculation [1,2,4]. Later, we acquire bacteria from our food. From this time of infancy the microbiome starts to interact with our immune system cells to learn “good bacteria” from the “bad pathogens”. The bacteria help stimulate cell responses that help ramp up and differentiate our immune system cells. It helps create our adaptive immune system or acquired immune system [1,2].

2. One of the main points of entry for pathogens to enter the body is the mouth. Most microbes are destroyed by acid in the stomach, but some can move on into the intestines. The microbiome creates a physical barrier to other harmful bacteria or pathogens. They play a role in maintaining the tight junction between epithelial cells in our gut. They reduce bad microbes capability to adhere to the intestinal lumen. The good bacteria will also release toxins to make pathogens incapable of adhering and reproducing in our gut [3].

3. The good bacteria in our gut will signal to our immune system that we need to create an immunologic response. For example when infected with cholera, our good bacteria will trigger an IgA response from our immune system to fight the infection. This system actually helps stimulate our innate immune system as well. Going all the way back to our bone marrow to produce specific immune cells to fight infection if needed. When there is no infection to fight our good bacteria will induce an anti-inflammatory response, promoting a healthy and calm intestinal wall [1,3]

4. One important interaction between us and our microbiome includes the breakdown of fibers into  short chain fatty acids such as butyrate, propionate, and acetate. These short chain fatty acids promote cellular repair and cell proliferation. They are vital for intestinal homeostasis and for proper cell maintenance and function. We need proper cell function to ensure once again pathogens cannot invade past our intestinal epithelial cells [1,2,3].

Things That Offset A Healthy Microbiome

1. Long term or excessive antibiotic use. Antibiotics can be very useful to treat systemic infections that are not clearing out on their own, but unfortunately the bacteria in our gut is killed off as well from these medications. When our good bacteria is killed off, it leaves opportunity for bad bacteria or pathogens to invade. Proton pump inhibitors, cancer treating drugs, laxatives, steroids have also been suggested to influence or change our microbiome. I am not suggesting coming off these medications if they are needed- talk with your primary care provider first [2].

2. Inadequate plants in our diet. Carbs are used as fuel for our bacteria. Fiber is the most readily fermented carb and beneficial to our microbiome, and once again fiber is essential to create those SCFA (short chain fatty acids) that we need in order to maintain a healthy, un-inflamed GI tract. These SCFA also have anti-cancer properties [4]. They also need a balance of protein, but too much protein can create harmful byproducts that can damage our bacteria. So a rich plant based diet with protein and fat in moderation is recommended for optimal gut flora [1,2].

3. Here’s no surprise, stress and lack of sleep. Disruptions in our circadian rhythm can result in a microbial “dysbiosis” or imbalance. This along with chronic stress can upregulate stress hormones and inflammatory factors that will be harmful to our good bacteria. Stress hormones are hypothesized to change the surface of our intestinal surface.

4. Toxins, environmental exposures. Toxins, pesticides, artificial sweeteners, smoking and alcohol have all been shown to be harmful to our microbiome.

Now this is a simplified version of the symbiotic relationship that exists between us and our gastrointestinal microbiome. The truth is these bacteria do SO MUCH MORE than help regulate and improve our immunity. They have been associated in protecting us from autoimmune, inflammatory diseases and even cancer. They can even help regulate our mood. The complexity of it is quite magnificent. I cited 4 articles that I found interesting and helpful, but there are literally hundreds of peer reviewed articles out there on this stuff. I encourage you all to check it out to learn more about this. It is quite interesting and profound. I also attached a video that gives a pretty good explanation of the immune cell interaction and the mucosal lining of our GI tract with our microbiome. Again it is simplified to a degree, but it gives you a general idea of the main components going on.

Without our microbiome we cannot function as a healthy individual. It’s something worth thinking about and maybe exploring some ways to improve your gut biome. I would suggest that everyone should be taking prebiotics and probiotics. Both are important. It’s a simple way to try to jumpstart your microbiome. Yogurt, Kefir, Kimchi, Saur-kraut are all great foods with a variety of types of probiotics. Once again, when we don’t have a healthy gut flora we lose our anti infectious barrier and are at risk for increased environmental infections.

Stay healthy out there, good luck families!


1. Lazar V, Ditu L, Pircalabioru G, Gheorghe I, Curutiu C, Holban A, Picu A, Petcu L, Chifiriuc C. Aspects of Gut Microbiota and Immune System Interactions in Infectious Diseases, Immunopathology, and Cancer. Front. Immunol., 15 August 2018 | https://doi.org/10.3389/fimmu.2018.01830

2. Wen L, Duffy A. Factors Influencing the Gut Microbiota, Inflammation, and Type 2 Diabetes. J Nutr. 2017 Jul; 147(7): 1468S–1475S. Published online 2017 Jun 14. doi: 10.3945/jn.116.240754.

3. Shi, N., Li, N., Duan, X. et al. Interaction between the gut microbiome and mucosal immune system. Military Med Res 4, 14 (2017). https://doi.org/10.1186/s40779-017-0122-9

4. Thursby E, Juge N. Introduction to the human gut microbiota. Biochem J. 2017 Jun 1; 474(11): 1823–1836. Published online 2017 May 16. doi: 10.1042/BCJ20160510

Check out this video:


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