Penn Medicine Basic and Translational Research
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The Microbiome as an Evolutionary Force

Streptococcus pneumonia can cause disease, but many people carry the bacteria in their nasal passages without bother. Recently, Jeffrey Weiser, PhD, professor of Microbiology and Pediatrics, and colleagues at Penn and the University of Oxford in Cambridge, England, found that it is competition for space that drives these bystanders into disease-causing agents.

When S. pneumonia has to share space with another common and often asymptomatic bacteria called Haemophilus influenzae problems start. H. influenzae calls in the host's immune cells, telling them to attack S. pneumonia. (If the trick works, H. influenzae gets more space and nutrients to grow.) To avoid the attack, S. pneumonia starts making a sugar-like slick coat that allows it to escape the immune cells. The coat also allows it to slip into other tissues, where it causes serious illnesses including pneumonia, bacteremia, septicemia, and meningitis.

Although much of the microbiome research has focused so far on bacteria, Frederick Bushman, PhD, professor of Microbiology, notes that viruses are also common members of the clan. When his group isolated DNA from the stool samples from 12 people, they uncovered 48 billion bases of viral DNA. Bushman estimates that the sequences represent hundreds to thousands of different viruses. Nearly all of the viruses appeared to come from bacteriophage, which are virus that live inside bacteria.

The most striking feature of the viral DNA was the fact that the vast majority of the genomes encoded unique proteins. That variability – technically referred to as hypervariation – implies that the viral microbiome is creating new variations of itself at a rapid clip. The researchers aren’t sure what is pushing the viruses to evolve so quickly, they may be trying to evade the host immune system or to adapt to changes in the bacteria. Whatever the reason, though, the data show the viral microbiome is evolving even as it lives in a single human intestine.