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."
