A close look at the gut microbiome in people with COVID-19 may predict who will develop severe disease.

A close look at the gut microbiome in people with COVID-19 may predict who will develop severe disease.

What you need to know

A dynamic ecosystem of microbes called the gut microbiome resides inside of our digestive systems. A healthy microbiome contains a diverse variety of microbes (bacteria, fungi, parasites, and viruses), which keeps our immune system working well. Changes to its diversity can make us sick.

Previous research has found that SARS-CoV-2, the virus that causes COVID-19, reduces the diversity of bacteria in the gut microbiome of people with the disease. Researchers wanted to know whether the variety of microbes present can predict how sick someone with COVID-19 may become.

In a study supported by the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) and the National Heart, Lung, and Blood Institute (NHLBI), researchers looked at gut microbiomes in people with different severities of COVID-19. They found that the microbiome was less diverse in people with severe COVID-19 than in people who were less sick. The difference is significant enough that researchers can predict who has severe disease based on the microbes in their gut microbiome.

What did the researchers do?

The researchers studied 127 people who went to the hospital with COVID-19. About two-thirds of those people (79) had severe COVID-19 and required intensive care. The other 48 had moderate COVID-19 that required hospitalization but not intensive care. The researchers used stool samples to investigate the gut microbiomes of the participants.

The researchers sequenced and identified all of the bacteria in the stool samples. People with a greater variety of species of microbes in their guts are considered to have more diverse microbiomes. Microbes of different species network together to help fight inflammation. Previous research showed that COVID-19 disrupts these networks, so the researchers in this study examined the quality of the gut microbe networks in people with moderate or severe COVID-19.

What did they learn?

The researchers found that gut microbiomes in people with more severe COVID-19 had fewer unique species of microbes, indicating an overall microbe community with less diversity. Additionally, the gut microbe networks in people with severe COVID-19 were disrupted more than those who had more moderate cases.

Based on the analysis, the researchers built a computer model that successfully predicted who had moderate or severe COVID-19 in a separate group of 38 people with COVID-19.

Interestingly, the researchers also found two strains of gut bacteria that were nearly wiped out in people with severe COVID-19. These strains are also severely reduced in people diagnosed with Long COVID. This suggests that microbiomes with fewer of those microbes may be an early warning sign of Long COVID.

Why is this research important?

The gut microbiome plays a significant role in our immune response, and COVID-19 can disrupt that microbiome’s balance. This study shows that people with moderate and severe COVID-19 have distinct differences in their gut microbiomes compared with healthy people and each other. Future research could find ways to target the gut microbiome with treatments and help prevent severe COVID-19.

Where can I go to learn more?

How COVID-19 Changes the Gut Microbiome

  • Researchers supported by NIH found that SARS-CoV-2 reduces the diversity of microbes in the gut microbiome and changes the gut lining to make blood infections more likely.

The Healthy Human Microbiome

  • Researchers have mapped the normal bacteria that live in and on the healthy human body. The accomplishment sets the stage for a better understanding of how bacterial communities affect human health and disease.

Decoding the Genetics Behind COVID-19 Infection

  • Researchers are studying the human genes that make some people resistant to SARS-CoV-2 infection and other people more likely to develop severe disease.


Nguyen, L. H., Okin, D., Drew, D. A., Battista, V. M., Jesudasen, S. J., Kuntz, T. M., Bhosle, A., Thompson, K. N., Reinicke, T., Lo, C. H., Woo, J. E., Caraballo, A., Berra, L., Vieira, J., Huang, C. Y., Das Adhikari, U., Kim, M., Sui, H. Y., Magicheva-Gupta, M., McIver, L., … Lai, P. S. (2023). Metagenomic assessment of gut microbial communities and risk of severe COVID-19. Genome Medicine, 15, 49. https://doi.org/10.1186/s13073-023-01202-6


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Page last updated: September 1, 2023