Does the Gut Microbiome Play a Role in the Individual Response to the COVID-19 Virus?

By Emeran A. Mayer, MD with Juliette Frank

While the wave of COVID-19 infections is spreading rapidly around the world and taking its devastating human and economic toll, many questions are being asked about the nature of this pandemic. What are its root causes, when and how will it end, and most importantly, why does the impact on infected people range from a barely noticed infection to failure of the respiratory system and death in a small percentage of patients. We already know that there are high risk populations, such as the elderly and those with underlying conditions, in particular the metabolic syndrome – including obesity, diabetes, high blood pressure, and cardiovascular disease, all diseases which are influenced to a large amount by the diet affected patients eat. Because of the greater prevalence of these chronic, metabolic disorders in African Americans and Latinos, there has been a dramatically higher impact of the COVID-19 infection on these segments of the US population. We also know that several mechanisms in the gut are altered in many of these chronic diseases, including changes in the gut microbiome, in intestinal permeability and in low grade activation of the gut associated immune activation. Two important factors play a role in these alterations in the gut: The North American diet and chronic stress. Could it be that these changes in gut health play a role in the vulnerability to the COVID-19 virus, explaining the greater toll that this virus takes on populations with such changes?

Even though we probably won’t know all the answers to vulnerability question for a while, one can speculate about the possible role of the gut microbiome and its interactions with the gut associated immune system in determining the trajectory of the disease, once somebody is exposed to the virus. In order to understand this speculation, here is a short primer of the gut microbiome.

The gut microbiome is made up of vast ecosystem composed of trillions of microorganisms including bacteria, viruses, protozoa, and fungi. These microorganisms work together to protect our gut and its immune system from invading pathogens, e.g. viruses and bacteria which can cause great harm to our health. However, far from being a peaceful world of coexistence, there is a constant struggle between these micro organisms using antibiotic molecules suppress each other and to preserve ecological niches. Viruses living in our gut prey on bacteria and kill approximately 10% of the microbial population every day, and gut microbes fight back with a vast battery of antibiotic like molecules. While the members of the microbiome compete with each other, they strictly adhere to a peace treaty with their host, e.g. our gut. This world of competing microorganisms is only separated by a thin layer of mucus from the largest part of our immune system, which resides in our gut. Once this barrier becomes compromised through an unhealth diet for example, the microbes come into direct contact with the powerful immune system, ready to launch an attack on the invader. So whatever goes on in our gut microbiome has a potentially huge impact on the activity of our immune system not just in the gut but throughout our body.

The effectiveness of the gut microbial defense against enemies from the world around us determined in large parts to the diversity of the microbial ecosystem, which provides stability, resilience and resistance to infections. There are many influences that are responsible for this diversity of the gut microbiome, from early life influences to dietary habits in the adult, to the exposure to antibiotics and environmental chemicals resulting in a considerable variation in the ability and resistance of the gut’s immune system.

Even though the entry of the COVID-19 virus into our body occurs primarily through our respiratory system, viruses have also been isolated from the stool of infected patients. Other than the fact that one of the symptoms of a COVID infection is diarrhea, we don’t know at this point how the COVID-19 virus interacts with our gut microbiome and our gut’s immune system, and how important these interactions are for the clinical outcome of an infection. However, what we do know is that a healthy, largely plant-based diet made up of a large variety of plants and fruits increases gut microbial diversity, resulting in increased resilience and resistance to infections. We also know that many health promoting molecules produced by plants such as polyphenols, antioxidants and anti-inflammatory molecules exert their beneficial actions through the gut microbiota.

So while everybody is anxiously awaiting the availability of widespread testing for exposure to the virus, the development of a vaccine, and the results from clinical trials with potential anti COVID-19 medications, we all can do something to strengthen the resilience and resistance of our gut microbiome, and prevent the catastrophic consequences of an excessive immune system activation. An action step we can all take towards building a more resilient immune system is to practice eating a nutritious diet in order to boost gut microbial microbiome health. An unhealthy diet weakens this ecosystem, compromising the protective microorganisms that fight off potential threats such as pathogens and viruses. Foods that will promote a healthy gut microbiome include a largely plant-based diet consisting of large amounts of fiber (the essential food for our microbes), anti-inflammatory molecules (such as turmeric and ginger) and naturally fermented foods, polyphenols, antioxidants and omega-3 fatty acids. These nutrients can be found in a diverse range of foods such as fresh fruits, vegetables, nuts, seeds, healthy fats such as olive oil and avocado, and fermented foods such as yogurt, sauerkraut, and kimchi. Such a gut health promoting diet should be devoid sugar, ultra processed foods, and artificially flavored beverages. While we all take precautions and anxiously await time when the infection curve declines and approximates zero, we can all take steps towards strengthening the resilience of our gut microbiome, and optimize gut health.


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