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Germs - your friends.


Microorganisms, germs, can only be seen under a microscope. There are of three main types, bacteria, viruses and fungi. Parasites are larger and can often be seen with the naked eye, lice, bed bugs and worms are good examples.

Bacteria can cause pneumonia, sinus infections, Strep throat, meningitis, urinary infections, and skin infections including boils. Common viral infections include head colds, most sore throats, flu, pneumonia, bronchitis and many childhood illnesses with rashes. Fungi cause ring worm, athletes foot and jock itch. Parasites tend to make their homes in your intestines or on your skin. But these diseases are but a minuscule part of the microbial world.

The so-called dirty germs

So-called germs. This concept is both outdated and actually dangerous. It has led us to a strange place.

If you are like most people you have been raised to believe that bacteria and viruses are all “dirty” and dangerous. So-called germs. This concept is both outdated and actually dangerous. It has led us to a strange place. The story goes that to be healthy and well you need to live in a germ free environment. In fact the truth is totally the opposite. In our natural state we have evolved surrounded by all sorts of microorganisms. Most so-called germs are actually beneficial to us and indeed without them we would be unhealthy. We need to be constantly exposed to so called germs to keep our immune system robust and healthy. Not only protecting us from infection but also cancers and other illnesses.

Get dirty

This does not mean that it is appropriate to live in a filthy environment without sanitation and clean running water. Humans did not evolve in these conditions either. But the need to provide appropriate sewage systems and clean water for drinking and bathing does not mean that we should attempt to live in sterile environments. In fact we should strive for the opposite. Children need to get dirty and play in the mud. At home, other than our kitchens, cooking surfaces and bathrooms, our homes should be clean not sterile. We should let things be.

Gardening, a walk in the woods, stroking pets and other animals are all activities that are good for us. Part of the benefit comes from coming into contact with microorganisms. For example walking in the woods has been shown to boost our immune system for several days. One of the documented beneficial effects is an improvement in the function of specific cells, Natural Killer cells (NK cells) whose role is to kill tumour cells and virus infected cells. The Japanese even have a name for it, Shinrin-yoku or Forest Bathing. There are other benefits to this actively including improving mental health. Talk about a great way to improve your health.

For example walking in the woods has been shown to boost our immune system for several days.

You need to have a different concept in your mind about germs. Far from being dangerous they assist us in so many ways. Besides protecting us from disease, soil organisms allow our food plants to grow with high levels of nutrients that benefit us.

So why am I mentioning this here? Because these microorganisms did not just evolve around us. They evolved with us and indeed inside us.

The resident colony

One of our primary defences against infection the invasion or overgrowth of a disease causing strain of bacteria and fungi is the resident bacterial colony. In some cases disease causing bacteria and fungi are already present as part of the resident colony in the very same location in which they cause disease, but are kept in their place by healthy competition with other resident bacteria and of course a healthy immune system.

We need to think differently about infection. In reality it is a breakdown of the local ecology and microbiota allowing the overgrowth of a one particular strain that if present in sufficient number can cause disease.

The presence of a healthy diverse colony at any particular site in the body protects us from this occurring. The resident microbiota does this in several ways. The first is simply a matter of space. Bacteria and fungi need room. So if if the surface area is covered by friendly organisms then there is no room for the bad guys. They also compete for other resources including nutrition.

The local microbiota influences the local immune system. It does so by directing our immune systems response. Not only alerting our immune cells that there is an overgrowth of a potentially aggressive species but also directing the correct military response based on the type of organism. We have seen that the presence of certain species can enhance the defensive response to other potentially disease causing species.

The microbiota is also intolerant of any particular group getting ahead. In my part of the world this is known as crabs in a bucket. If any individual manages to reach high enough to climb out, typically by climbing on others, the rest of the crabs will pull it back in. This restores equality. The bacteria in a colony employ a wide array of techniques which include cross talk (diplomacy and negotiation) and armaments (weapons and toxins). In other words if the colony gets out of balance it has mechanisms to restore itself to a balanced state. The benefit to us is the infection is controlled.

Caution with antibiotics

This is one of the reasons why antibiotics need to be treated with extreme caution because they have the potential to damage these normal protective mechanisms by throwing the system into even deeper disarray both in the short and long term. Antibiotics significantly damages the microbiota’s ability to defend itself and and the human body.

It is also exemplified by the way we manage a potentially life-threatening antibiotic induced infection in the gut called C-diff. In the past we often had to give months of heavy antibiotics to cure the problem. Now we just offer a faecal transplant from a healthy individual with a 95% success rate which is almost instantaneous.

We are also beginning to understand how the microbiota influence this defence process from being to end. Influencing transmission, immunity, the actual damage done and finally the process of tissue repair.

This process is not just confined to bacteria and fungi but includes viruses. Its not confined to the gut either. It has been shown that your response to infection to the flu virus is in part influenced by the quality of your gut microbiota.

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