The Future of Supplementation Goes Viral

The Diverse Community In Your Gastrointestinal Tract

You may have heard about the health benefits of probiotic foods like yogurt, kombucha, and pickles. Probiotics contain a live culture of benevolent bacteria that may settle down in your gastrointestinal (GI) tract as they move through it. These microbes pay their rent by participating in a wide range of human activities including digestion, vitamin production, and maintaining immune cells. However, recent research shows that we may have been overlooking another family of tiny tenants in our body — the viruses! Yes, viruses: the family that brought us Human Immunodeficiency Virus (HIV), smallpox, and Ebola. 

It should come as no surprise that the GI tract would be a popular residential area for commensal (friendly) bacteria and viruses due to the abundance of nutrients. The intestine’s constant exposure to foreign substances, including food and pathogens, requires a complex immune system with many specialized cells. Specialized cells in the intestine play an important role in interacting with the tiny tenants and maintaining intestinal health. Much of the existing literature focuses on characterizing the impact of commensal bacteria. However, there is some evidence that an imbalance in the viral community in the human and animal intestine may also be associated with intestinal inflammatory diseases. A research team at the University of Science and Technology of China have recently conducted a mice study to explore the role of commensal viruses.

When the Viruses Are Gone…

The first and most important question to address is what changes might happen to the host in the absence of commensal viruses? To understand this, the researchers compared the immune cell population in the control mice to that in the mice treated with antiviral drugs, which eradicate most of the commensal viruses. The scientists observed that the mice treated with antivirals had a reduced population of specialized lymphocytes, specifically intraepithelial lymphocytes (IELs), than controls.  IELs are lymphocytes found in the epithelial layer of mammalian mucosal linings, such as the gastrointestinal (GI) tract and reproductive tracts. 

Furthermore, the researchers examined the health consequences of viral loss by injecting the control and antivirals-treated mice with dextran sulfate sodium (DSS), a drug that induces intestinal inflammation. This set up allows the scientist to disentangle the connection between viruses and inflammatory disease. The researchers observed that the antiviral-treated mice were not only more likely to develop inflammation but their symptoms were more severe. These results strongly suggest that the commensal viruses somehow offer a protective effect on the mice’s intestinal health.

It’s All About Stimulating the Immune System

What if the antiviral-treated mice have poorer intestinal health due to other, unintended effects of the antiviral drugs (off-target), you may ask? This question was answered using mice that have been modified to be deficient of a virus recognition receptor called RIG-I. Rig-1 deficient mice are them less sensitive to the presence of commensal viruses (all viruses, really). As expected, the mice with RIG-I deficiency exhibit a reduced number of IELs in comparison to the control.  This reinforces that the presence of viruses has an effect on the presence and variety of immune cells

If the viruses maintain the IEL population by interacting with RIG-I receptor, then the role of commensal viruses should be replaceable by an alternative stimulant of RIG-I receptor, right? The researchers proceeded to test this hypothesis. When the antiviral-treated mice were injected with an artificial stimulant of RIG-I receptor, the IEL loss was successfully recovered to a level comparable to the healthy control mice. Together, these results affirm the hypothesis that viral stimulation of the host immune system plays a critical role in maintaining intestinal health.

Tracing the Missing IELs

At this point, the researchers have identified many of the important players in maintaining the IEL count in mice, but how -exactly- do these players affect the IEL count? One way they could is by preventing IEL death by apoptosis- or they could increase numbers by stimulating proliferation. These researchers answered this question by staining the IEL samples with annexin V and bromodeoxyuridine (BrdU), which can be used to assess cell death (apoptosis) and proliferation respectively via flow cytometry. During flow cytometry, a mixture of fluorescently-tagged antibodies that bind specifically to annexin V and BrdU are added to the IEL samples. The samples then pass through a laser beam that activates the fluorescent tag corresponding to either annexin V or BrdU. The flow cytometer collects the fluorescence signals, which are used to quantify the IELs containing annexin V or BrdU. The results showed that the IELs from RIG-I deficient mice showed greater cell deaths and fewer cell divisions than that from the control mice.

Although it appears that this discovery marks viruses as a new potential target for the treatment and prevention of inflammatory diseases, the magnitude of viruses’ contribution is unclear. Despite its significance in this study, RIG-I recognizes only a small subgroup of viruses that stores their genetic materials in the form of RNA, as opposed to the DNA we see in animals, plants, and bacteria. Though this may be in part attributed to the technical limitations in the identification and characterization of viruses. Nonetheless, this study indicates that some viruses have been under-appreciated and that some are more commensal than parasitic. 


Liu, L., Gong, T., Tao, W. et al. Commensal viruses maintain intestinal intraepithelial lymphocytes via noncanonical RIG-I signaling. Nat Immunol (2019) doi:10.1038/s41590-019-0513-z 

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