Germs are everywhere – On your kitchen surfaces, your computer keyboard, even your children’s toys! They’re poised and ready, waiting to jump down your throat and up your nose where they can multiply and cause you to become ill, unless your immune system manages to fight them off.

The best course of action is to try and kill all the micro-organisms in your environment, through the use of disinfectants, sterilisation techniques and bacterial soaps. If you fail to do this, and get infected, antibiotics are the solution, as a strong enough dose will kill all the infecting pathogens and restore your health.

Before the modern inventions of disinfectants and antibiotics, humans were constantly at risk from pathogenic microbes in the environment, with only their immune systems to protect them, but thank-fully modern medicine has saved us!

This is the commonly accepted view, or conventional wisdom, on what is known as “The Germ Theory”. Although many people are coming around to the fact that much of the conventional wisdom with regards to chronic degenerative disease, good diet, and exercise is flawed (if not completely fraudulent), very few people tend to question the germ theory of modern medicine.

Well folks, I’m about to do just that…

First a bit of background.

Although he was certainly not the first to propose it, Louis Pasteur is generally recognised as “the father of the germ theory of modern medicine”1. Prior to the widespread acceptance of the germ theory, the conventional wisdom of the time supported the “spontaneous generation” theory. This theory held that diseases generated spontaneously from within (the clue is in the name), and had held sway for almost 2000 years since it was first proposed by Aristotle.

Pasteur put paid to the spontaneous generation theory through a series of experiments:

He exposed boiled broths to air in vessels that contained a filter to prevent all particles from passing through to the growth medium, and even in vessels with no filter at all, with air being admitted via a long tortuous tube that would not allow dust particles to pass. Nothing grew in the broths unless the flasks were broken open; therefore, the living organisms that grew in such broths came from outside, as spores on dust, rather than spontaneously generated within the broth. This was one of the last and most important experiments disproving the theory of spontaneous generation.2

Through his work in the field of microbiology, most notably his development of vaccines for rabies and anthrax, and the process of heat treating milk and wine (later called pasteurisation in his honour), Pasteur became a legend of modern medicine, and the germ theory became the new conventional wisdom.

Pasteur’s germ theory holds, that like these boiled broths, if we are exposed to micro-organisms present in the environment, we too can become infected, allowing them to proliferate within us causing illness and disease.

Image: jscreationzs / FreeDigitalPhotos.net

Bacteria Spores searching for a Human Host to Infect!

Pasteur was not the only scientist investigating germs and disease at the time however. Two of his contemporaries, Calude Bernard and Antione Béchamp were conducting similar research, which challenged the simplicity of Pateur’s Germ Theory. Béchamp proposed the “Terrain Theory”, which stated that germs would not simply infect any healthy subject, but only one which exhibits favourable conditions – i.e. one which is already unhealthy.

It was Pasteur’s theory that was accepted by the scientific community, and now informs conventional wisdom. There is however, a minority that argue that the wrong horse was backed! There is even a contingent that have suggested that Pasteur was less than rigorous in much of his research, plagiarised the work of others and even forged results. He is also rumoured to have admitted he was wrong on his death bed, his final words allegedly being “Bernard was right! The bacteria are nothing, the soil is everything”.

Do I subscribe to the conspiracy theories surrounding Pasteur, or that Béchamp’s Terrain Theory had it all figured out, but was suppressed due to clandestine and sinister forces that believed they could profit from the Germ Theory?

No, not really. Though his scientific method may not have been as meticulous as it could have been, and perhaps he did not always give credit to his influences where it was due, Pasteur’s breakthroughs were incredibly important, and have undoubtedly saved countless lives.

This does not mean however, that Pasteur’s theory was perfect, nor that the work of Bernard and Béchamp should be ignored.

Bernard and Béchamp acknowledged the existence of microbes, and that they played a role in disease, but argued that infections were not a simple case of unwitting exposure to pathogens, as with the flasks of broth, but would only occur when conditions were favourable for the pathogenic microbes to flourish.

Essentially, both Bernard and Béchamp believed that it was only after a tissue became diseased, that microbes would become attracted to it, and infection could occur. Legend has it that Bernard was so convinced by his theory, he drank a glass full of cholera infected water to prove his point!

Regardless of what actually happened in history, contemporary medical research is starting to show us that the truth lies somewhat in-between the two conflicting theories.

As Pasteur theorised, there do exist pathogenic microbes, which can infect a living host and produce specific disease symptoms. The immune system will fight against this infection, and in many cases antibiotics can be effective in killing the microbes and curing the infection.

