What's In Your Gut Virome?
By Dr. Marvin Singh, MD
October 14, 2018
Category: Microbiome
Tags: @healthygutmd  

What’s In Your Gut Virome?

The gut microbiome is a hot topic these days. It seems like everywhere you turn someone is talking about gut health and bacteria. But is it all about bacteria? What is the gut microbiome? Let me break it down for you.

The gut microbiome is basically the ecosystem of trillions of microorganisms that live inside of our intestinal tract, mainly in the colon. Some have estimated that there are about 100 trillion microorganisms that live in the gastrointestinal tract. By the way, this is just the gut we are talking about; there are even more organisms on our skin, in our mouths, and in many other parts of our bodies. These little bugs make up an intricate network and ecosystem and are largely responsible for our health (or lack thereof). There are ten times more microorganisms in our digestive tract than there are human cells on our body. The DNA from these organisms outnumbers our human DNA by a factor of 100 to 1. This is definitely a force to take seriously!

We often think about the gut microbiome in terms of bacteria. In fact, it is predominantly bacteria. However, there are also fungi, yeasts, parasites (in some cases), and viruses. It’s the viruses I want to spend some time talking about. We are probably going to discover in the years to come that certain viruses alter the ecology of the gut microbiome and this can lead to certain conditions. For example, a recent study suggested that infection with the Reovirus could trigger an inflammatory response to certain foods and lead to the development of celiac disease (https://www.ncbi.nlm.nih.gov/pubmed/28386004). Another study suggested that infection with Rotavirus could lead to the development of non-celiac gluten sensitivity (https://www.ncbi.nlm.nih.gov/pubmed/29736406). Even a decade ago, in the literature, researchers described the Epstein-Barr virus (the virus that causes mono) as being associated with autoimmune diseases like Lupus, Rheumatoid Arthritis, and Sjogren’s syndrome (https://www.ncbi.nlm.nih.gov/pubmed/19028369).

What some of us biohackers are discovering is that there are viruses that are living in the gut. For the most part, these happen to be plant viruses. For example, some people may have a cucumber mosaic virus living in their gut. This is a virus that was first discovered in 1934 and it was found to infect cucumbers and a variety of other plants. We probably don’t think too much about plant viruses when we are eating vegetables but maybe we should. Humans make a good go-between for a plant virus and when we ingest them they could potentially change the ecology in the gut microbiome before they depart the gastrointestinal tract. Although we don’t know too much about all these different viruses yet, it is generally felt that the more viruses you have, the more issues with health you may have as well. Some bacteria in the gut can inhibit viral infections while other bacteria can promote viral infections, so there is definitely an interaction there (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4373533/). Remember, 70% of the immune system exists in the gut. When you take a snapshot of your gut microbiome and get it tested, it is hard to know if the viruses that are being detected are related to food recently eaten or persistent infections. Either way, it could be a sign that you are not eating the best quality vegetables. While it is unclear if the viruses are a part of the picture when it comes to food sensitivities, it makes sense to try to avoid a particular plant if you know you are infected with a virus that infects that plant.

What is even more interesting are the viruses that infect the bacteria. These are called bacteriophages. One of the more common ones is referred to as crAssphage or cross-assembly phage (I love the name, don’t you?). This is a common phage in the gut, actually. It is felt to predict infection to the family Bacteroidetes. While the function of this virus in human health is not really clear, it does make one wonder about its role in human health if it can infect certain kinds of bacteria. It also makes one wonder about particular drug or therapy targets in certain diseases or conditions that involve a virus at the root of its cause.

In the meantime, here are a few things you can do to help protect your gut from viruses:

  1. Make sure your produce is organic and comes from a reliable source. If the vegetable looks infected or just doesn’t look right, think twice before eating it
  2. If you know you have a particular plant virus living in your gut, consider taking a break from that plant at least for a while.
  3. Work towards eating plenty of colorful fruits and vegetables that come from a reliable source so that you can build the diversity of your gut microbiome.
  4. Reduce stress, exercise, avoid toxins, have fun in life, avoid sugars and processed foods; basically, do all the things that help build a strong resilient gut microbiome

We don’t yet have enough information about the gut virome but it is clear that there are viruses that live in the gut as well. It is fascinating how a plant virus can settle down in the gut microbiome. It is even more fascinating to wonder about what it is actually doing. In some cases, these viruses may be doing nothing. However, in other cases, it is possible they could be shifting the balance of the microbiome and contributing to significant health effects. While I wouldn’t lose too much sleep over this, I would definitely try to be more aware that it exists and perhaps pay more attention to the quality of plants we are eating on a regular basis. 

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