Over 140K Virus Species Found in Your Gut

Analysis by Dr. Joseph Mercola Fact Checked

virus in your gut

Story at-a-glance

  • Analysis of over 28,000 gut microbiome samples revealed there were over 140,000 highly diverse virus species in the gut microbiome, some of which had never been seen before
  • The viruses were bacteriophages that infect bacteria, which are important as they help drive adaptations by creating gene flow networks
  • Processed and ultraprocessed foods negatively affect the balance of beneficial and harmful bacteria in your gut, which can lead to inflammation and many chronic diseases, including diabetes and cardiovascular disease
  • Sun exposure and optimizing vitamin D are two ways of improving the diversity of your gut bacteria; also consider fermented foods and avoiding or eliminating ultraprocessed foods, including food with added sugar


This is an older article that may not reflect Dr. Mercola’s current view on this topic. Use our search engine to find Dr. Mercola’s latest position on any health topic.

Researchers have studied the human microbiome to understand the relationship between these microorganisms and health. A recent analysis found the human gut also has over 142,809 different virus species that reside with your gut bacteria.1 In recent years, scientific evidence has made it apparent that your gut microbiome plays a vital role in your health and disease prevention.

Your unique set of microbes influences the function of many organ systems. Microbes inhabit nearly every part of the human body. Work published in Nature in 20162 found that microbes outnumbered human cells 10-to-1. But, a team of researchers from Israel and Canada re-estimated it using a wide range of experimental data in the literature and discovered the number could vary.

For example, a "reference man" who is 20 years old, weighing 154 pounds (70 kilograms) and standing 5 feet 7 inches (1.7 meters), might have 30 trillion human cells and 39 trillion bacteria.

But, this number could vary from person to person and the ratio may change after each bowel movement. And, “those numbers are approximate,” the study authors say. “… another person might have half as many or twice as many bacteria, for example — but far from the 10-to-1 ratio commonly assumed.”

Dozens of health conditions have been traced to the diversity and health of your gut microbiome, including cancer, obesity, depression, chronic fatigue syndrome, Parkinson's disease and allergies.

One of the main reasons for this connection is that your gut is vital to your immune system. When your gut microbiome is disrupted, it automatically disrupts your body's immune function. As noted in a paper published in Clinical and Experimental Immunology:3

"The crucial position of the gastrointestinal system is testified by the huge amount of immune cells that reside within it. Indeed, gut-associated lymphoid tissue (GALT) is the prominent part of mucosal-associated lymphoid tissue and represents almost 70 percent of the entire immune system; moreover, about 80 percent of plasma cells … reside in GALT."

Virus Database Catalogs Over 140,000 Species in the Gut

Scientists from the Wellcome Trust Sanger Institute have identified 142,809 nonredundant genomes4 from the Gut Phage Database (GPD), some of which had never been seen before. The results were a compilation of over 28,000 gut microbiome samples collected from around the world.5

The researchers found the diversity was "surprisingly high,"6 which opens new avenues for research into human health. Years of study have been dedicated to identifying the role bacteria play in human health, but little is known about the interaction between viruses and bacteria in the gut.

The researchers used DNA sequencing to catalog the biodiversity. One of the researchers from the Wellcome Trust Sanger Institute commented in a press release about the types of viruses found and the important roles they play:7

"It's important to remember that not all viruses are harmful but represent an integral component of the gut ecosystem. For one thing, most of the viruses we found have DNA as their genetic material, which is different from the pathogens most people know, such as SARS-CoV-2 or Zika, which are RNA viruses.

Secondly, these samples came mainly from healthy individuals who didn't share any specific diseases. It's fascinating to see how many unknown species live in our gut, and to try and unravel the link between them and human health."

The viruses were a specific type called bacteriophages that infect bacteria.8 A lack of understanding of bacteriophages had stalled the study of the interrelationship of viruses and your gut microbiome, but recent advancements expanded scientists’ ability to identify and examine the community of viruses living in your gut.

The cataloging also revealed over one-third of the virus clusters do not infect just one species of bacteria and roughly 280 included the newly identified viral clade Gubphage, which is the second most prevalent virus clade. Bacteriophages are important to bacterial communities as they help drive adaptations by creating gene flow networks.9

The researchers stress there is a lot left to learn about these viruses, how they interact with gut bacteria and the role they play in human health. However, they also concluded from the data:10

“Having a comprehensive database of high-quality phage genomes paves the way for a multitude of analyses of the human gut virome at a greatly improved resolution, enabling the association of specific viral clades with distinct microbiome phenotypes. Importantly, GPD provides a blueprint to guide functional and phenotypic experiments of the human gut phageome, as we linked over 40,000 predictions to 472 cultured gut bacteria species.”

Microbiome Dysbiosis Can Develop With a Poor Diet

Processed and ultraprocessed foods have become the mainstay of a Western diet. Yet, there is much evidence11 to demonstrate these foods have a significant impact on your gut microbiome, leading to inflammation, weight gain, cancer and cardiovascular risk. 

One animal study12 aptly demonstrated the negative effects that a Western diet has on health. Eric Berg, Ph.D., is an expert meat scientist at North Dakota State University. He believes that pigs are an excellent substitute for humans to analyze the nutritive value of dietary intake.

“Like humans, pigs are omnivores and their anatomy and physiology are very similar,” Berg explained to a reporter from Tri-State Livestock News.13 Their gastrointestinal system and nutrient requirements are comparable to humans.

