Sep 23 2008

Bacteria Are Your Friend

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In the Robot series of science fiction books by Isaac Asimov, which take place in the far future, there are “Spacers”, who are those who live on colonies off earth. The Spacers live in a germ-free environment, since the planets that they colonized were initially sterile and access to those worlds includes the requirement of being treated to remove any bacteria or viruses. This created worlds free of infectious disease, but as a consequence the Spacers have impaired immune systems. Without the regular workout of fighting off germs, their immune systems are weak.

The Hygiene Hypothesis

Like many ideas Asimov cooked up, there is some legitimate science to this science-fiction. The modern industrialized world is obsessed with hygiene. There is undoubted benefit to this cleanliness (other than its putative divine propinquity) – crowding together in cities, airports, schools, and shopping malls creates a friendly playground for viruses and bacteria, and good hygiene is the best prevention against infection.

But perhaps we are heading toward having too much of a good thing. From watching TV commercials you would think that the goal of healthy living is to have a germ-free environment. Clean your hands regularly with anti-bacterial soap, wash all surfaces with germ-killing agents, keep your food vacuum packed, and don’t play in the dirt.

There are those who think this obsession has gone too far – that lack of exposure to germs is turning us into Asimov’s Spacers.  In addition to having weakened immune systems it has been proposed that excess hygiene is leading to increased incidence of allergies, asthma, and other immune disorders, including type I diabetes. This is the so-called hygiene hypothesis (here is a good summary of the possible mechanisms).

Now new research in mice give support to the hygiene hypothesis (here is the technical paper in Nature, and here is a press discussion of the paper). Essentially what the researchers shows is that exposing a certain kind of mice to bacteria similar to the bacteria found in the human gut reduced their incidence of type I diabetes, presumably by reducing immune dysfunction.

What all this likely means is that there is a range of optimal exposure to germs: too much leads to excessive and possibly dangerous infections; too little and the immune system is out of whack. In practice this means that we should be clean but not sterile. A little dirt is a good thing.


The hygiene hypothesis is partly responsible for the probiotics movement.  Probiotics is the use of friendly bacteria to promote bowel health or other health benefits. There is some logic to this – we need a healthy colony of friendly bacteria in our guts, so why not help is along by eating live bacteria in yogurt?

There is some evidence that giving Lactobacillus (a friendly GI bacteria) to infants reduces the incidence of asthma. While this question is far from settled, such strategies may play a role in reducing autoimmunity.

The evidence for probiotics and GI symptoms, however, is less clear. The problem is that the intestinal flora, as it is called, is comprised of many species of bacteria. It is a little ecosystem. Simply adding one or a few species does not seem to have a significant impact.

Studies looking at probiotics to restore intestinal flora after treatment with antibiotics generally show no effect. Mark Crislip (of QuackCast fame, and also a blogger over at Science-Based Medicine) likened this to cutting down a rainforest and then planting corn as a replacement. It doesn’t replace the lost ecosystem.

At present the science of probiotics is immature. This is a solid scientific approach, and I think will yield useful treatments for certain conditions, but at present the research is largely preliminary.  This hasn’t stopped the marketing of probiotics for general health or a host of conditions for which there is little evidence of efficacy. At present such products are mostly hype.

The Future

If I were to wildly speculate about the future of friendly bacteria in health care the, then I would say that I think this technology will play an increasing, and possible very large role, in future medicine. Bacteria cells outnumber human cells in an average human by 10 to 1.  Bacteria colonize all of our mucous membranes – mouth, nose, intestines, etc., and they serve vital functions for digestion and keeping out more harmful bacteria, fungus, parasites, and viruses. It seems that they also play an important role in the maturation of the immune system as well.

Therefore friendly bacteria present another method of altering our biological function. Perhaps we can develop a GI ecosystem of bacteria to replace lost bacteria from antibiotic use, for example.

We are already genetically engineering bacteria (have been for a long time) and are learning how to make them do interesting stuff. It is not difficult to imagine colonizing ourselves with dozens of specific engineered bacteria designed to serve specific functions – remove toxins from food, reduce absorption of too many calories or bad fat, actively fight off infections, aid digestion, reduce or perfume flatulence, improve overall immune function, prevent tooth decay, or infect and kill cancer cells.

Right now this is all science fiction, but as Asimov has demonstrated before, the plausible and well-reasoned science fiction of yesterday can be the science of tomorrow.

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