Bugs ‘R’ us

After a couple of posts focusing on the bad guys, I thought I should set the record straight.

Ever since Louis Pasteur established germ theory about 150 years ago, it seems we’ve been trying to eradicate everything microbial from our lives.  Even though we’ve tackled this with gusto and science, the task is ultimately futile (they will always out-evolve our efforts), and the indirect consequences to our health seem to be mounting.

Our well-being is affected by the well-being and diversity of the bacteria that inhabit us (mostly in the gut, but also mouth, skin, vagina, nose, lung). As we increasingly sanitize ourselves, our environment and our food, we increasingly disturb and deplete our complex microbial ecology.

We wouldn’t have existed without bacteria. It was the bacterial strain cyanobacteria that bio-engineered Earth and made us possible. Originally, Earth had an oxygen-free atmosphere made up of nitrogen and carbon dioxide, and was bathed in intense ultraviolet radiation. Life could only exist in an anaerobic form, protected from radiation undersea. Cyanobacteria evolved the earliest form of photosynthesis for energy, harnessing CO2 and releasing oxygen as a byproduct. This added oxygen to the oceans, and enabled oxygen-based sea life to evolve. As cyanobacteria continued their work and oxygen also accumulated in the atmosphere, radiation hitting the upper levels converted the oxygen gas (O2) to ozone (O3), forming the ozone layer that blocks ultraviolet radiation from reaching the earth’s surface. Only then, protected from radiation, could land-based life evolve. The irony is that, as their name suggests, cyanobacteria are toxic to us (they are closely related to blue-green algae). After billions of years, Cyanobacteria can still be found today, working away in Stromatolites like these at Shark Bay (Western Australia). Astonishing stuff.


It is not clear at what point multicellular life began, however it is clear that bacteria and more complex cellular and aerobic life-forms co-evolved together, and a genetically diverse bacterial pool came to be incorporated into our bodies. We have about 10 times more bacteria in us than we have cells (and about 500 bacterial species, although mostly concentrated in 30-40).

By constantly eating, we supply these bacteria with a nutrient rich environment, and we benefit from the physiological functions that they provide and that we didn’t need to evolve for ourselves.

Some of what they do for us:

1. Primarily, they ferment indigestible or undigested carbohydrates and so break down these carbohydrates and make them available for us to absorb. For example, we are unable to digest beans, but because of the action of our gut bacteria, beans become not only nutritious but a food staple. Flatulence from gases the bacteria release during fermentation is a small price to pay for the nutritional benefit we obtain.

2. The process of fermentation creates a slightly acidic environment in the gut that reduces the proliferation of harmful species of bacteria.

3. Bacteria synthesise vitamins B and K for us.

4. Our bacteria help regulate the balance between energy use and storage, and their disturbance may be a factor in obesity.

5. A healthy and diverse microflora can out-compete harmful bacteria that we may ingest.

6. Bacteria regulate our immune system. They colonise an infant’s digestive tract almost immediately after birth (and perhaps even before). While our immune system is still naive, they train it to recognise them as friends, and other bacteria as the enemy. They continue to influence the immune system throughout life (gut bacteria can up-regulate the immune response to a lung infection for example). Disturbance of our bacterial colonies may be related to an increased incidence of immune-related allergies and asthma.

Whenever we take an antibiotic we attack not only the harmful bacteria that have invaded us, but also these helpful bacteria. Antibiotics are widely prescribed, and they are ubiquitous, turning up in hand-washes, toothpaste, fed to our livestock and distributed across our food chain. Antibiotic resistance is the inevitable and disturbing outcome, and is a top concern for the Centers for Disease Control and medical scientists. Add to this that we now preserve our food not by fermentation (which had all the benefits of microbial digestion, nutrient release and our ingestion of the good guys), but rather by pasteurisation, irradiation and canning, which kill everything. And we chlorinate our tap-water.

There is no question that public health has been improved dramatically by these strategies. However, it seems maybe we’ve gone too far. Rather than continuing our futile all-out war on bacteria, a more intelligent and balanced strategy makes sense as the awareness of our bacterial co-dependence increases.

Principal sources: SE Katz “The Art of Fermentation“, Chelsea Green, Vermont. H McGee “On Food and Cooking“, Scribner, New York