Blog 74: Rethinking Germ Theory:
A New Look at Health and Disease
Cody Vagle, PA-C
After the COVID-19 pandemic, many people—including doctors, scientists, and everyday individuals—began to take a closer look at how we understand disease and health. This has led to renewed interest in whether our current medical approach, especially the long-standing Germ Theory, is the whole picture.
For more than a century, Germ Theory has been the foundation of modern medicine. It teaches that bacteria, viruses, and other microorganisms are the leading causes of illness. This idea sees the body and its immune system as constantly fighting off harmful invaders. However, some researchers suggest that this view might be too simple.
Are Germs the Cause or the Result?
Even in the 1800s, doctors observed that injecting bacteria into animals didn’t always make them sick. Researchers also pointed out that many bacteria live naturally in the human body, even in healthy people. In fact, scientists didn’t deny that bacteria were found in sick or dying tissue. However, many believed that bacteria appeared after the tissue was already damaged, not before. In other words, instead of causing disease, bacteria were hypothesized to grow where the body was already weakened.
The Microbiome: Life Inside Us
Modern research has confirmed that bacteria and other microbes live throughout the human body, not just in the gut. Places once thought to be sterile—like the bladder, placenta, and even the brain—are now known to contain their own unique groups of microbes. This collection of microbes, known as the microbiome, plays a key role in digestion, immunity, and overall health. Instead of trying to eliminate all germs, some scientists believe we should focus on maintaining a healthy balance of microorganisms inside the body.
Beyond the “Germ-Free” Model
Germ Theory suggests that a healthy body is a germ-free body. But this idea is being challenged. Many scientists now argue that sterility isn’t a sign of health—balance is. The immune system doesn’t just destroy harmful microbes; it also works alongside helpful ones. A balanced body is less likely to become sick, even when exposed to germs. This supports the idea of terrain theory, which says that a person’s internal environment—the “terrain”—determines how well they resist disease. If the terrain is strong and balanced, microbes are less likely to cause harm.
What About Antibiotics?
Antibiotics have saved many lives by killing harmful bacteria. But they also kill helpful bacteria, which can disrupt the microbiome. This can lead to a condition called dysbiosis, where the body’s microbial balance is thrown off, increasing the risk of infections and diseases related to the immune system and metabolism.
Surprisingly, modern life expectancy rose well before antibiotics were introduced in the 1940s. Improved sanitation, clean water, and nutrition likely had a much greater impact. Even in the Victorian era, life expectancy was similar to today’s after accounting for infant mortality. Also, antibiotics are one of the top causes of emergency room visits related to medication reactions. This shows that while antibiotics are helpful, they’re not without risks.
How Microbes Shaped Human Evolution
Recent genetic research has shown that microbes may have played a role in human evolution. In fact, a recent study found at least 17 genes in the human genome that came from microbes through horizontal gene transfer, where genetic material moves between species. This means that microbes didn’t just coexist with humans—they helped shape who we are. It challenges the idea that microbes are simply enemies of the human body.
A Healthier View of Health
If microbes have been part of human life since the beginning, it may not make sense to see them only as threats. In fact, life on Earth wouldn’t exist without them. Health isn’t just the absence of disease or germs. It may depend more on how well the body can stay balanced and strong, even when exposed to microbes. This view shifts the focus from fighting germs to supporting the body’s internal systems.
Final Thoughts
It’s time to take a broader view of health and disease. Germs may not be the leading cause of illness, but a sign that the body is already unwell. A healthy immune system doesn’t just destroy—it also supports balance. By focusing on the body’s internal environment and working with, not against, the microbiome, we may find better ways to prevent and treat illness.

