COVID-19 and the Gut Microbiome

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There’s a lot of emphasis on the immediate and long term pulmonary manifestations of COVID-19; from pneumonia and Acute Respiratory Distress Syndrome to sepsis and lung scarring, COVID is no joke. But it is important not to forget that this virus can leave its mark on the entire body, not least of which is the gut!


Not surprisingly, COVID-19 had an effect on the microbiome of affected individuals. Even in patients who had no antibiotics (used to deal with secondary bacterial infections common in COVID patients), there was a clear decrease in commensal (good) bacteria and a marked increase in the presence of opportunistic pathogens (1). This reduction in good bacteria is detrimental, as those microbes aid in the maintenance of digestive health, help modulate the immune system and manage inflammatory responses throughout the body (4). Furthermore, the more severe the disease, the higher the density of gut pathogens, increasing the likelihood of the patient developing a life-threatening infection.


In a US study of 318 confirmed COVID-19 cases, 61.3% of patients reported at least one gastrointestinal symptom, with loss of appetite (34.8%), diarrhea (33.7%), and nausea (26.4%) being the most common (2). These same symptoms may even appear before other signs and symptoms of the virus.


This is because Sars-CoV2 virus binds to ACE2 receptors found throughout our digestive system. A SARS-CoV-2 infection occurs when the virus enters into a host cell, which is dependent on its dense glycosylated spike protein, or S protein (these are the bulbs that come off of the main body of the virus in all the pictures you’ve seen). Angiotensin-converting enzyme 2 (ACE2), one of many receptors on many of the cells in our lungs and intestines, is a functional receptor for SARS-CoV-2 (3). If you think of ACE2 protein as the lock to our cells,

SARS-CoV-2’s S protein is the key.

SARS-COV-2 binding to a cell’s ACE2 receptor.
How COVID works; Image taken from
How COVID works; Image taken from
It turns out that the ACE2 protein is present in significantly higher amounts in our small intestines than in any other organs, including lungs (2).


And this is not the most distressing part! Studies show that people with underlying conditions, including heart disease, hypertension, obesity and diabetes, are more likely to develop more severe COVID-19 (1). These are the same diseases normally associated with lifestyle choices like a poor diet and lack of exercise. Coincidentally, these lifestyle choices are also associated with microbiome dysregulation (5).


But even people without these underlying conditions are at risk. We’ve all heard of COVID long-haulers, or patients who, months after clearing the virus, have chronic symptoms similar to an autoimmune disease. I have patients who were previously plant-based and healthy who now suffer from chronic fatigue, weight loss and muscle wasting, insomnia, hair loss, thyroid inflammation and anxiety and depression.


The key here is, again, the gut microbiome; as the commensal microbe communities in our guts decrease, we open ourselves up to a whole host of other issues, including an increased risk of obesity, diabetes, colorectal cancer, anxiety, depression, and autoimmune-style disorders (4, 6, 7).


As the commensal microbe communities in our guts decrease, we open ourselves up to a whole host issues.
As the commensal microbe communities in our guts decrease, we open ourselves up to a whole host issues.

COVID-19 is not a disease we want to get. Even once you’ve “recovered,” the long term effects on the microbiome won’t be known for years to come. This is all unprecedented and scary, and one could be forgiven for falling into despair, right?

Hope is not lost! We have learned many important lessons from this pandemic and first among them is that health should be at the top of our priorities! There’re many habits we can adopt beginning now that can change our microbiomes and have them work for us instead of against us!


