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The Gut Microbiome and COVID-19

There are many different factors that relate to COVID-19, but something that scientists haven’t fully considered is the fact that there is a connection between the gut and COVID-19. 

Graphical representation of the different types of microorganisms present within the gut.

(NIH Image Gallery via Flickr)

What is the Gut Microbiome?

Contained within your intestines and stomach is a living community of around 1014 microorganisms including bacteria, fungi, and archaea (ancient cells!). These bacteria belong to many different families with the four main ones being: Actinobacteria, Firmicutes, Proteobacteria, and Bacteroidetes. Why would we want these living things in our body? Because microbes are beneficial! While we provide them with a safe habitat to grow, they help us digest our food and strengthen our immune system (Dhar & Mohanty, 2020). 

Connection to COVID: Inflammation

One theory behind the connection between the gut microbiome and COVID-19 is through inflammation. Many of the risk factors and diseases related to COVID-19 include aging, cardiovascular disease, asthma, and Alzheimer’s disease. All of these risk factors have been linked to an increase in inflammation and changes in gut microbiota (Villapol, 2020). 

Inflammation can sometimes be good (if you have a healthy microbiome), but too much inflammation (caused by bad bacteria) can be detrimental.

(Immuno Laboratories)

Gut microbiota play a key role in regulating inflammation. When inflammation is initiated, some bacteria release molecules called cytokines that increase inflammation (pro-inflammatory). Other bacteria release cytokines such as IL10 that decrease inflammation (anti-inflammatory) (Dhar & Mohanty, 2020). It is the balance between these types of microbes that dictates a person’s susceptibility to COVID-19. If a person were to have more pro-inflammatory bacteria in their gut, they would have an increased number of ACE2 receptors on cells in their gut. The ACE2 receptor is what the virus uses to enter and infect cells (van der Lelie & Taghavia, 2020).

Gut Dysbiosis

Two recent studies done by Zuo et al (2020) and Guo et al (2020) revealed an increase in pro-inflammatory bacteria such as Coprobacillus, Clostridium ramosum,  Klebsiella , and Streptococcus along with a decrease in anti-inflammatory bacteria such as Faecalibacterium prausnitzii and Lactobacillus in COVID-19 patients. The change in the types of microbes found in the microbiome is called “gut dysbiosis”. Gut dysbiosis is also seen in the elderly, those that are immuno-compromised, and those with diseases related to COVID-19 (as described above). Especially in the elderly, we see a decrease in the diversity of the gut microbiota (Dhar & Moharty, 2020). This change decreases immunity and increases susceptibility to inflammation, overall increasing susceptibility to COVID-19.

The Gut-Lung Axis

Another way COVID-19 can affect the gut microbiome is through the gut-lung axis. It’s crazy to believe, but your lungs and your gut talk to each other! Molecules (including cytokines and immune cells) released by microbes can enter the circulatory system and travel to the lungs where they are released and can help the lungs fight infection or cause more inflammation. The same occurs when going from the lungs to the gut, where changes in the microbial community induce changes in the gut’s microbial community. Thus, if COVID-19 affects the lungs, it is possible that it indirectly affects the gut too (Ahlawat et al, 2020).

Visual of how the gut-lung works, especially in dysbiosis that is seen in diseases like COVID-19.

(Dumas et al, 2018)

As you can see, the gut microbiome plays an important part in how well the body handles infectious diseases including COVID-19. It’s surprising that there aren’t any treatments that focus on changing the gut microbiota to treat COVID-19 (Ahlawat et al, 2020). Hopefully, researchers look into this more as it could also help discover new treatments for other diseases involving the gut.


Ahlawat, S., Asha, & Sharma, K. K. (2020). Immunological co-ordination between gut and lungs

in SARS-CoV-2 infection. Virus Research, 286, 198103.


Dhar, D., & Mohanty, A. (2020). Gut microbiota and Covid-19- possible link and implications.

Virus Research, 285, 198018. https://doi.org/10.1016/j.virusres.2020.198018

Gou, W., Fu, Y., Yue, L., Chen, G., Cai, X., Shuai, M., Xu, F., Yi, X., Chen, H., Zhu, Y. J., Xiao, M.,

Jiang, Z., Miao, Z., Xiao, C., Shen, B., Wu, X., Zhao, H., Ling, W., Wang, J., … Zheng, J.-S. (2020).

Gut microbiota may underlie the predisposition of healthy individuals to COVID-19.

MedRxiv, 2020.04.22.20076091. https://doi.org/10.1101/2020.04.22.20076091

van der Lelie, D., & Taghavi, S. (2020). COVID-19 and the Gut Microbiome: More than a Gut

Feeling. MSystems, 5(4). https://doi.org/10.1128/mSystems.00453-20

Villapol, S. (2020). Gastrointestinal symptoms associated with COVID-19: Impact on the gut

microbiome. Translational Research. https://doi.org/10.1016/j.trsl.2020.08.004

Zuo, T., Zhan, H., Zhang, F., Liu, Q., Tso, E. Y. K., Lui, G. C. Y., Chen, N., Li, A., Lu, W., Chan, F. K. L.,

Chan, P. K. S., & Ng, S. C. (2020). Alterations in Fecal Fungal Microbiome of Patients With

COVID-19 During Time of Hospitalization until Discharge.

Gastroenterology. https://doi.org/10.1053/j.gastro.2020.06.048

Article Author: Vanessa Wong

Article Editors: Stephanie Sahadeo, Valerie Shirobokov