Through his experiments, Berg has learned that pigs do poorly on a diet that lacks protein with a good balance of amino acids. A food product may be high in protein, he explains, but if it is low in essential amino acids that make up the protein, the animals don't do well.

In a unique experiment, Berg fed pigs a typical Western diet and was forced to stop the study because the animals’ health was failing rapidly, including stunted growth, intramuscular fat, brittle bones, hair loss and pimples. Commenting on the link to human diets, he said:14

“We would never just feed corn to pigs, but balance their diet with a legume like soybeans to balance essential amino acids and then add vitamins and minerals … [Yet] we snack ourselves into non-nutrition. We may have a whole-grain bagel for breakfast and then snack on something else for lunch. As a result, our diet is out of balance.”

The overconsumption of ultraprocessed foods in the typical Western diet is also likely a culprit in the growing number of adults and children who are obese. In one analysis of results from the National Health and Nutrition Examination Survey,15 researchers found that ultraprocessed foods make up 57.9% of the average American's caloric intake.

Your Gut Health Impacts Disease Risk

This link between processed foods and obesity has taken on new meaning during the pandemic since even mild obesity may raise the risk of severe COVID-19. In one study16 of patients with COVID-19, researchers from Italy found patients with mild obesity had a 2.32 times greater risk of respiratory failure and 4.96 times greater risk of being admitted to the ICU compared to patients who were not obese.

When you consider that many people eat foods with added sugar at all three meals, it's easy to see how obesity has become the norm, rather than the exception. Yet, sugar is only one problem with processed and ultraprocessed foods. Industrially processed seed oils, often referred to as vegetable oil, may be an even worse offender.

Processed vegetable oils negatively impact your health in several ways but affect your gut microbiome by exposing you to toxic 4-hydroxynonenal (4HNE), which forms when the oil is heated for cooking and frying.17 4HNE is highly toxic, especially to your gut bacteria, and consumption has been correlated with inflammatory bowel disease.18

Sun Exposure Improves Gut Diversity and Health

Research also highlights the role vitamin D plays in gut health and systemic autoimmunity. A review article, published January 21, 2020, in Frontiers in Immunology, notes,19 “Autoimmune diseases tend to share a predisposition for vitamin D deficiency, which alters the microbiome and integrity of the gut epithelial barrier.”

The paper reviews the several direct and indirect regulatory effects that vitamin D has on your immune system, including promoting regulatory T cells (Tregs), inhibiting differentiation of Th1 and Th17 cells, impairing the development and function of B cells, reducing monocyte activation and stimulating antimicrobial peptides from immune cells.

The relationship between vitamin D and autoimmunity is complicated. Aside from immunosuppression, vitamin D also appears to improve autoimmune disorders by the way it affects your microbiota composition and gut barrier.

The review also cites research showing that your vitamin D status alters the composition of your gut microbiome. Generally speaking, vitamin D deficiency tends to increase Bacteriodetes and Proteobacteria while higher vitamin D intake tends to increase the prevalence of Prevotella and reduce certain types of Proteobacteria and Firmicutes.

One research team20 from the University of British Columbia was interested in the relationship between exposure to UVB light and the effect on the human gut microbiome. Past research suggested vitamin D could alter gut microbiome diversity and demonstrated that exposure to sunlight has a positive effect on people with inflammatory bowel disease21 and multiple sclerosis.22

Since insufficient sunlight exposure could exacerbate or trigger chronic gut inflammatory diseases and vitamin D has an impact on microbiome diversity, the team designed the study to look at the influence these factors may have on each other.23 After the intervention researchers found an increased number of species in the stool, including those associated with good health.

These results have the potential to affect those who live with immune-mediated or inflammatory diseases, which respond to changes in the gut microbiome. The combination of raising your vitamin D24 level through sensible sun exposure and improving your gut microbiome diversity25 can also have a significant impact on your body's ability to fight viral infections, including COVID-19.

How to Positively Influence Your Gut Microbiome

In the past decade, and more recently in the past year, it has become increasingly evident that optimizing your gut microbiome and vitamin D level is important for your health. You can keep pathogenic microbes and fungi in check by reseeding your gut with beneficial bacteria.

Regularly eating traditionally fermented foods is one of the easiest, most effective and least expensive ways to make a significant impact on your gut microbiome. Fermented vegetables are also high in fiber, which helps to feed your beneficial bacteria.

While I'm not a major proponent of taking many supplements, probiotics are an exception if you don't eat fermented foods on a regular basis. Spore-based probiotics, or sporebiotics, can be particularly helpful when you are taking antibiotics.

Processed foods and foods high in sugar and net carbohydrates negatively affect your gut microbiome as they damage beneficial bacteria and provide the necessary “food” for harmful bacteria to thrive.

It's also important to maintain optimal levels of vitamin D. While sensible sun exposure is the best way, this is not an option for many during the winter months. Before considering supplementation, though, it's important to get your vitamin D level tested. This helps you determine the amount of vitamin D3 you need to take.

It's important to remember that if you're taking vitamin D supplements you also need vitamin K2 to move calcium from your blood into your bones and teeth. Magnesium also helps optimize your vitamin D level. You can read more about the relationship between these three nutrients in “Magnesium and K2 Optimize Your Vitamin D Supplementation.”


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