🔬 Best of BEG News

Bacteriophage Ecology Group News, or BEG News, was published mostly quarterly as an online newsletter for a total of 26 issues, starting July 1, 1999 and continuing through December 31, 2007. As follows is a reprint of the editorial from the newsletter. Also included in issues were lists of new members to the Bacteriophage Ecology Group, an introduction to new website features, a list of upcoming meetings, phage images found on the web (remember, this was 1999, so effectively pre-Google), etc., but most of all, a listing of new phage ecology-related publications. The newsletter was modelled after T4 News, which was a printed newsletter distributed earlier in the 1990s. The newsletter's successors are the ongoing Phage.org website, phage-therapy.org, and the Bacteriophage Ecology Group Facebook page.

The Bacteriophage Ecology Group (BEG) was born during the Summer of 1995 at the biannual Population Biology of Microorganisms Gordon Conference. The original group consisted of myself (Steve Abedon) plus a number of graduate students and post-docs including Brendan Bohannan, Greg Krukonis, Sharon Messenger, John Mittler, Tom Palys, and Ing-Nang Wang. At that moment I was in transition from a somewhat unsuccessful post-doc at the University of Pennsylvania (studying AIDS immunology of all things) to a tenure-track position in the department of Microbiology at The Ohio State University. Also at the time, I had a vague idea that service toward the profession counted for something, and that taking on a project such as BEG could contribute toward my college's service expectations.

Of course, as with all reasonably OK ideas, this one had its genesis long before the Summer of 1995. In fact, BEG's roots may be found in two locales. First, there is the obvious precedent of Max Delbrück's Phage Group as a means of motivating camaraderie among researchers and to promote outstanding phage research ("Phage Group" → "Bacteriophage Ecology Group," get it?). Second, by working with mentors highly influenced by the phage group--Harris Bernstein, the man who (by some tangled turn of logic that I don't fully understand) gave his mother's "name" to the amber mutation (amber is the English translation of the German word "bernstein"), was my Ph.D. advisor and John Spizizen, Emory Ellis' first post-doc, was both my department head and on my Ph.D. committee--I found myself immersed in bacteriophagy but nevertheless isolated from bacteriophage ecologists. This isolation was perhaps more one of attitude than of geography since a mere one mile south of the Bernstein laboratory there were not one but two laboratories actively engaged in bacteriophage ecology research: Conrad Istock's group with their ecology of bacteriophages in soil and Chuck Gerba's applied bacteriophage ecology. As far as I am aware, none of us were extensively talking with each other! This travesty, combined with my ongoing frustration, during the late 1980s, early 1990s as I attempted to proselytize the relevance of ecology to molecular geneticists (my supposed Ph.D. area of concentration), resulted in an observation that would eventually become BEG: Bacteriophage ecologists seem to interact with just about anyone but other bacteriophage ecologists. The surprisingly large concentration of bacteriophage ecologists at the 1995 Gordon conference made me realize that not only should this sad situation change, but that it could.

Additionally, in the simpler systems of biology, it should be possible for the proximate causation people (e.g., molecular biologists, physiologists, and biochemists) to talk to the ultimate causation people (ecologists and evolutionists), and vice versa, and there aren't too many biological systems that are much simpler than bacteriophages. Thus, my agenda is both broader and more ambitious than just the organization and development of bacteriophage ecology: I additionally hope to merge bacteriophagy into a coherent whole. Or, more precisely, remerge these two camps since, in fact, the roots of bacteriophagy can be found in an organismal biology that embodied a concern for both philosophies (see, for example, the translation of Félix d'Hérelle, 1917, below).

BEG, from the start, was a child of the internet. BEG began with e-mail but by July of 1996 consisted of a web site. The bulk of the work involved in getting this web site into its current form began in the following months as a catharsis aimed at getting me past the dual crises of my mother's death (as well as both of her parents, my grandparents) and my ongoing inability to complete the set up of my laboratory (the most humorous delay involved the loss of my centrifuge during its shipment when a box containing a motorcycle apparently fell upon it). Part of this development included putting on line my collection of bacteriophage ecology references that I had been collecting and assembling since my graduate-school days. We are now up to 2344 references in this bibliography! Milestones in the further development of the BEG site included the incorporation of a search engine for these references (late Summer, 1998) and my obtaining the www.phage.org URL (ditto). These two events are correlated since it was my need to run the search engine on a Windows-based machine that forced me off of our (Unix) campus web server (now used as a mirror site) and it was my frustration employing an IP address for this new site, rather than an URL (plus my dislike of long URLs, e.g., www.mansfield.ohio-state.edu/~sabedon/), that motivated me to purchase www.phage.org. Right from that start BEG has also proudly emphasized bacteriophage ecologists and currently our membership consists of 40 individuals. My guess is that this represents about half of the world's bacteriophage ecologists. Where/who are the rest of you?

If creating a web presence for bacteriophage ecology represented phase II of BEG, then here allow me to introduce phase III: Bacteriophage Ecology Group News. BEG News represents a continuation of our efforts to forge bacteriophage ecology (indeed, all of bacteriophagy) into a cohesive discipline. My hope is to publish BEG News quarterly, as a single web page, with issues put to rest with whatever I have written or received as of July 1, October 1, January 1, or April 1. I envisage BEG News as a means of introducing BEG members to new members; to publicize newly published research, newly discovered links, and new features found on the BEG site; to remind people of upcoming meetings, to advertise (for free, of course) job positions available as well as job positions wanted; etc... Most important, though, is to foster communication between all of us. Toward that latter end, I would like to highly encourage the submission of material for publication in BEG News. For example, we all would like to hear of any developments that are relevant to phage ecology and those of you that are closest to these developments should consider writing up short articles. We additionally would appreciate the submission of notes on relevant bacteriophage ecology research that, for whatever reason, may not be published elsewhere or in a timely fashion. In other words, people, lets start talking to each other!

BEG News will be posted as it is drafted and suggestions as well editorial comments are welcome from all. Any material not completed by the quarterly deadlines will be scheduled for tentative publication in the subsequent issue. As usual, send any materials to me at abedon.1@osu.edu (microdude@osu.edu works just as well). Please send all submissions as Microsoft Word documents if possible (I'll let you know if I have trouble converting any other document formats), and in English. I anxiously look forward to everybody's participation.

Bacteriophage Ecology Group News, or BEG News, was published mostly quarterly as an online newsletter for a total of 26 issues, starting July 1, 1999 and continuing through December 31, 2007. As follows is a reprint of the editorial from the newsletter. Also included in issues were lists of new members to the Bacteriophage Ecology Group, an introduction to new website features, a list of upcoming meetings, phage images found on the web (remember, this was 1999, so effectively pre-Google), etc., but most of all, a listing of new phage ecology-related publications. The newsletter was modelled after T4 News, which was a printed newsletter distributed earlier in the 1990s. The newsletter's successors are the ongoing Phage.org website, phage-therapy.org, and the Bacteriophage Ecology Group Facebook page.

