🔬 Calling a Phage a “Phage”

Bacteriophage Ecology Group News (BEG News) was published mostly quarterly as an online newsletter for a total of 24 issues, July 1999 through April 2005. As follows is a reprint of the editorial from Volume 13. The newsletter’s successors are the ongoing Phage.org website, phage-therapy.org, and the Bacteriophage Ecology Group Facebook page.

by Stephen T. Abedon Assembling the Bacteriophage Ecology Group Bibliography can be challenging, particularly since not all phage-ecology references are obviously phage-ecology references. Generally my strategy has been to do "phage" searches on the various online databases. For example, with Medline I use this search:

$phage$ not $phageal not macrophage$ which assures that I catch references by all those individuals who insist on referring to "bacterial viruses" as "phages" or "bacteriophage" or "actinophages," etc., rather than simply as "phage." Typically I customize the output of my search results so that 400 references are displayed per page. Still, even though I often don't need to go more than 1,000 references into these lists before I start seeing references I caught during the last quarter's search, that's a lot of references to consider. Thus, to save time, I've attempted to eliminate a few very common terms that contain "phage", such as "macrophage," but which often have nothing to do with bacterial viruses.

Consistently, what I don't do are searches for the terms "virus" or "viral" since the number of phage papers I would find that I wouldn't find using only a "phage" search would be small. Still, it bothers me that clearly I must be missing at least some phage-ecology papers because, as I've found, sometimes authors neglect to call a phage a phage. The purpose of this editorial, therefore, is to suggest that it would be helpful if papers that considered phages actually had the term "phage," or a derivative (e.g., phages or bacteriophage or, indeed, all three), somewhere in their title, or, at the very least, in their abstract. Not only would this be helpful to me, but consider everyone else who might need to wade through endless "virus" searches to find the few papers that refer to "the viruses of bacteria" but not to "phage."

Is this really a problem? To attempt to address this question I have employed my handy-dandy BEG bibliography to do a "virus" or "viral" but not "phage" or "bacteriophage" search. Considering only the more modern references (i.e., 1998 through 2001; see below), there are over 40 seemingly phage-ecology (or evolution) references that do not use the word "phage" in their title nor, if I had it to search, in their abstract as well. That's an average, of course, of over 10 "phage"-less phage-ecology papers per year. I observe that avoidance of "phage" is particularly common among ecosystem ecologists. I note that if I am having trouble finding (or noticing) these or, particularly, other "phage"-less references, then clearly at least some of our more "phage"-minded colleagues might as well. What have we missed?

Special thanks to Steven McQuinn for the wonderful "phage-virus" gif found at the top of this editorial.

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