The Anti-Viral Gut

Our gut microbes have been evolving with us for a long time-we can trace their origins to a common ancestor more than fifteen million years ago, but our formal understanding of these tiny creatures dates to the 1600s, when the Dutch scientist Antoni van Leeuwenhoek first looked at his own dental plaque under the microscope and saw "little living animalcules." A few centuries later, in the 1800s, the French chemist Louis Pasteur proposed his "germ theory" that certain diseases are caused by the invasion of the body by microorganisms and avoiding contact with them is the way to stay healthy. (It's hard to believe that prior to these groundbreaking findings, people thought foul odors or "evil spirits" were the cause of illness.)


This concept of avoiding germs like the plague has become foundational to modern Western medicine and is the driving force behind our efforts to find new and more effective ways to assault dangerous bugs, like the development of antibiotics and vaccines-discoveries that save countless lives every day. We've formulated medications like monoclonal antibodies that can help us combat viruses and illness if our bodies aren't strong enough to fight them naturally and instituted widespread precautions to keep ourselves protected from pathogens. And simple yet important innovations in sanitation and hygiene, like Florence Nightingale's introduction of handwashing into British Army hospitals during the Crimean War, combined with social distancing and quarantining, have also become effective ways of limiting infectious outbreaks.

But as we've decreased the amount of germs on our bodies and in our environment, something else has increased at an alarming rate-and that's our susceptibility to viruses. The increased risk of viral infection includes completely new ones like human immunodeficiency virus (HIV), as well as reemerging oldies like measles, and more transmissible and deadlier versions of some we were already familiar with, like coronavirus. And with COVID-19, we have seen how a global pandemic can impact our daily existence. This paradox of increased infection as we get rid of germs isn't really a paradox at all-it's confirmation of the critical role our microbes play in protecting us from viruses.

The Hidden World Inside You

Since the days of Leeuwenhoek and Pasteur, we've also made another incredibly important discovery: not all germs are bad! In fact, the trillions of microbes that call our body home are primarily helping rather than hindering us, with a specific purpose that's very much aligned with our own survival. Without these microscopic critters, your immune system wouldn't be able to protect you from infections or cancer; your heart, lungs, and liver wouldn't function properly; and you wouldn't be able to digest food, assimilate nutrients, or synthesize essential vitamins and growth factors that your body can't make on its own. Even your mental health would take a major hit because of the lack of neurotransmitters that microbes produce and the close and necessary interaction between bacteria in your gut and your brain health and development. Why is understanding the relationship we have with our microbes so important? Because these organisms are, in fact, intimately involved in every aspect of our health-and they're especially critical for protecting us from viruses. Viruses can't survive on their own. They rely on their host's cellular machinery to allow them to live, reproduce, and go on to infect other hosts-a process known as replication. How easily they're able to hijack that machinery is what determines your outcome when infected with a virus, and that is in turn dependent on the trillions of microbes that inhabit your body. To understand how it all works, let's take a closer look at this hidden world inside you.

Multiple Microbial Parts

The microbiome refers to all the organisms that live in or on your body-from your scalp to your toenails and everywhere in between, but mostly in your gut. This diverse universe includes bacteria, viruses, fungi, protozoa, helminths (worms, for those of us who have them), as well as all their genes. A staggering hundred trillion microbes that include thousands of different species inhabit your body-with more than a billion bacteria in just one drop of fluid in your colon alone. We are single individuals, but we're composed of multiple living, breathing, moving microbial parts.

To appreciate the role and function of your microbes, it's helpful to think of your body as a factory. Organs like your lungs, heart, and liver represent the machinery that keeps production moving: extracting oxygen, pumping blood, removing toxins, synthesizing hormones, and performing all of the other complicated tasks that keep us alive. Some of these tasks are automated, but most of the assembly lines require constant monitoring, maintenance, and adjustment. We house the machinery, but who operates it? How does a complex process like, for example, digestion, actually happen? How does the food get broken down into its basic constituents and carried across the gut lining into the bloodstream where it can be transported to cells that utilize it as an energy source? Who helps produce the substances your body requires but can't make on its own, like B complex vitamins B12, thiamine, and riboflavin, and vitamin K? How does your body distinguish between serious infection with a dangerous virus and colonization with a harmless one? How does your immune system know when to rally the troops to defend you, and when to ignore benign intruders that don't pose a threat? Your microbes are the ones carrying out all of these tasks-and more! They even turn your genes on and off, activating those you need and dismantling those you don't.

Like David Vetter, the famous "boy in the bubble" who had a disease that weakened his immune system, you'd have to live in a sterile and isolated environment with no contact with the outside world in order to survive without your multitude of microbes, and even that wouldn't be enough to keep you alive because of all the other necessary functions your microbes perform. Since you're their host and they rely on you for their survival, most of your microbes are very much invested in your well-being. If you die, they die, too, and when you prosper, so do they. It is the ultimate symbiotic relationship, and when it's healthy and well maintained, both you and your microbes thrive.