The Bacteriophage Ecology Group (BEG) is concerned, of course, with the ecology of bacteriophages. When modeling bacteriophage growth, especially in liquid culture, the dynamics of host acquisition by bacteriophages should essentially resemble those of any organism that acquires its "prey" through random diffusion. Of organisms that obtain their resources directly from other living organisms, we may, of course, further subdivide into (i) those that acquire no more than one "prey" per lifetime (the parasites) and (ii) those that acquire more than one "prey" per lifetime (the predators). An individual bacteriophage clearly cannot acquire more than one "prey" (or host) in a lifetime so clearly, by these definitions, is more parasite-like than predator-like.

Among parasites we may further subdivide into (i) those parasites that infect multicellular organisms and (ii) those parasites that infect unicellular organisms. From the standpoint of a parasite, the former, but not the latter, is supplied with additional "prey" by the infected host. This is most easily visualized when considering obligately lytic intracellular parasites in which host cells represent discrete "prey." Thus, acquisition of a single host cell can lead to the generation of parasite progeny which can then go on to acquire new "prey," all without any parasite ever leaving the original host. This is not the case for the parasites of unicellular hosts (or unicellular organism parasites, i.e., UOPs). The progeny of UOPs must leave their host (e.g., an individual bacterium) to acquire new "prey." It has been my policy to define UOP rather broadly to include such parasites as Bdellovibrio as well as the viruses of yeasts and those of protozoa.

Nevertheless, ambiguity rears its ugly head in defining multicellularity. An important component of the first night of the 1999 Gordon Conference on Microbial Population Biology (held July 18-23) was the argument that bacteria often exist effectively as multicellular organisms. That is, individual cells interact in ways such that the whole of a bacterial population is greater than (or, at least, different from) the sum of its parts. If bacteria can be multicellular, then are bacteriophages truly UOPs? Is anything?

I won't attempt to answer that question but instead will address the implications of bacterial multicellularity on bacteriophage replication, based on a contrast between the environments represented by multicellularity versus those represented by unicellularity. I will then question whether, from the standpoint of bacteriophage growth, eukaryotic cells growing in tissue culture are any more multicellular than, for example, bacteria growing in a biofilm or bacteria growing within an agar lawn or colony.

With regard to the population-wide growth of obligately intracellular parasites, two considerations may occur during the jump from unicellularity to multicellularity. First, the susceptibility of individual host cells to parasite infection may decline. Second, the dynamics of host-cell acquisition may change. Considering the former, we may envisage barriers to parasite diffusion, changes in host cell-surface markers, or even mechanisms of parasite inactivation both prior to and following host-cell infection (e.g., an immune system). Alternatively, with regard to the dynamics of host-cell acquisition, clearly with multicellularity the odds of finding two host cells that are adjacent is no longer a statistically independent product of global host-cell densities. Thus, within a multicellular system the acquisition of a single host cell increases the likelihood or rate with which progeny may find additional host cells. Clearly these two factors would result in (i) a decrease in host-cell susceptibility and (ii) an increase in host-cell clumping.

Together these factors affect parasite replication in opposite directions with the former decreasing and the latter increasing host susceptibility in terms of the spread of progeny parasites to adjacent cells. We may thus envision that if parasitism has significant negative impact, then the benefits of multicellularity to the host must either outweigh the costs of increased parasite susceptibility by multicellular organisms or that along with multicellularity comes at least an opportunity for increased defense against parasites. If the latter is the case then one might even go so far as to argue that multicellularity could have evolved in general as a mechanism of parasite (or predator) evasion. For example, the evolution of metazoa could have been motivated as a mechanism of protection against protozoa-mediated engulfment (i.e., big things are harder to engulf and multicellularity is one route toward bigness). Alternatively, as well as additionally, multicellularity may have evolved as a means toward more-effective predation of, for example, multicellular cyanobacterial mats.

Thus, a multicellular organism represents both a juicier, perhaps more obtainable target for parasitism, but simultaneously a less appetizing morsel to the extent that colonial living leads to mutual protection against parasitism. Since prokaryotes are probably as capable of at least some mutual protection as eukaryotes, then I suppose I must concede that bacteria, from the point of view of a bacteriophage, are not nearly as unicellular as I might otherwise like to think. How, then, might we classify eukaryotic cells living together in a tissue culture flask? Are such cells any less susceptible to a parasite than bacteria living in an agar lawn or within a biofilm? My intuition suggests no. I welcome (and would like to publish) any good arguments either for or against this assertion.

All of this pontification stems from a debate I've been having with myself over whether we should include an article — found in the September 10 issue of Science on vesicular stomatitis virus evolution — into the BEG bibliography: Rosario Miralles, Philip J. Gerrish, Andrés Moya, and Santiago F. Elena, Clonal Interference and the Evolution of RNA Viruses, Science 285(5434):1745-1747 (Clonal Interference). Since the primary experimental technique used in this study involves little more than growing viruses on "baby hampster kidney cells... grown as monolayers under Dulbecco's modified Eagle's minimum essential medium," it strikes me that what we have here is an example of UOP-mediated experimental evolutionary biology. Therefore, along with UOP ecology and evolutionary biology in general, it is my tentative contention that Miralles et al. should be included in the BEG bibliography (along with, for example, papers on the viruses of protozoa). What do you think?

Bacteriophage Ecology Group News, or BEG News, was published mostly quarterly as an online newsletter for a total of 26 issues, starting July 1, 1999 and continuing through December 31, 2007. As follows is a reprint of the editorial from the newsletter. Also included in issues were lists of new members to the Bacteriophage Ecology Group, an introduction to new website features, a list of upcoming meetings, phage images found on the web (remember, this was 1999, so effectively pre-Google), etc., but most of all, a listing of new phage ecology-related publications. The newsletter was modelled after T4 News, which was a printed newsletter distributed earlier in the 1990s. The newsletter's successors are the ongoing Phage.org website, phage-therapy.org, and the Bacteriophage Ecology Group Facebook page.

"Ecologists who are not thoroughly familiar with the organisms involved risk wasting a great deal of time." — Nelson G. Hairston, Sr.

For years now I've straddled the divide between the bacteriophage molecular and the bacteriophage ecological, never quite understanding the motivations of those who are dedicated to only one but not the other. The problem as I see it is one of using bacteriophages as model systems. Regardless of one's orientation, such an attitude is degrading to bacteriophages, as it is any individual who is objectified rather than treated as a whole. Take molecular types. With enormous success organisms have been reduced to their component parts, unless there is some economic incentive to do otherwise, with little regard for the subtleties of environmental interactions. The phage has a nucleic acid polymerase, the better to understand polymerases! But who cares where that phage uses that polymerase, nor how many phages it makes with it, much less why.

Purely ecology types are not much better. Sure phage populations do interesting things, and they are so simple that experimentation is far simpler than, say, setting up the Serengeti in the laboratory. Lions, and even zebras, are complex creatures, living in complex environments; so much easier it is to study a simple bacteriophage, infecting a simple bacterium, living together in a simple broth culture. However, simplicity can be deceiving. We only know that lions, zebras and the Serengeti are complex systems because we can see those complexities. As any molecular type could tell you, however, bacteriophages and bacteria (and even broth cultures as the ecology types might retort) can also be pretty darn complex. But it's easy to pretend otherwise because we can't see these complexities with our own eyes.

