Phages are everywhere but almost none of them can be easily studied. We can scoop up their DNA (and sometimes RNA), sequence it, and try to put the pieces of their biology together. But often we cannot figure out which bacteria they would infect unless we bring them into the lab, coddle their host into culture, and then experimentally mix the two. Now it is becoming feasible to isolate single bacterial cells to see which phage is lurking within, according to a new publication by Labonte et al

Start by using a cell sorting machine to isolate single bacterial cells from an environmental sample of interest (in this case, surface ocean waters). Along with each cell comes any phage bound to it surface, or already inside the cell. Those phages already inside may be lysogenic, i.e., have inserted their genome into the host chromosome, or they may be lytic and producing thousands of progeny virions. 

Next, sequence all of the DNA from each cell isolated. Here we can tell whether there is phage DNA present, and its copy number relative to the host DNA tells us whether that phage is lytic (higher DNA copy number than host) or lysogenic or bound to the cell surface (same DNA copy number as host). 

Sounds pretty simple, right? Not really of course. These researchers have taken great pains to be remarkably thorough, for example, by testing whether a phage could be sorted with a cell by 'hiding' in the cell's shadow, rather than actually having bound to or infected that cell. They also had to perform a number of experiments and analyses to determine how abundant phage DNA is compared to host bacterial DNA. This is not an easy task with the best-studied organism, and it becomes even more challenging when dealing with newly discovered phages, as the databases used for comparison would have little or nothing related. 

What was learned? 33% of cells were associated with a phage. So, 1/3 cells isolated from nature were actively infected (or being infected by) a phage. 15/20 of the phages were isolated in bacteria for which no other phages have been identified. Only 1 of the 20 phages appeared to be temperate, whereas 4 were likely in late lytic phase. The life cycle stages for 14 phages were unclear. And the last phage? Its genome sequence suggested it was similar to a virus that infects a microbial eukaryote, suggesting that the association between this virus and its "host" may have been simply a matter of non-specific binding to the cell surface. That must happen all the time in the marine milieu. 

Where will this take us? Perhaps within a few years we can regularly isolate millions of bacterial cells and see who is attached to or infecting them. Statistical associations can tell us about how loyal phages are to particular hosts, and whether they change their attitude depending on the host (e.g., more likely to lysogenize host A and lyse host B). Just a scratch on the phage-host surface, but a badly needed scratch.