We can categorize your microscopic roommates into three main groups:

1.            Commensal bacteria that cohabit peacefully with you, like Streptococcus salivarius in your mouth that are simply part of your normal bacterial ecosystem.

2.            Symbiotic organisms (sometimes called mutualists) that play an active role in keeping you healthy, like certain strains of Escherichia coli in the gut that synthesize vitamin K, which is required for your blood to be able to clot properly.

3.            Pathogens (including opportunistic flora) that can do you harm, like Pseudomonas aeruginosa, which can cause ear infections.

In a balanced healthy microbiome, groups 1 and 2, the quintessential "good" bacteria, far outnumber the pathogens or "bad" bacteria. There's no requirement for a microbiome composed entirely of good bacteria, but without sufficient commensals and symbiotic species, your microbiome can't function properly-and neither can the rest of your body, particularly your immune system.

What Do Your Gut Bacteria Do?

Symbiotic organisms-the quintessential "good" bacteria-perform lots of important functions. They help you digest food, maintain the integrity of your gut lining (the barrier that keeps bowel contents-and viruses-separate from the rest of your body), crowd out harmful pathogens, and train your immune system to distinguish between friend and foe. They also convert carbohydrates into critical metabolites like short-chain fatty acids (SCFAs) that help guide your immune response, and they synthesize many of the enzymes, vitamins, and hormones that you can't make on your own. Food can't be properly broken down and its constituent parts can't be fully absorbed without these essential gut bacteria, which means that even if you're eating a super-nutritious diet, if you don't have a healthy microbiome, you may not be able to absorb and assimilate all of the vitamins and nutrients in your food.

Role of Gut Microbes

Digest food

Produce digestive enzymes

Convert carbohydrates to short-chain fatty acids (SCFAs)

Help your body absorb nutrients such as calcium and iron

Synthesize B-complex vitamins like thiamine and folate

Synthesize fat-soluble vitamins like vitamin K

Synthesize hormones and neurotransmitters

Maintain the integrity of the gut lining

Keep the pH in your gut balanced

Metabolize drugs

Neutralize cancer-causing compounds

Promote angiogenesis (growth of new blood vessels)

Crowd out pathogens

Train the immune system to distinguish friend from foe

Activate anti-viral efforts

Modulate genes

You're Only as Healthy as Your Gut Bacteria

Ever notice how some people never get sick when everyone else has the flu or a cold? They're exposed to the same virus as everyone else, but because of their healthy microbiome populated with lots of essential "good" microbes, they're able to defeat the virus and stay healthy. The very young, whose microbiome is still developing and who therefore lack the microbial diversity necessary for a strong immune system, and the very old, who also have fewer microbial species and less diversity, tend to be the most vulnerable, but there are lots of external factors at play, too, in which we have a key role. The medications we take, the food we choose to put on our plates every day, and the environments we expose ourselves to are some of the major influences that we have control over. Overzealous use of antibiotics can put you at risk for viral infection by killing off good microbes along with the bad ones; a low-fiber diet literally starves many of the bacterial species that are essential for proper immune function; and a super-sanitized environment can also put us at risk by exposing us to pesticides and other microbe-depleting chemicals and limiting our contact with soil microbes that can enhance our own internal bacterial communities.

Now that you have a better sense of your microbiome and the many important functions it performs throughout your body, letÕs focus on the connection between your gut microbes and your immune system and how that relationship, when itÕs healthy, protects you from viruses.

Hand and Glove

Your body is in constant contact with external and internal threats that pose a direct danger to your health: harmful viruses and other pathogens in the environment, plus internal waste and toxins that can build up in your body and lead to chronic inflammation and disease. Your immune system protects you from all of it-cancer, infection, and more-and helps you recover after injury. It's your first and best line of defense, and it's especially important now, with the reality of global pandemics, plus all the chemicals and carcinogens we're exposed to on a daily basis. But how does this internal surveillance system actually work to protect you from viruses? It turns out that your gut microbiome and your immune system have an extremely close interdependent relationship, and that hand and glove interaction is critical to a properly functioning immune system that can keep you safe and healthy.

Your immune system tolerates an enormous and constantly changing mass of harmless microbes, while at the same time recognizing and responding to dangerous viruses that it's able to spot amid a pool of trillions of other organisms. How is it able to distinguish friend from foe so precisely and then launch an attack that destroys one while preserving the other? The fact that more than 70 percent of your immune system is located in your gut provides an important clue. The thin lining of your intestinal wall, known as your epithelial barrier, has immune cells on one side and bacteria on the other, and both sides interact continuously with each other. Immune cells in your gut lining pump out substances to help defend against invaders, while microbes help guide and modulate those cells, ensuring a balanced immune response.