So let’s dig into the fun stuff! What are some ways that we can both keep ourselves healthy (and therefore less likely to have a severe reaction to the disease) and get ourselves back to our old selves if we do catch COVID?
  1. Practice physical (not social!) distancing! Staying, at minimum, 6 feet away from other people and minimizing your time indoors when outside our homes goes a long way towards keeping you safe.
  2. Wear a mask if you are near people who are not in your immediate family.
  3. Eat plant-based or plant-forward: our beneficial gut microbes use fiber as their energy source to maintain our gut health and balance our immunity. Eating 30 or more different plants per week is associated with microbial diversity and improved health (9).
  4. Minimize the consumption of refined sugars, emulsifiers and saturated fat. Disease promoting gut microbes feed on these foods and replicate to cause inflammation (13, 14, 15).
  5. Minimizing alcohol, tobacco and environmental toxins when possible. These toxins are associated with promotion of the same microbial imbalance we are trying to prevent (16).
  6. Exercise at least 30 minutes daily. Moderate exercise is associated with increased gut microbiome health (10).
  7. Prioritize 7-8 hours of restful sleep every night. Our bodies need rest to thrive and lack of sleep is associated with poor microbiome diversity (11).
  8. Go out into nature as much as possible. Breathing fresh air, getting vitamins from the sun and exposure to natural environments for at least 120 minutes per week is associated with optimal health (8).
  9. Manage your stress by being mindful of what you are reading, watching and listening to so as not to overload yourself with negative news. Try to stay present and focus on the now. Stress has been associated with poor health outcomes, especially when one is not in any real danger (12).
  10. Maintain social connectivity. In the age of COVID, this is easier said than done, though there are some tricks: make sure you are talking to your friends and loved ones over social media or a video platform, and maybe plan an physically distanced get together at a park or other outdoor venue (remember to always wear your mask!)
  11. Lastly, and probably most importantly, is being patient with yourself and your body, giving yourself grace and allowing your good habits to take effect without searching for quick solutions that often don’t yield lasting healing.
We are almost there guys! The COVID-19 finish line is in sight. As more people become aware of the severity of the virus and do the right thing, and with the development of multiple vaccines, we’re almost there! However, prioritizing our physical and mental health is and should continue to be our top priority.
This information is for education only, for medical advice contact your doctor.


To optimize your Gut Health, download Dr Mendez Gut Health Guide! If you are looking for support to help improve your diet and boost your gut microbiome, then get in touch today or register to make an appointment to discover how Doctor Méndez can help you to optimize your health.


Manage your stress.
Manage your stress.
  1. Zuo T, Zhang F, Lui GCY, Yeoh YK, Li AYL, Zhan H, Wan Y, Chung ACK, Cheung CP, Chen N, Lai CKC, Chen Z, Tso EYK, Fung KSC, Chan V, Ling L, Joynt G, Hui DSC, Chan FKL, Chan PKS, Ng SC. Alterations in Gut Microbiota of Patients With COVID-19 During Time of Hospitalization. Gastroenterology. 2020 Sep;159(3):944-955.e8. doi: 10.1053/j.gastro.2020.05.048. Epub 2020 May 20. PMID: 32442562; PMCID: PMC7237927.
  2. Redd WD, et al. Prevalence and characteristics of gastrointestinal symptoms in patients with SARS-CoV-2 infection in the United States: a multicenter cohort study. Gastroenterology. 2020;159:765.e2–767.e2. doi: 10.1053/j.gastro.2020.04.045
  3. Zhong, P., Xu, J., Yang, D. et al. COVID-19-associated gastrointestinal and liver injury: clinical features and potential mechanisms. Sig Transduct Target Ther 5, 256 (2020).
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  5. Shreiner AB, Kao JY, Young VB. The gut microbiome in health and in disease. Curr Opin Gastroenterol. 2015;31(1):69-75. doi:10.1097/MOG.0000000000000139
  6. Kho ZY, Lal SK. The Human Gut Microbiome – A Potential Controller of Wellness and Disease. Front Microbiol. 2018;9:1835. Published 2018 Aug 14. doi:10.3389/fmicb.2018.01835
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  9. De Luca F, Shoenfeld Y. The microbiome in autoimmune diseases. Clin Exp Immunol. 2019;195(1):74-85. doi:10.1111/cei.13158
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  17. Bancil AS, Sandall AM, Rossi M, Chassaing B, Lindsay JO, Whelan K. Food additive emulsifiers and their impact on gut microbiome, permeability and inflammation: mechanistic insights in inflammatory bowel disease. J Crohns Colitis. 2020 Dec 18:jjaa254. doi: 10.1093/ecco-jcc/jjaa254. Epub ahead of print. PMID: 33336247.
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