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Gut Health - Microbes and the Microbiome


Did you know when it comes to the number of cells that make you up you are mostly microbes and bacteria? Before you get grossed out, deny that its true or shower extensively, in this post let's examine how these bacteria got a bad rap in the first place.

Bacteria have long been thought to be at the root cause of disease, but most of our research has been around pathogens, bacteria, or viruses that cause disease. Before we blame bacteria, it was originally thought that bad air was the culprit. This was a time when sanitation wasn’t great, streets were filled with cesspools and it was thought that the foul stench was why people were getting sick. Well, this was partially true; it was due to the bacteria in the sewage that was being poured in the street. The prevailing idea back in the day was that disease was not passed from person to person but by the environment. The Germ theory is the idea that disease is caused by bacteria or microorganisms in the body


The Germ theory was first proposed in 1546 by Girolamo Fracastoro an Italian scientist, but this idea really didn’t take root until the 1860’s when Louis Pasteur & Robert Koch brought this idea into the mainstream. You may have heard of Louis Pasteur, the inventor of pasteurization, a process that kills bacteria. Pasteurization is the process of heat treating many of our products so that their shelf-stable.

Pasteur was the first to prove the germ theory. A germ refers to a pathogenic organism but looking at the word germ it was originally proposed to mean beginning or formation of something. Like the germ of an idea. Remember we didn’t know much about organisms in the body at this point.

Pasteur first noticed that microorganisms caused food to spoil. He identified a microorganism as the root cause of the silkworm disease which saved the entire silk industry. So, germs were quickly labeled as the troublemakers and Pasteur was the savior.

Germs then became known as disease-causing pathogens that could spread from person to person. In 1876, Robert Koch continued to prove that microorganisms were at fault. He proved that anthrax, cholera, and tuberculosis were all caused by germs. And then he created a series of rules to identify germs called Kotsiopoulos. There are many pathogens that don’t fit into Kotsiopoulos criteria, but they were a critical step to identifying the cause of disease. In response to the germ theory, soap became a necessity rather than a luxury. Doctors started washing their hands and many lives were saved due to reduced infection during surgery.

This discovery then lead to a large focus on developing antibiotics. Rightly so because there was an epidemic of infectious disease. By eradicating bacteria, we hoped to end the disease. The Germ theory sent us down a path of eradicating as many bacteria and germs as possible with antibiotics, hand sanitizers, soap, and sanitation. People wanted everything to be clean, but microbes vastly outnumber us, and not only did we kill the bad but the good too.


It would be difficult if not impossible to get rid of our microbial friends and given the amount of good they do for us; we might be getting rid of ourselves too. As it turns out our relationship with bacteria not only keeps us healthy, but it is also essential to our survival.

Until recently we’ve been pointing the finger at bacteria for most disease but now as we dive into the research around the human microbiome, we are learning the error in our assumptions. For example, H-pylori a bug in our gut has been linked to the cause of stomach ulcers and stomach cancer. So now based on the germ theory we tried to eradicate it but now we’re seeing it may have been foolish to try and eradicate an entire species. A lack of H-pylori in the body may be linked to the rise of many other conditions such as type 2 diabetes, obesity, celiac disease, and other autoimmune diseases and allergies. It appears that H-Pylori is responsible for stimulating stomach acid and regulating ghrelin and leptin telling your body when it is full or hungry. And here we’ve been obliterating H-pylori for years.



Rather than viewing microbes solely as pathogens, it looks like Claude Bernard may have been right. It may actually be, that imbalance in the ecosystem causes particular bacteria to act up. Who’s Claude Bernard? He’s the other guy, Pasteur’s colleague who believed that the ecosystem or environment the bacteria live in determines whether they become pathogenic or beneficial.

We now know that bacteria in the gut play a role in regulating hormones, eliminating toxins, and even serve as an internal pharmacy by creating natural antibiotics. We’ve also learned that they are key influencers in obesity, diabetes, and directly affect the immune system. We can positively influence this community and keep a range of bacteria in the gut through diet, probiotics, or even sticking our hands in the dirt. But, on the flip side, we can negatively alter this community of bacteria and create dysbiosis or imbalance of bacteria with illness, stress, aging, bad dietary habits, the overuse of antibiotics, and our lifestyle choices.

After the introduction of soap, sanitation, and antibiotics we’ve seen a steady decline in infectious disease but now we’re in an epidemic of chronic disease. What is a chronic disease? It’s a disease that lasts longer than 3 months and generally can’t be treated.

Chronic disease eats away at one’s quality of life and takes a huge toll on our health care system. In the late 1980s, the Hygiene Hypothesis was introduced. This states that a lack of exposure to germs may actually be responsible for suppressing the immune system. This is not to say that we need to get sick more but that we need more exposure to good bacteria.

So in summary we’ve spent the last century viewing germs as the victims. As it turns out we may have gotten it wrong. This belief led us to eliminate infectious disease which was a wonderful thing but we’re also seeing a rise in chronic diseases. It’s possible that we may have taken a good thing too far. We see now that it’s possible to wipe out the good bacteria along with the bad. This may lead the body to be vulnerable to whatever is dominant in our environment and this brings us back to the notion that health and possible treatment for chronic disease may lie in the health of our gut and gut bacteria.


Next week we are going to discuss: The Microbiome in Health and Disease

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