The Surprising Part of Your Body that Supports a Healthy Immune System

Want to support a healthy immune system? A Doctor of Osteopathy explains how this one surprising system is crucial for good health.
smiling hispanic woman on yoga mat. Discover which surprising part of the body supports a healthy immune system.

Imagine living in a city where crime is happening non-stop. Calls are constantly coming into the local police and fire departments. What happens when a real emergency happens at your home? By the time the police, paramedics, or firefighters arrive, crucial time is lost.

If only help could have come right away, they might have been able to save your home, property, or even your life.

Unfortunately, a scenario similar to this is played out in our bodies quite regularly. Our immune systems rely on our gut flora or microbiome to get information about potential dangers and pathogens, yet chronic problems can mix up the message and delay help from coming to the rescue.

How Your Microbiome Supports Immune Health

It has been estimated that there are roughly 40 trillion microbes present in the human body. In a lecture for the Living Proof Insititute titled “The Microbiome and Immune Defense,” scientist Kiran Krishnan claims there are about 200 million immune cells in your body. That means there are over 200,000 microbial cells in the body to every 1 immune cell.

Imagine if you alone were in charge of policing a crowd of 200,000 people. That would not be an easy task.

Your microbiome does not want you to get sick. In fact, your survival is crucial to their survival so in general, they want you to be as healthy as possible. Think of yourself as their planet: When it is gone, so are they. So when a pathogen arrives, your microbiome signals to your immune system that something is wrong. Your immune system relies on communication and even training from your gut microbiome to direct it.

Now, wouldn’t it be much easier if the crowd of 200,000 people was actively helping you find a criminal, act as backup for you, and even provide you the tools necessary to neutralize the criminal?

That’s what your microbiome does. It signals to your immune system when it comes in contact with a virus, bacteria, or any other pathogen that could cause you harm. It shines a guiding light to your immune system signaling where to go to deal with the pathogen. In certain cases, they’ll supply cells with tools to fight the pathogen. One could say, “the gut makes the drugs.”

It is when the gut microbiome becomes damaged or imbalanced that problems can arise. Not just from the external pathogens, but also normal gut bacteria that are usually kept in check. Under these circumstances, they can overgrow, cause damage, and prevent healing of the gut. This starts the process of chronic infections in the gut.

How Inflammation Signals Your Immune System

We tend to think of inflammation as a “bad” thing in our bodies. Under normal, healthy environments, the microbiome will use inflammation to signal to your immune system as to where there is a problem. In this case, the inflammation is not bad. Your immune system immediately can go to where it needs to, fight the infection, and deal with it as quickly as possible. Time can be crucial when viruses are hijacking cells to replicate more copies. This is an example of a healthy response.

Unfortunately, a normal, healthy environment is not so common anymore. There are many things that disrupt our microbiome including medications (especially antibiotics), chemical exposure, processed foods, and more.

Once the microbiome and gut lining is damaged, it is no longer healthy and then infections of the gut can take hold and turn into chronic infections.

The pathogens don’t have to come from other places, disrupting the microbiome can cause certain bacteria that are normally kept in check to overgrow and start causing and perpetuating chronic disease. Chronic infections can look differently in the gut from being asymptomatic to bloating, headaches, low energy, to autoimmune issues.

Suddenly there’s chronic inflammation in one or several other places that require attention and resources from the immune system. So when you have inflammation that is widespread throughout the body, it is damaging to health, but it also mixes the signal going to the immune system.

So under conditions of chronic inflammation when suddenly the microbiome comes in contact with a pathogen and signals to the immune system, the immune system may take longer to get there and cannot come in full force.

This has been proposed as a reason for why people with comorbidities are at much higher risk with COVID19.

Do All Infections Start In the Gut?

You can think of the microbiome in your gut as the “control center” that is in contact with the microbiome of the rest of your body. Perhaps you may have heard of the gut-brain axis? It is where the gut communicates with the brain and vice versa. A cranial nerve called the vagus nerve gets information from your microbiome. Your microbiome can then have an effect on your food cravings, mood, and even inflammation in your head.

But there is much more than a gut-brain axis. There are unique environments in the body with different microbiomes. There is a “gut-lung axis,” a “gut-skin axis,” and probably many more. Scientists have found that there is cross-talk between the microbiome of the lungs and the microbiome of the gut. So if you inhale a pathogen such as the flu or even the COVID19 virus, your lung microbiome is disrupted and it warns the host and the gut microbiome.

The gut microbiome will go to work in getting the immune system activated and primed to fight the infection as quickly as possible. So even if the virus or pathogen does not directly infect the gut, the gut is still playing a significant role in the immune response to the pathogen.

If you’re looking to boost your immunity, you want to make sure that your gut microbiome is diverse, balanced, and healthy. 

How to Promote a Healthy, Balanced Gut Microbiome

Healing a gut when chronic diseases have taken hold is not easy. Once pathogens take hold, they do their best to prevent your gut from healing. So it can take persistence, commitment, dedication, and time.

Some things that can help positively move your gut towards healing are:

  • Get outside: A little bit of dirt is helpful for your immune system. It needs to come in contact with other microbes to differentiate between self and non-self.
  • Eating a large variety of fruits and vegetables daily: Your microbiome adapts to what foods you put into it. Food variety increases the diversity of healthy microbes that can help your gut heal and make your gut more resilient.
  • Fasting: Fasting promotes repair and healing of the gut. It gives your gut a rest and favors good bacteria that help restore the protective mucin barrier.
  • Keep your gut moving: Staying regular is important. Constipation can negatively impair the delicate balance of a healthy microbiome. Exercise, fiber, coffee, and oils are examples of ways to promote gut motility.
  • Eat fermented foods: Fermented foods such as sauerkraut, kimchi, and kombucha can help promote diversity in your gut.
  • Manage stress: Chronic stress is a part of modern life. With the COVID19 pandemic, it is even truer than ever. Chronic stress negatively affects the bacteria in the gut. Practices like meditation and taking adaptogens can help you deal with stress.
  • Prebiotics and spore-based researched probiotic: Spore-based probiotics made from soil-based microorganisms can help boost the good bacteria and make the gut more resilient.

When chronic infections have taken hold, even if subclinical, the immune system will have a more difficult time dealing with harmful pathogens. Boosting immunity is important for overall health and well-being. Restoring the health of the microbiome should be a priority for anyone wanting to be as healthy as possible and have the best immune response possible when needed.

Healing the gut can be a difficult challenge, but understanding that it can positively boost everything about your health and well-being should be a priority to nearly everyone.


Daniel Lopez, DO is an osteopathic doctor that specializes in helping people feel better inside and out. From getting rid of pain to healthier-looking skin and hair, he is passionate about helping transform you into your optimal self. Sign up for his free upcoming course on healing the gut so you can support a healthy, balanced immune system.

Dr. Daniel Lopez, D.O.
Daniel Lopez, D.O. is a regenerative medicine physician and board-certified specialist in osteopathic manipulative medicine. He specializes in many problems, including headaches (tension and migraine), tongue and airway related bodywork, traumatic brain injuries, TMJ dysfunctions, eye problems, neck pain, back pain, and much more. He is always looking for answers, real answers. He is not interested in masking symptoms but resolving them. He loves learning and teaching. Take one of his courses to optimize your health at