Viruses are parasites; they need to live inside another organism to survive. Figuring out just who a virus's host is can be difficult, however. Especially when you're talking about bacteriophages—a particularly pervasive group of bacteria-infecting viruses.
The problem lies in identifying which bacteriophages are infecting which bacteria, without having to culture either the viruses or their hosts in the lab, which can often be a difficult if not impossible task.
To address that issue, a team led by Caltech biophysicist Rob Phillips has created a genetic-analysis technique—called microfluidic digital polymerase chain reaction (PCR)—that can "physically link single bacterial cells harvested from a natural environment with a viral marker genes," the scientists report in the July 1 issue of the journal Science.
The team looked at the bacterial community found in the hindgut of a termite—specifically, a termite collected in 2005 in Costa Rica. The typical termite hindgut contains over 250 different species of bacteria, "making it ideally suited to explore many potential, diverse phage-host interactions," the scientists say.
What they found was that microfluidic digital PCR allowed them to see interactions between the viruses and their bacterial hosts in uncultivated cells harvested directly from the hindgut. They noted, for instance, that variants of a viral packaging gene had made their way into hosts across an entire genus of bacteria; in another gene-tracking experiment, however, they found little evidence of lateral gene transfer or switching of the gene from one host to another, despite plenty of opportunity.
"Our approach does not require culturing hosts or viruses," the researchers write, "and provides a method for examining virus-bacteria interactions in many environments."
For more on the new technology and its potential applications, check out the paper's abstract or this press release from the National Science Foundation, one of the funders of the research.