The solely molecular biology types have created a world in which phages are highly complex molecular model systems that have no ecology, while the solely ecological types have created a world in which phages are represented as simple ecological model systems. Obviously both views are quite misleading. And just as obvious, bacteriophage ecology is an irrelevant discipline, and increasingly so, unless it is based on a robust understanding of bacteriophage complexity. Only with such an understanding can one argue that the experimental manipulation of phages is justifiable because robust conclusions are possible only with systems that are understandable. But just because bacteriophages have that potential does not mean that the potential will be realized.

Ideally all bacteriophagologists would take a strong interest in both the molecular and the ecological. Minimally, bacteriophage ecologists should never lose sight of the molecular (and physiological) complexity of the organisms with which they work.

Bacteriophage Ecology Group News, or BEG News, was published mostly quarterly as an online newsletter for a total of 26 issues, starting July 1, 1999 and continuing through December 31, 2007. As follows is a reprint of an article from the newsletter, authored by Hans-Wolfgang Ackermann. Also included in issues were lists of new members to the Bacteriophage Ecology Group, an introduction to new website features, a list of upcoming meetings, phage images found on the web (remember, this was 1999, so effectively pre-Google), etc., but most of all, a listing of new phage ecology-related publications. The newsletter was modelled after T4 News, which was a printed newsletter distributed earlier in the 1990s. The newsletter's successors are the ongoing Phage.org website, phage-therapy.org, and the Bacteriophage Ecology Group Facebook page.

Hansjürgen Raettig, MD, was born in Stralsund, Germany. He studied medicine and obtained his medical degree in 1939. His doctoral thesis was on the influence of season and climate on pulmonary embolies. His early career can be summarized as follows. He was inducted into the army in 1939, worked during the war in a military hospital in France and in the Hygiene Institute in Greifswald, was a member of the Public Health Institute of the same city from 1946 to 1948, and was recruited in 1948 by the Robert-Koch-Institute in Berlin. The institute was then in dire straits, lacking basic furnitures and facilities, yet charged with heavy public health responsibilities. In 1952 Dr. Raettig became the equivalent of an assistant professor at the Free University of Berlin. He became a full professor in 1961 and then became acting director of the Robert-Koch-Institute, holding that position from July 10 of that year until March 7, 1976 and retiring from the institute October 10, 1976.

Dr. Raettig published more than 200 papers or books. Most were on vaccination, namely against typhoid fever, shigellosis, poliomyelitis, and cholera. He was also very concerned with epidemiology, public health, and seriological diagnosis of infectious diseases. In the early fifties, he became interested in bacteriophages, mainly in intestinal phages and their variability. This led to experimentation with phage media and inactivation experiments and culminated in a two-volume book entitled "Bakteriophagie", a literature documentation aimed at covering the whole vast phage literature and classifying it by using a large number of key-words. Two volumes covered the literature from 1915 to 1956 and from 1956 to 1965, respectively. The first volume was in German only and the second one was in English and German [Raettig, H., 1958, Bakteriophagie, 1917 bis 1956; Zugleich en Vorschlag zur Dokumentation Wissenschaftlicher Literatur & 1967, Bakteriophagie 1957-1965 (Bacteriophagy 1957-1965), both G. Fischer, Stuttgart]. The two volumes covered a total of 11,405 references.

Dr. Raettig was also interested in electron microscopy and offered a course on this subject which I had the good fortune to attend in 1958 or 1959. I remember him as a friendly and engaging teacher who took great pride to show how he had assembled and categorized the vast phage literature using perforated cards. The book "Bakteriophagie" is now a bibliophile rarity, much sought after by phage workers and extremely useful for its near complete coverage of the early literature on this subject. To my knowledge, nobody in the field of biology has ever assembled a similarly vast and structured documentation. It is certainly Dr. Raettig's most enduring legacy.

Hans-Wolfgang Ackermann
Félix d'Hérelle Reference Center for Bacterial Viruses
Department of Medical Biology
Faculty of Medicine
Laval University

Bacteriophage Ecology Group News, or BEG News, was published mostly quarterly as an online newsletter for a total of 26 issues, starting July 1, 1999 and continuing through December 31, 2007. As follows is a reprint of an article from the newsletter. Also included in issues were lists of new members to the Bacteriophage Ecology Group, an introduction to new website features, a list of upcoming meetings, phage images found on the web (remember, this was 2000, so effectively pre-Google), etc., but most of all, a listing of new phage ecology-related publications. The newsletter was modelled after T4 News, which was a printed newsletter distributed earlier in the 1990s. The newsletter's successors are the ongoing Phage.org website, phage-therapy.org, and the Bacteriophage Ecology Group Facebook page.

"The phage group wasn't much of a group. I mean, it was a group only in the sense that we all communicated with each other. And that the spirit was — open. This was copied straight from Copenhagen, and the circle around Bohr, so far as I was concerned. In fact, the first principle had to be openness. That you tell each other what you are doing and thinking. And that you don't care who has the priority."

— Max Delbrück, quoted on p. 42 of Horace Freeland Judson's The Eighth Day of Creation, Cold Spring Harbor Laboratory Press (1996)

"We are not primarily interested in the destruction of the bacteria, intent on applying what we find to the therapy of infectious diseases caused by bacteria. Nor are we interested, primarily, in devising means to frustrate the growth of the viruses, intent on applying such knowledge to the therapy of infectious diseases in plants, animals and men caused by viruses. Such motives, noble though they are, are ulterior to our cause."

— Max Delbrück, 1946, The Harvey Lectures, 41:161-187, p. 163.

"Today, a bacterial virus is a parasitic microbe in ecology, a bacterial organelle during its existence as prophage, a marker on the bacterial chromosome in breeding experiments with lysogenic bacteria, a subgamete for which names are lacking when it transmits lysogeny, a vector of unrelated bacterial organelles, including other prophages, in transduction experiments, and the inciter of an explosive disease of nucleic acid metabolism when it mimics T2. Bacteriophages are all these things, and probably more to be discovered. To ask which is the correct view is to ask what is the proper function of a window: to admit light, to let in air, to keep out wind, to exclude rain, to frame a pleasing landscape, or to pique the peeping Tom."

— Alfred Day Hershey, 1957, Bacteriophage T2: parasite or organelle?, The Harvey Lectures, Series LI, 1955-1956, Academic Press, pp. 229-239 (quote is on page 238).

"Our inability to find phenotypes for so many mutants (of the newly completed Caenorhabditis elegans sequence) only reflects our ignorance of life. The advocates of 'modern' molecular biology, many of whom are trained in the art of cloning genes, will need to go back to their friends and colleagues versed in physiology, neurobiology, ecology and population biology; these disciplines will be critical in teasing apart the function of all of those genes. 'Functional genomics' is synonymous with 'biology' — biology against rich tableaux of sequence information. Who does not remember the seminars in which the speaker professed an interest in some biological phenomenon, and then nose-dived into a 40-minute description of gene mapping, cloning and sequencing? With the completion of the genome projects, one senses that these days will soon be over: back to biology."

