The Microbiome – Gate Keeper against Viral Infections

Unlike the treatment of bacterial infections traditional lines of defense against viruses have been less successful. Antiviral drugs and vaccines are difficult to develop, can produce undesirable side effects in some, and may lose efficacy if the virus mutates.

In the past few decades, scientists have learned a great deal about the gut microbiome, particularly the immune defence component. The gut microbiome is host to 70-80% of the immune system.

New research is showing that a healthy gut microbiome can block a virus from entering a cell by making it a less desirable place for the virus to set up residence. This concept is starting to get the attention of infectious disease researchers in regard to treatment and prevention of various viral infections.

(see the Microbe or the Terrain below)

Viral infections in general, and more recently SARS-CoV-2, has heightened the interest in the potential connection between a person’s microbiome and their ability to fight a viral infection. Why is it that COVID-19 caused by the SARS-Cov-2 virus produces few to no symptoms in many people but can become life-threatening in others? Current studies are suggesting that the state of the persons microbiome could be a contributing factor.

Viral infections are usually harder on the elderly as well as others of any age who have preexisting conditions such as obesity, diabetes, or cancer. Preliminary studies have documented imbalance in gut microbiota (dysbiosis) in those hospitalized with COVID-19.

It is interesting that the elderly who are generally more prone to serious consequences of viral infections like influenza or pneumonia, commonly have dysbiosis as well as less gut microbiome diversity. (see more information on aging and the gut microbiome below).

If we consider the microbiome as a gatekeeper against infection one can appreciate that in some people the ‘gatekeeper’ will be more effective than in others at fighting off infections based on the health of the microbiome.

How does the gut microbiome help defend against viral infections?

What happens when the gut protective barrier is damaged and becomes more permeable, commonly referred to as leaky-gut? A leaky-gut enables waste products and pathogens to enter the bloodstream and reach other organ systems, where they can cause inflammation or infection.

At this point research has found various ways the gut microbiome can help combat viral infections:

  1. Researchers found that viruses, including SARS-CoV-2 alter the gut microbiome and decrease the production of short-chain fatty acids (SCFAs), which are produced in the gut through bacterial fermentation of dietary fibers. SCFAs play a key role in the immune system defence. In a healthy gut, SCFAs travel via the bloodstream to other areas of the body, including the lungs, and protect from respiratory viruses.
  2. The microbiomes also battle viruses by producing chemicals that interfere with the viral life cycle. Some bacteria produce toxins called bacteriocins and studies suggest they inhibit the activity of certain viruses. One of the bacteriocins blocks entry of West Nile virus, Dengue, and Ebola virus from entering into their host cells, others halt the replication of herpes viruses (HSV); cold sores (HSV 1), genital herpes (HSV 2) and shingles (HSV 3) and more.  
  3. Other gut bacteria trigger intestinal immune cells to release interferons – key factors that ramp up the body’s response to viruses and help eliminate cells that are infected.  These bacteria called bacteroidetes, make up about 40 to 50 percent of the microbial species in the gut. Dysbiosis interrupts the balance of these viral fighting bacteria and can make people more susceptible to the various viral infections.
  4. The microbiome plays critical roles in the training and development of major components of the host’s innate and adaptive immune system.

We cannot ignore the mounting evidence of the microbiome’s role in fortifying the immune system to fight viruses.  How the microbiome interacts with viruses is complex and more recently being explored, but as time goes on we will learn even more about the importance of the gut microbiome and the virome in health and disease.

Germ theory vs terrain theory or BOTH?

The ‘germ theory’ is basically the argument that germs are what we need to worry about and we need to keep finding ways to kill them off. Terrain theory argues that if the body is healthy, then germs that are a natural part of life and the environment will be handled without causing sickness.

It wasn’t until the 1800’s that a French chemist Louis Pasteur proposed that microorganisms caused most diseases and by 1910 and the Flexner report this became the accepted approach in Western medicine. This paved the way for the ongoing development of various pharmaceuticals which seek to treat single disease or antibiotics that attempt to kill the microbes without consideration for the terrain. Today, over 200 years later, this is still western medicine’s approach to pathogens and disease treatment.

In contrast Pasteur’s friend, physiologist Claude Bernard, taught that the ‘terrain’ of the human body was more important than the ‘pathogens’ that infect it.  We are surrounded by, and even harbor, microorganisms in our bodies.  When exposed to pathogens, we become ill if our defenses are weakened by chronic stress, nutritional deficiencies or toxicities.

Unlike the germ theory, the terrain theory explains why some people get sick while others do not when exposed to the same pathogens. It is said that on his death bed, Pasteur admitted, “Bernard was right: the pathogen is nothing, the terrain is everything.”

Both theories are in fact important in today’s world. Because of nutrient deficient soils, the prevalence of toxic chemicals in our foods, air and water, our bodies are generally weaker. Add to this chronic stress, poor dietary and lifestyle choices, and electromagnetic fields (EMFs), both our outer terrain and our inner terrain are out of balance.

It is very important that we have medicines to help us combat invading microbes and to help treat various diseases if our bodies do not have a strong enough immune response to deal with them naturally.

It is not either/or, it is both. Our first focus in medicine should be prevention; to nurture the body with healthy food and a lifestyle that promote a strong immune system thus making it more inhospitable to opportunistic microbes like viruses, and parasites and development of disease.

Gut Microbiome and Aging

The gut microbiome keeps on fluctuating during different stages of life. Our microbiota undergoes the most prominent deviations during infancy and old age and, interestingly, our immune health is also in its weakest and most unstable state during these two critical stages of life

For decades, it has been known that the aging process causes a less robust and less efficient immune and metabolic response.

Current research on the importance of the gut in health and immunity is helping us to understand some of the mechanisms underlying some of these age-related deficiencies and changes. Exposure to multiple drugs/antibiotics, poor nutrition and dietary modifications and constipation, that generally accompany aging are closely correlated with imbalance in the gut microbiome composition and functions.

The gut microbiome, as previously discussed, is also closely associated with increased gut permeability resulting in systemic inflammation which in turn can lead to cardiovascular, metabolic and gut-brain disorders. Probiotics are a very important intervention for a strong immune system and overall healthy aging.

The two-way connection between the gut microbiome and aging

The Importance of Cultivating a healthy microbiome

Everyone’s microbiome is different, populated through a complex mix of genetic, dietary, and environmental influences. There is general consensus, however, that a diet rich whole foods and prebiotics and probiotics, along with regular exercise, helps promote a healthy microbiome.

Prebiotics are a type of fiber and are only found in plants or certain supplements. Foods high in fiber include artichokes, asparagus, onions, beans, and berries. Prebiotics have been well studied and have been shown to improve gut integrity. Probiotic foods contain live bacteria or yeast that are beneficial for digestive health; they include fermented foods like kefir, sauerkraut, kimchi, yoghurt and probiotic supplements.

The importance of prebiotic fibres and probiotics, healthy diet and exercise cannot be overemphasized when it comes to our immunity and prevention of viral infections and chronic disease throughout our life.


Karen Jensen was in clinical practice for 25 years and although she is retired, she continues to write books and educate on the naturopathic approach to wellness. She is author or co-author of seven books, her most recent is Women’s Health Matters: The Influence of Gender on Disease.


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