What has come to light more recently, however, is that:

  1. Not Everyone is Equally Susceptible to an Infection
  2. The Immune System is Not (or should not be) the First Line of Defence
  3. The Use of Antibiotics can have Undesirable Side-Effects

If infection by a pathogenic microbe was a simple case of exposure, then why is it that when a bug is going around, not everybody catches it?

Micro-organisms are not so dissimilar from larger organisms such as plants and animals, in that each has its own niche or environment in which it will flourish. Take plants for example. Any gardener knows that growing a plant from seed is not simply a case of throwing some seeds in your back yard and waiting for it to grow. For the plant to take hold, there must be the right set of environmental conditions – The pH of the soil, correct temperature, the right amount of light, sufficient minerals in the soil, etc. I’d love a grove of mango trees in my back garden, but throwing mango stones out of the window each time I eat one isn’t going to do it!

Another major factor not recognised at the time by Pasteur, was the existence of the beneficial microbes which populate every surface, both external and internal, of healthy individuals. The growing body of research into gut flora over the last few years has shown that it is not the immune system that should provide the first line of defence, but your microbiome.

Again using the ecosystem analogy, it is a lot harder for a new plant’s seeds to take root in an environment where other plants are already well established, and utilising what resources are available for themselves. Think of the difference between scattering seeds on an empty field, as opposed to one that already has fully fledged crops growing on it.

The protection offered by good bacteria goes far beyond out competing pathogens for nutrients, however. Good bacteria actively defend their host by producing anti-microbial chemicals which only target unwanted intruders, preventing foreign agents from passing through the tight junctions into the blood stream, and also communicating with the body’s immune system to make it better able to identify bad bacteria and destroy them.

The problem with antibiotics, is that while they may have the desired effect of killing pathogenic microbes which have managed to infect the body, they are indiscriminate in their actions, and will also kill all your beneficial bacteria too.

To use an analogy again: Imagine your immune system as a fortress, and your gut flora as soldiers. Pathogenic microbes are like an invading army. Under normal circumstances, where the fortress is in good repair and the soldiers are well supplied, the invasion should be held at bay.

Antibiotics are the equivalent of a powerful biological weapon, which would not only kill all members of the invading army, but also, all of your own soldiers. Though this may provide temporary respite from danger, it also leaves the fortress unprotected, and open to invasion from any other hostile forces in the area.

In some extreme circumstances, perhaps such drastic measures may be necessary. If for example, the invading army were extremely powerful, and had the defending army overpowered and beaten, had stormed the gates and had taken the fortress, such a measure may be necessary.

All too often, however, doctors are way too eager to push the red button and prescribe antibiotics, long before our natural defences have had a chance to put up a fight. This leaves the host even more susceptible to future, and possibly more severe infections.

This can lead to a chronic cycle of one infection after another, as once the antibiotics have left the system, the body is akin to one of Pasteur’s broths, ready and waiting for the next microbe to come along (in fact, depending upon the individual’s health and nutritional status, they may even be a more favourable environment for pathogens). To make matters even worse, pathogenic microbes such as Staphylococcus aureus and Clostridium difficile are becoming resistant to even the strongest anti-microbial drugs, meaning that a course of antibiotics may actually just kill your beneficial gut flora and leave the bad ones!3

The potential negative consequences of antibiotics go far beyond increased susceptibility to the very illnesses they are intended to cure however, with over-use of antibiotics having been linked to increased risks of obesity, diabetes (types I and II), inflammatory bowel disease, allergies and asthma4, autoimmune conditions such as M.S.5 and cancer.6

In the next, and final, instalment of this series, we shall be looking at how to foster a healthy microbiome, thereby maximising your health, digestion and resistance to illness and disease, how to avoid dysbiosis, and what to do if you’re already affected.


1. Pasteur-Koch: Distinctive Ways of Thinking about Infectious DiseasesAgnes Ullman, 2007

2. Wikipedia entry on Louis Pasteur and Germ Theory

3. Decreased Diversity of the Fecal Microbiome in Recurrent Clostridium difficile—Associated Diarrhea Ju Young Chang et al 2006

4. Antibiotic overuse: Stop the killing of beneficial bacteria Martin Blaser, 2011

5. Use of Penicillin and Other Antibiotics and Risk of Multiple Sclerosis: A Population-based Case-Control Study Mette Nørgaard, 2011

6. Is antibiotic use a risk factor for breast cancer? A meta-analysis. Sergentanis TN

Thanks for reading, I hope you found this post of interest. I would love to hear your thoughts and comments below, or feel free to tweet me at @Simon_Whyatt

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