— Ronald H. A. Plasterk, 1999, Hershey heaven and Caenorhabditis elegans, Nature Genetics 21:63-64 (quote is the last paragraph of the article).

Bacteriophage Ecology Group News, or BEG News, was published mostly quarterly as an online newsletter for a total of 26 issues, starting July 1, 1999 and continuing through December 31, 2007. As follows is a reprint of the editorial from the newsletter. Also included in issues were lists of new members to the Bacteriophage Ecology Group, an introduction to new website features, a list of upcoming meetings, phage images found on the web (remember, this was 2000, so effectively pre-Google), etc., but most of all, a listing of new phage ecology-related publications. The newsletter was modelled after T4 News, which was a printed newsletter distributed earlier in the 1990s. The newsletter's successors are the ongoing Phage.org website, phage-therapy.org, and the Bacteriophage Ecology Group Facebook page.

"The power to lysogenize is the property of temperate phages, as opposed to virulent ones."
— André Lwoff, 1953 (Lysogeny. Bacteriological Reviews 17:269-337), p. 273.

Welcome to the wonderful world of bacteriophage classification based on phage-host interaction. It turns out that there is some confusion as to how one classifies these interactions. Here, then, are a few definitions, which I follow with a proposition that we stop describing lytic, non-temperate phages as "virulent." I find all of these terms useful (except virulence as typically defined), but only when properly employed. Thus, there is no such thing as a "lysogenic phage" and temperate phages typically are perfectly capable of lysing their bacteria hosts.

Lytic:	In order to release progeny into the extracellular environment, a lytic phage must terminate its lytic infection and breach its host's cell envelope. "Lytic phage" and "Virulent phage" are used synonymously (Lwoff, 1953. Lysogeny. Bacteriological Reviews 17:269-337).
Chronic (Continuous):	A lytic infection contrasts with a chronic (or continuous) infection. A chronically infecting bacteriophage (or virus) can release progeny into the extracellular environment without terminating its infection. That is, phages are extruded across the host cell envelope continuously (a.k.a., chronically).
Lysogenic:	"A lysogenic bacterium is a bacterium possessing and transmitting the power to produce bacteriophage" (p. 271, Lwoff, 1953). During the lysogenic cycle an infected bacterium does not produce phage progeny nor release phage progeny into the extracellular environment.
Temperate:	A temperate phage is one that is capable of displaying a lysogenic infection. Note that temperate phages typically display a lytic cycle as their vegetative (i.e., non-lysogenic) phase. Nevertheless, one does not refer to temperate phages as lytic phages.
Virulent:	Unfortunately, the standard term used to describe a lytic but not temperate phage is virulent. A virulent phage is one that does not display a lysogenic cycle.

Common practice has been to differentiate phages into at least two types, temperate versus virulent or lytic, to which a third type, chronic or continuous, should be habitually included. Temperate phages can produce reductive (lysogenic), productive, or abortive infections while non-temperate phages can give rise only to productive or abortive infections. Chronically infecting phages extrude their progeny from infected cells without lysing their hosts, while both temperate and lytic (or virulent) phages lyse their hosts to release progeny phages. Unfortunately, this contrast between chronic release and lytic release gives rise to an ambiguity: Temperate phages, in practice, are lytic, but, strictly speaking, are not "Lytic phages." Less ambiguous, temperate phages are not virulent phages, but as I will consider, this latter term, too, is problematic.

The term "Virulence" dates from early phage characterization in which it was noted that some phages more readily lyse bacterial cultures than others. For instance:

The question of virulence has been mentioned and emphasis placed upon the necessity of utilizing a race of maximum virulence. By this is meant a race of bacteriophage which will cause a complete and permanent dissolution of the organisms actually present in the infectious process. (p. 178, F. d'Hérelle as translated by G. H. Smith, 1930. The Bacteriophage and its Clinical Applications. Charles C. Thomas, Publisher. Springfield, Illinois)

Only subsequently did the term "Virulent" come to designate those phages that fail to display lysogeny in the modern sense of that term:

Phages have been classified in two categories, temperate and virulent according to the presence or absence of the power to lysogenize. (p. 319, Lwoff, 1953)

Regardless, I am of the opinion that it is time to stop employing the term virulent as a synonym for not temperate. Why? First, it is very likely that by doing so we do not use the term in its original sense. Second, especially as we ponder the use of phages as antibacterial agents, it is probably useful (taking d'Hérelle's lead) to have a term that distinguishes those phages that more readily lyse bacterial cultures from those that less readily lyse bacterial cultures. Virulent is the obvious and perhaps original term used for this purpose. Third, without extensive molecular characterization there is always significant uncertainty surrounding our declarations of phage virulence in the Lwoff sense:

Unfortunately, the definition of the character virulent is purely negative. If, after the action of a temperate phage, most survivors are nonlysogenic, the rare lysogenic survivors, because of their low proportion, may be practically impossible to find. Thus, as a result of the study of a system with a low lysogenization quotient, a temperate phage could be considered as virulent... and one may conceive of a phage behaving as a strong virulent in one bacterium and able to be reduced to a prophage into another. (p. 319, Lwoff, 1953)

Lastly, as pointed out by Michael DuBow during this past June meeting [June 2000, at the Millennial Phage Meeting, hosted by Michael DuBow], the term VIRULENT has some serious PR baggage as phage therapists ponder injecting what we hope are harmless little viruses into people's arms.

What's the alternative? Except for the various vir derivatives of temperate phages (the description of which is sufficiently ingrained that there is no going back), I propose using "Obligately lytic" to describe those phages that obligately initiate their lytic cycle upon successful adsorption, especially if one has demonstrated to some reasonable degree that a "Lytic phage" truly is not capable of inducing lysogeny on any host. I reject "Non-temperate" as a synonym because chronically infecting phages are also non-temperate but are not obligately lytic.

We should reserve virulent as a description of the ability of a phage to kill some (large) proportion of the cells found within a bacterial culture.

See Also

Hobbs, Z. & Abedon, S.T. (2016). Diversity of phage infection types and associated terminology: the problem with 'Lytic or lysogenic'. FEMS Microbiology Letters 363(7):fnw047. 10.1093/femsle/fnw047

Abedon, S.T. (2026). Broth optical density-based assessment for phage therapy: turbidity reduction, antibacterial virulence, and time-kill. Viruses 18(1):97. 10.3390/v18010097

Bacteriophage Ecology Group News, or BEG News, was published mostly quarterly as an online newsletter for a total of 26 issues, starting July 1, 1999 and continuing through December 31, 2007. As follows is a reprint of the editorial from the newsletter. Also included in issues were lists of new members to the Bacteriophage Ecology Group, an introduction to new website features, a list of upcoming meetings, phage images found on the web (remember, this was 2000, so effectively pre-Google), etc., but most of all, a listing of new phage ecology-related publications. The newsletter was modelled after T4 News, which was a printed newsletter distributed earlier in the 1990s. The newsletter's successors are the ongoing Phage.org website, phage-therapy.org, and the Bacteriophage Ecology Group Facebook page.

