Bugs Inside

I’ve talked here before about the hygiene hypothesis: the idea that our environments, which are extraordinarily clean by evolutionary standards, are keeping some children’s immune systems from developing normally, because they are not exposed to the range of microorganisms that the immune system needs to “see” in order to calibrate itself.

There is a recent article at Scientific American that raises another unsettling possibility: that a combination of excessive hygiene and other anti-microbial measures, such as antibiotics, may be decimating the population of helpful organisms that live on, and in, us.  The human body contains ~10 trillion cells; however, there are about ten times as many bacteria, fungi, and other microbes that live on the skin, in the gut, or elsewhere in the body, most of which are benign or actually beneficial. (This does not count the mitochondria that are present in most cells, which probably evolved from bacteria.)  We have evolved along with these organisms, and the concern is that we may be engaged in a giant uncontrolled experiment to see what happens if some of them are removed from the scene.

With rapid changes in sanitation, medicine and lifestyle in the past century, some of these indigenous species are facing decline, displacement and possibly even extinction. In many of the world’s larger ecosystems, scientists can predict what might happen when one of the central species is lost, but in the human microbial environment—which is still largely uncharacterized—most of these rapid changes are not yet understood.

As with hygiene in general, most of these changes have occurred as a result of medical interventions that were well-intentioned and in fact have had an overall positive effect on human health.  Antibiotics are a case in point.  It is certainly a good thing that we are able to prevent many people from dying as a result of bacterial infections every year.  But the perspective of evolutionary biology that took a while for us to grasp is that antibiotics  create selection pressure for antibiotic resistance, and that has led to the development of new nasties like MRSA (methicillin-resistant Staphylococcus aureus).  There are subtler effects, too.  Yeast infections can be a side effect of antibiotic treatment, because the antibiotic, as it attacks the primary infection, can also wipe out large numbers of the beneficial bacteria that normally keep the yeast organisms in check.

Another potential example is the vaccine for pneumonia.  It has been a success in reducing the number of cases of pneumonia, which can be life-threatening in susceptible individuals.  But the organism against which it builds immunity, Streptococcus pneumoniae, is frequently present in healthy individuals.  Moreover, it is a natural competitor to S. aureus; the concern is that getting rid of one bacterium may make the environment more congenial for another that is at least as nasty.

We’ve begun to see some reflection of this in popular culture, with the introduction of so-called “probiotic” products, like yogurt, that are claimed to replenish the helpful microorganisms in the body.  At present, though, this is something of a “Ready, Fire, Aim” approach, since it is hard to adjust things to a normal state when we don’t know what a normal state looks like.

The first step in understanding these systems is simply taking stock of what archaea, bacteria, fungi, protozoa and viruses are present in healthy individuals. This massive micro undertaking has been ongoing since 2007 through the National Institutes of Health’s (NIH) Human Microbiome Project.

This project is an enormous undertaking, and is unlikely to produce any definitive results quickly.  Yet it is fascinating to realize how much of what happens not only under our noses but inside them (not to mention other places) we don’t understand.