How COVID-19 Affects the Gut Microbiome

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COVID-19, caused by the SARS-CoV-2 virus, is known as primarily a respiratory disease. However, between 11% and 39% of people diagnosed with COVID-19 report having gastrointestinal (GI) symptoms such as diarrhea, vomiting or belly pain. GI symptoms are associated with a high risk of hospitalization and disease severity. As our understanding of the pandemic has grown, research now indicates that SARS-CoV-2 can infect and replicate in the intestinal cells (called enterocytes) that express high amounts of angiotensin-converting enzyme 2 (ACE2) receptors. ACE2 is a main entry route for SARS-CoV-2 to infect human cells. 

People who have had COVID-19 also report having disruptions in the gut microbiome. The gut microbiome is made of the trillion microbes—bacteria, fungi and viruses—living in the gut. Although there is an association between COVID-19 severity and changes in the microbiome, scientists are still uncovering more about the direct effect of SARS-CoV-2 on the human microbiome. 

The authors of a recent study asked if being infected with COVID-19 has any effect on gut microbiome function and if it increases disease severity. The study showed that not only does SARS-CoV-2 cause destruction in the respiratory tract, but it can also damage the lining of the gut, which allows harmful bacteria to move from the gut into the bloodstream. Once the bacteria enter the circulatory system, it causes secondary life-threatening conditions such as sepsis.  

Other studies found—from examining the stool of people with COVID-19—that they had significantly altered gut microbiomes when compared to people who haven’t had COVID-19.  The people who had COVID-19 had fewer beneficial microbe species that support the immune system and nourish human intestinal cells. This creates an environment where dangerous bacteria can thrive.

Many people who are critically ill with COVID-19 are treated with antibiotics. These medications may also affect gut microbial populations. Broad-spectrum antibiotics have been found to have a negative impact on the gut microbiota, reducing microbial diversity and the number of beneficial microorganisms. It’s not clear if COVID-19 or antibiotic therapy is to blame for these changes in the microbiome. 

There is still more for researchers to learn about the long-term implications of COVID-19. It is becoming more evident that addressing these GI and gut microbiome alterations will play a significant role in the healing process.

Raz Abdulqadir is a PhD candidate in the biomedical science program at Penn State College of Medicine. Her research examines the role of probiotic-host interactions on the modulation of the intestinal epithelial tight junction barrier.

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