For some time whenever I've been asked that simple question, "What exactly is it that you do?" I've had a hard time coming up with an answer. I suppose that the simplest answer is that I am a microbiologist since I received my Ph.D. in a department of microbiology, I post-docced in a department of microbiology, and I now hold a faculty position in a department of microbiology. But this answer has never been terribly satisfying to me, and can be downright terrifying when this prompts individuals to ask questions pertaining to medical microbiology. I certainly am not a medical microbiologist (though I certainly wish I could pass for one). For a while I've answered that I am a microbial evolutionary ecologist. This is satisfying since I actually do see myself as an evolutionary ecologist and I do work with microbes. But there are four problems with this answer. The first is that it is not nearly specific enough. The second is that I don't have much formal training in evolutionary ecology. The third is, "Just what the heck is evolutionary ecology anyway?" And the fourth is that I live in a very small, conservative town located in the upper fringes of the U.S. Bible Belt. The just what the heck is evolutionary ecology is actually rather easy to answer: I am interested in how evolution has adapted organisms to their environments.

But microbial evolutionary ecologist is just something I say when I'm trying to impress (overwhelm, drive crazy, etc.) non-biologists. When speaking with biologists, one is obliged to employ a touch more precision. One solution is to pick some topic that I've recently been interested in such as the evolution of lysis timing in T-even bacteriophages (actually, I've been interested in this topic for over a decade). However, too much precision can be excluding. It's always nice to fit oneself within a group. Obviously I can call myself a phage ecologist, and thereby include all of you in my defining group, but from experience I've noted that if there is one thing a phage ecologist yearns to do, it is to command the respect of biologists, e.g., ecologists, who don't work with phages. So, for example, in terms of phages, what constitutes organismal biology, population, community, or ecosystem ecology, and which ecology am I?

Clearly there is a big world out there of organismal phage biology and just as clearly much of that world has far more of a molecular bent than an ecological one. Nevertheless, I see a number of areas of phage organismal ecology that I would equate without hesitation with phage organismal ecology, e.g., any circumstance in which a virion particle or phage-infected cell interacts chemically or physically with a component of an ecosystem in such a way that this interaction impacts on a phage growth parameter. Phage growth parameters include: (i) the duration of the phage eclipse period, (ii) the likelihood of reduction to lysogeny, (iii) the rate of progeny production once the eclipse period has ended, (iv) the timing of lysis, (v) the duration of the rise period, (vi) adsorption kinetics, (vii) phage inactivation kinetics, etc. That is, I see phage organismal ecology as being intimately entwined with the study of phage single-step growth (a.k.a., one-step growth) and survival along with all those complications on the phage life cycle introduced by such things as lysogeny, etc.

What, then, is phage population ecology? This I see as equivalent, minimally, to phage batch culture growth, either within a liquid medium or associated with a solid substrate. At the level of experimentation, what is the difference between phage organismal ecology and phage population ecology? In essence this comes down to a degree of control over phage adsorption including phage multiplicity considerations. That is, phage population ecology typically involves cultures that begin with multiplicities that are less than one while phage organismal ecology need not. In addition, the study of phage single-step growth typically involves a significant level of control over phage adsorption either during the initial addition of phages to hosts or following phage progeny release. Batch culture growth is the antithesis of such control and therefore can involve multiple rounds of phage adsorption and infection. Phage population ecology can also encompass phage growth in continuous culture so long as one does not dwell too greatly upon the doings of the bacterial hosts.

Phage community ecology considers the phage host as something more than simply a fancy nutrient or complex growth environment. Indeed, the concern of the phage community ecologist often (gasp!) has more to do with the welfare of bacteria than with their lovely little parasites, as well as that dreaded experimental complication: Coevolution! The practitioners of phage community ecology often employ such fancy set ups as phage-host chemostats. Still, other than the bias of phage community ecologists towards considerations of the bacteriophage host, much of phage growth within chemostats probably consists of brief periods of phage batch-culture-like excitement punctuating long intervals of waiting-for-those-dang-bacteria-populations-to-grow-back-to-a-decent-density boredom.

Ecosystem ecology is the consideration of the interactions between organisms as well as their interactions with their chemical and physical (abiotic) environment, e.g., nutrient movement through trophic structures. Clearly the impact of phages on the aquatic microbial loop is a fine and deservedly popular example of phage ecosystem ecology.

There is more, in my opinion, to phage ecology than just these examples. Phage systematics is highly relevant to an understanding of phage ecology and encompasses phage nucleic acid analysis as well as studies of bacteriophage comparative morphology, while phage therapy is an example of applied community ecology. Even phage behavioral ecology is not completely oxymoronic. My lack of sympathy for the plight of bacteria clearly limits my forays into community ecology and real ecosystems are much too complex for my blood. Perhaps, then, I am a bacteriophage organismal or population ecologist with a no-doubt unfortunate weakness for considerations of behavior? I wonder what my neighbors would say?

Bacteriophage Ecology Group News, or BEG News, was published mostly quarterly as an online newsletter for a total of 26 issues, starting July 1, 1999 and continuing through December 31, 2007. As follows is a reprint of an article from the newsletter, authored by J.-Y. Maillard, and originally published in Letters in Applied Microbiology 23:273-274, 1996, reprinted here with permission. Also included in issues were lists of new members to the Bacteriophage Ecology Group, an introduction to new website features, a list of upcoming meetings, phage images found on the web (remember, this was 2000, so effectively pre-Google), etc., but most of all, a listing of new phage ecology-related publications. The newsletter was modelled after T4 News, which was a printed newsletter distributed earlier in the 1990s. The newsletter's successors are the ongoing Phage.org website, phage-therapy.org, and the Bacteriophage Ecology Group Facebook page.

It is important to assess and control the presence of viruses and their inactivation from surfaces (e.g. inanimate surfaces, body Tissues, Nosocomial equipment) and Water (e.g. drinking, Sewage and sea water). Since the detection and use of Mammalian viruses can be fastidious, bacteriophages (bacterial viruses) offer potential alternatives in the following areas:

1. bacteriophages as a model system

Alongside the use of bacteriophages as index micro-organisms, their development and their employment as analogues of human viruses are due to the advantages they present. Bacteriophages infect only bacterial cells and are therefore not Pathogenic. Their infection cycle is more rapid than that of human viruses, and complex and expensive culture media are not needed for their propagation. Also, the lytic infection cycle ends with lysis of the Bacterial host, subsequently forming plaques, which are easy to assess, whereas the lysogenic cycle ends ultimately with the expression of 'foreign Genes' in the host Cell, providing a tool for the study of gene transfer. Finally, bacteriophages are widespread in the environment and are extremely diversified in their structure and can thus be used to study a variety of viruses of higher organisms.

2. Bacteriophages as an index system for enteric pathogens

The index function of bacteriophages is used to predict the possible presence of pathogenic organisms. In this respect several Phages have been investigated as potential index systems for the contamination of swimming pools, and ground, drinking, sewage and Shellfish water by faecal Micro-organisms such as enteroviruses (Hedberg and Osterholm 1993). Three major groups of phages have been considered to achieve this function: Somatic, F-RNA and Bacteroides fragilis bacteriophages. The last two are thought to be the most adequate as index micro-organisms (Havelaar and Pot-Hogeboom 1988; Havelaar 1993; Nasser et al. 1995). Bacteroides fragilis phages appear to be of particular interest due to their faecal origin (Grabow et al. 1995). However, Callahan et al. (1995) recently described the use of somatic Salmonella bacteriophages as index micro-organisms for enteric viruses in sea water. Therefore, the use of bacteriophages as index organisms depends upon the type of waters which are contaminated with pathogenic viruses. Furthermore, their use has to be subjected to several well-defined criteria (Havelaar 1993).

3. Bacteriophages as an indicator system for enteric viral pathogens

The indicator function of bacteriophages is used to predict the efficacy of Antimicrobial treatments. In this respect, coliphages, such as MS2 and f2 (Kott et al. 1972; Tartera et al. 1988; Maillard et al. 1994; Havelaar et al. 1995), have been widely studied, mainly to monitor the 'removal' of human enteroviruses (i.e., poliovirus, human rotavirus, Hepatitis A virus and adenovirus) from various water sources. However, Finch and Fairbain (1991) showed that MS2 treatment by ozone was not indicative of the inactivation of poliovirus type-3. Therefore, the use of bacteriophages as indicators depends upon the type of antimicrobial treatments and the type of viruses investigated. Other bacteriophages such as the Bact. fragilis phages have also been considered as indicators for enteroviral contamination because of their resistance to decontamination processes (Abad et al. 1994; Armon and Kott 1995; Bosch et al. 1995; Jofre et al. 1995a, b).

4. Bacteriophages as tools for studying mechanisms of viral disinfection

Bacteriophages are also potential tools for studying rapidly and accurately the mechanisms of action of viricidal processes. Several biocides, as well as heat and Radiation, have been tested against coliphages such as MS2 (Davies et al. 1993) and K (Maillard et al. 1994) and pseudomonad phages such as F116 (Maillard et al. 1993) and phi6 (Woolwine and Gerberding 1995). Bacteriophages are used as an investigating tool mainly because of their structure but also because of some particularly features. In this respect, Rheinbaben et al. (1992) investigated the disinfection of lactococcal phages P001, P008 and P109 and ϕX174 coliphage because of their thermal stability at high temperatures (i.e. 55-60°C). Woolwine and Gerberding (1995) studied the inactivation of the Pseudomonas syringae phi6 phage because of the presence of a surrounding Envelope. The Ps. aeruginosa F116 phage is currently being used as a tool for investigating the mechanism of the viricidal action of biocides. Its well-defined complex structure and its large size have been used to identify damage to the phage structure (Maillard et al. 1995a) after exposure to antimicrobial agents. Furthermore, F116 phage is also able to transduce. Maillard et al. (1995b) showed that the transduction process was extremely sensitive to disinfection.

J.-Y. Maillard
Welsh School of Pharmacy
University of Wales College of Cardiff
Cardiff CF1 3XF
UK

Reprinted with permission from Letters in Applied microbiology, 1996, 23:273-274.

References

Abad, F.X., Pintó, R.M. and Bosch, A. (1994) Survival of enteric viruses on environmental Fomites. Applied and Environmental Microbiology 60:3704-3710.
Armon, R. and Kott, Y. (1995) Distribution comparison between coliphages and phages of anaerobic Bacteria (Bacteroides fragilis) in water sources, and their reliability as fecal pollution indicators in drinking-water. Water Science and Technology 31:215-222.
Bosch, A., Pintó, R.M. and Abad, F.X. (1995) Differential accumulation and depuration of human enteric viruses by mussels. Water Science and Technology 31:447-451.
Callahan, K.M., Taylor, D.J. and Sobsey, M.D. (1995) Comparative survival of Hepatitis-A Virus, poliovirus and indicator viruses in geographically diverse seawaters. Water Science and Technology 31:189-193.
Davies, J.G., Babb, J.R., Bradley, C.R. and Ayliffe, G.A. (1993) Preliminary study of test methods to assess the virucidal activity of skin Disinfectants using poliovirus and bacteriophages. Journal of Hospital Infection 25:125-131.
Grabow, W.O.K., Neubrech, T.E., Holtzhausen, C.S. and Jofre, J. (1995) Bacteroides fragilis and Escherichia coli bacteriophages — excretion by Humans and animals. Water Science and Technology 31:223-230.
Finch, G.R. and Fairbain, N. (1991) Comparative inactivation of poliovirus type 3 and MS2 coliphage in demand-free phosphate buffer by using ozone. Applied and Environmental Microbiology 57:3121-3126.
Havelaar, A.H. (1993) Bacteriophages as models of human enteric viruses in the environment. ASM News 59:614-619.
Havelaar, A.H. and Pot-Hogeboom, W.M. (1988) F-specific RNA bacteriophages as model viruses in water hygiene: ecological aspects. Water Science and Technology 20:399-407.
Havelaar, A.H., Vanolphen, M. and Schijven, J.F. (1995) Removal and inactivation of viruses by drinking-water treatment processes under full-scale conditions. Water Science and Technology 31:55-62.
Hedberg, C.W. and Osterholm, M.T. (1993) Outbreak of food-borne and waterborne viral gastroenteritis. Clinical Microbiology Reviews 6:199-210.
Jofre, J., Ollé, E., Lucena, F. and Ribas, F. (1995a) Bacteriophage removal in water-treatment plants. Water Science and Technology 31:69-73.
Jofre, J., Ollé, E., Ribas, F., Vidal, A. and Lucena, F. (1995b) Potential usefulness of bacteriophages that infect Bacteroides fragilis as model organisms for monitoring virus removal in drinking treatment plants. Applied and Environmental Microbiology 61:3227-3231.
Kott, Y., Roze, N., Sperber, S. and Betzer, N. (1974) Bacteriophages as viral pollution indicators. Water Research 8:165-171.
Maillard, J.-Y., Beggs, T.S., Day, M.J., Hudson, R.A. and Russell, A.D. (1993) Effect of biocides on Pseudomonas aeruginosa phage F116. Letters in Applied Microbiology 17:167-170.
Maillard, J.-Y., Beggs, T.S., Day, M.J., Hudson, R.A. and Russell, A.D. (1994) Effects of biocides on MS2 and K coliphages. Applied and Environmental Microbiology 3:849-853.
Maillard, J.-Y., Hann, A.C., Beggs, T.S., Day, M.J., Hudson, R.A. and Russell, A.D. (1995a) Electron micrographic investigation of the effect of biocides on Pseudomonas aeruginosa PAO bacteriophage F116. Journal of Medical microbiology 42:415-420.
Maillard, J.-Y., Beggs, T.S., Day, M.J., Hudson, R.A. and Russell, A.D. (1995b) The effects of biocides on the transduction of Pseudomonas aeruginosa PAO by F116 bacteriophages. Letters in Applied Microbiology 21:215-218.
Nasser, A., Weinberg, D., Dinoor, N., Fattal, B. and Adin, A. (1995) Removal of hepatitis-A virus (HAV), poliovirus and MS2 coliphage by Coagulation and high-rate Filtration. Water Science and Technology 31:63-68.
Pintó, R.M., Abad, F.X., Roca, R.M., Riera, J.M., Bosch, A. (1991) The use of bacteriophages of Bacteroides fragilis as indicators of the efficiency of virucidal products. FEMS Microbiology Letters 82:61-66.
Rheinbaben, F.V., Bansemir, K.-P. and Heinzel, M. (1992) Virucidal effectiveness of some commercial disinfectants for chemothermal disinfection procedures tested against temperature resistant viruses and bacteriophages. Zentralblatt für Hygiene 192:419-431.
Tartera, C., Bosch, A. and Jofre, J. (1988) The inactivation of bacteriophages infecting Bacteroides fragilis by Chlorine treatment and UV-irradiation. FEMS Microbiology Letters 56:313-316.
Woolwine, J.D. and Gerberding, J.L. (1995) Effect of testing method on apparent activities of viral disinfectants and antiseptics. Antimicrobial Agents and Chemotherapy 39:921-923.

See Also

Maillard, J.-Y. (1996). Bacteriophages: a model system for human viruses. Letters in Applied Microbiology 23:273-274. 10.1111/j.1472-765X.1996.tb00187.x

Bacteriophage Ecology Group News, or BEG News, was published mostly quarterly as an online newsletter for a total of 26 issues, starting July 1, 1999 and continuing through December 31, 2007. As follows is a reprint of an article from the newsletter. Also included in issues were lists of new members to the Bacteriophage Ecology Group, an introduction to new website features, a list of upcoming meetings, phage images found on the web (remember, this was 2001, so effectively pre-Google), etc., but most of all, a listing of new phage ecology-related publications. The newsletter was modelled after T4 News, which was a printed newsletter distributed earlier in the 1990s. The newsletter's successors are the ongoing Phage.org website, phage-therapy.org, and the Bacteriophage Ecology Group Facebook page.

[Note: This article has been lightly updated on April 18, 2026. The solar mass figure, originally given in pounds, has been corrected to kilograms per the Wikipedia article on solar mass; the solar volume figure has been updated to liters accordingly. A bracketed note on current estimates of 10³¹ has also been added. Original text is preserved in HTML comments.]

Whitman et al. (1998) argue that there are between 10³⁰ and 10³¹ prokaryotic cells on our planet. If we assume numerically one virus for every prokaryote host, then we conservatively (e.g., Bergh et al., 1989) reach a total worldwide abundance of 10³⁰ virus-like particles. Is 10³⁰ virus-like particles a reasonable estimation? What does a number like that mean? Astronomers, for instance, can account for "only" about 10²² stars in the entire universe (Turner, 2000). The size of the universe is something on the order of 1.5 × 10¹⁰ light years across (depending on whose estimation of the age of the universe you choose to believe), while a light year is about 10¹³ kilometers (9,460,800,000,000, actually). That means that the universe is something like 10²⁹ mm wide (10¹⁰ × 10¹³ × 10⁶ mm/kilometer). If phages were one mm wide, then 10³⁰ phages placed end to end would form a single line that would stretch ten-times across the entire universe! Of course, phages (and bacteria) are something less than one mm wide.

From a now defunct website called About Big Numbers (ABN), 10³⁰ is approximately the mass of the sun in kilograms (2 × 10³⁰) and about the volume of the sun in liters (1.41 × 10³⁰), and that there are over 10⁴⁷ atoms of water on Earth's surface. Of greater relevance to our subject, ABN claimed that 10³⁶ is the "Maximum number of living things the Earth can accommodate." Therefore 10³⁰ would only be claiming that the Earth's smallest "organisms" would numerically represent only one-millionth of the Earth's total organismal capacity. From that perspective, 10³⁰ phages strike me as quite reasonable, perhaps even on the low side [indeed, current estimates are closer to 10³¹ (Mushegian, 2020)].

The chemist in me wants to know how many moles 10³⁰ represents. Avogadro's number is 6.022 × 10²³ atoms, molecules, or particles per mole. 10³⁰ / 6.022 × 10²³ = 1.66 × 10⁶ or over one million moles of bacteriophage! Given the examples in the above paragraph, my first impulse would be to compare this number with the number of moles that make up the Sun. Since the sun consists mostly of hydrogen gas (with a molecular weight of 2) then there are approximately 10³³ moles of hydrogen making up the sun! This would mean that the sun has nearly 10²⁷ molecules for every phage on Earth. However, far more humbling, the volume of the sun would accommodate approximately one million earth-size balls. That would be a lot of heat-inactivated phages!

Dubin et al. (1970) provide an estimation of the molecular weights of phages T4, T5, and T7 of 192, 109, and 50 × 10⁶ dalton, which we'll assume on average is something like 10⁸ grams per mole of phage. This is approximately the mass of a single blue whale, i.e., 100 short tons. 10⁸ grams per mole translates to about 10¹⁴ grams of phages (10⁶ moles) found on the Earth. That's about equal to the total mass of humanity (6 × 10⁹ people at 50 kilograms per person), and is slightly more than the total mass of the approximately 10⁸ cows in the U.S., where 10⁶ grams is one metric ton and a good-sized cow is about half a metric ton. The mass of the whole Earth is approximately 5 × 10²⁸ grams, so we need not worry about running out of planet to make our phages. In fact, a single mole of an average-sized bacterium weighs approximately 5 × 10¹¹ grams (30 × 10¹² "average-sized" bacteria per ounce) which means that 10³⁰ phages is equivalent in mass to 200 moles of bacteria (10¹⁴ / 5 × 10¹¹), or about 10²⁶ individual cells. Numerically, 10²⁶ is 10 orders of magnitude less than the above-noted guestimate for Earth's total organismal capacity.

So if there may be 10³⁰ phages then there are ~10⁶ moles of phages or something like 10¹⁴ grams in total. What phage density would be necessary to account for such numbers? Estimations of the surface area of the Earth can vary depending upon whether Earth is truly a sphere (in fact, the poles are flattened) or whether one insists on taking into account the degree to which that surface is rough (which can dramatically increase the Earth's surface area). For our purposes we will assume that Earth is a perfectly smooth sphere with a diameter of 1.28 × 10⁷ meters at the equator. The surface area of a sphere is 4πr² and 4 × 3.14 × (1.28 × 10⁷ / 2)² = 5 × 10¹⁴ square meters or 5 × 10¹⁸ square centimeters. The density of phages therefore is 10³⁰ / 5 × 10¹⁸ = 2 × 10¹¹ which, to be conservative, we'll call 5 × 10¹¹. To account for 10³⁰ total phages this is the number that would have to be present per ml to a depth of 1 cm over the surface of the entire world's oceans. A more reasonable density is 10⁶ phages per ml (or, at least, of virus-like particles), total count (Wommack & Colwell, 2000). Diluting 5 × 10¹¹ phages per ml to 10⁶ phages per ml requires a depth of 500,000 cm which is 5,000 meters of 10⁶ phages per ml to account for 10³⁰ phages worldwide. 5,000 meters is within the range of the average depth of the world's oceans, which is about 4 kilometers. So 10³⁰ represents an assumption of approximately 10⁶ virus particles per ml over (and under) the entire world's oceans.

More precisely, assuming 10⁶ virus-like particles per ml:

Ocean	Area	Ave. depth	Volume	Phages
Atlantic	8.20 × 1017 cm2	3.33 × 105 cm	3.22 × 1023 cm3	3.22 × 1029
Indian	7.36 × 1017 cm2	3.89 × 105 cm	2.92 × 1023 cm3	2.92 × 1029
Pacific	1.66 × 1018 cm2	4.28 × 105 cm	7.24 × 1023 cm3	7.24 × 1029
Total				1.33 × 1030

Thus, a total of 10³⁰ phages is, in fact, a reasonable and entirely plausible worldwide estimation of total virus particles.

References

1.  Bergh, O., K.Y. Børsheim, G. Bratbak, and M. Heldal. 1989. High abundance of viruses found in aquatic environments. Nature 340:467-468. 10.1038/340467a0
2.  Dubin, S.B., G.B. Benedek, F.C. Bancroft, and D. Freifelder. 1970. Molecular weights of coliphages and coliphage DNA. II. Measurement of diffusion coefficients using optical mixing spectroscopy, and measurement of sedimentation coefficients. Journal of Molecular Biology 54:547-556.
3.  Mushegian, A.R. 2020. Are there 10³¹ virus particles on Earth, or more, or fewer? Journal of Bacteriology 202:e00052-20. 10.1128/JB.00052-20
4.  Turner, M.S. 2000. More than meets the eye. The Sciences November/December:32-37.
5.  Whitman, W.B., D.C. Coleman, and W.J. Wiebe. 1998. Prokaryotes: The unseen majority. Proceedings of the National Academy of Sciences, USA 95:6578-6583. 10.1073/pnas.95.12.6578
6.  Wommack, K.E. and R.R. Colwell. 2000. Virioplankton: viruses in aquatic ecosystems. Microbiology and Molecular Biology Reviews 64:69-114. 10.1128/MMBR.64.1.69-114.2000

Bacteriophage Ecology Group News, or BEG News, was published mostly quarterly as an online newsletter for a total of 26 issues, starting July 1, 1999 and continuing through December 31, 2007. As follows is a reprint of the editorial from the newsletter, authored by Ry Young. Also included in issues were lists of new members to the Bacteriophage Ecology Group, an introduction to new website features, a list of upcoming meetings, phage images found on the web (remember, this was 2001, so effectively pre-Google), etc., but most of all, a listing of new Phage ecology-related publications. The newsletter was modelled after T4 News, which was a printed newsletter distributed earlier in the 1990s. The newsletter's successors are the ongoing phage.org website, phage-therapy.org, and the Bacteriophage Ecology Group Facebook page.

Phage biologists are accustomed to being treated as relics, hoary apostles of a classical discipline pedagogically useful but past its prime. It is thus heartening to see the burgeoning interest in bacteriophage at all levels and from so many different perspectives. Of course, there are legions of protein biochemists biochemists who suddenly have to titer M13 to monitor the enrichment cycles of their phage display libraries. Even a purely methodological interest makes them stakeholders, however marginally, in phage biology. More impressive is the wave of other scientists who have come to phage as an active research field in the pursuit of seemingly unrelated goals. Suddenly the virulence of otherwise harmless bacteria turns out to be due to pathogenicity islands, which turn out to be prophages. Indeed, phage don't just carry virulence characteristics but in fact, suddenly, it develops that major diseases like cholera and enterohemorrhagic diarrhea are fundamentally phage-borne diseases, that in a sense the bacteria are victims as much as the human hosts. Suddenly, understanding pathogenesis requires understanding the inheritance, organization and expression of phage genes. Mirabile dictu, suddenly phage ecology is discovered to have been ignored; we know more about kangaroo rats than about the "where"'s, "when"'s and "how many"'s of phage populations. We don't know where these disease-factor phages are, how they are transmitted, how they change, what makes them tick. Until study sections wake up to this, clearly our ability to analyze, understand, and predict the emergence of new infectious disease is limited.

It is not just molecular pathogenicists and epidemiologists who are scurrying for their dusty phage texts; now it's the drug companies and clinicians who have the bug as the "new" concept of phage therapy is making news and attracting investors. Ironically, there is little known about what is available to attack various pathogens, and few people have actually done phage hunts. Thus decades-old phage collections assembled in Stalin's Caucasus by contemporaries of Lysenko are now attracting U.S. government research funding.

All of this serves to bring the word phage back into play in public and general scientific discourse, which is good. It's also the best of times since the Golden Age for phage biology proper. Through the dogged efforts of a few people interested in phage per se and also, pari passu, as a result of the sequencing of so many bacterial genomes that contain multiple prophages, suddenly we have a phage genomics. Suddenly phage evolution turns out to be stunningly inventive and articulated. The momentum in phage biology extends beyond primary structure to tertiary and quaternary structure: suddenly self-assembly of phage virions has been revealed at the atomic level by focusing modern x-ray crystallography on genetically tractable bacteriophage. Suddenly, through Crystallography and high-resolution cryo-electron microscopy, we have a crisp picture of the operation of a phage injection system, geared by both RNA and protein components. The best of times.

But it is also the worst of times. Few students and post-docs are being trained in the classical traditions of phage biology. Classical phage systems are being depopulated through super-annuation; you can count the combined number of P1, ϕX174, and T5 labs on one hand and have fingers left over. Almost no grant proposals are being written on phage systems. In the early '90s I served on one of the NIH study sections that traditionally supported phage biology. The panel always had several phage people, as well as individuals who had been trained in the phage biology tradition. Now that same study section has about a third as many R01's to consider, the proportion of phage grants is even less, and the number of phage biologists on the panel is now exactly one.

And now comes the pitch. The professional association of phage biologists is under siege. Division M of ASM has been placed on probationary status because our membership has fallen below the minimum 150, out of 19,000 total members. We can no longer vote in the ASM council. To use an analogy very familiar to Texans, it is like being moved to the isolation chamber shortly before execution. As the 2000–1 chair, I am appealing to the phage community to help redress the situation. We need to recruit for Division M. We need past members who have let their dues lapse to renew their memberships. We need our colleagues who are doing phage biology to join ASM and select Division M as their primary division. We need to enroll graduate students as student members, to look to the future of the Division.

Division M has a lot to offer. Being a small division is not all bad; smallness means we can be cohesive and organized. Despite being less than 1% of the membership, we have influence at the top. For example, this year's General Meeting is chaired by Lucia Rothman-Denes of Division M. All this means is that new members get to be part of a small and influential group and can make an impact immediately; just come to our Division meeting at Orlando this year and see!

If you are interested in joining ASM and Division M, please check out the ASM website at https://asm.org. Remember, it's the new Age of Phage. Get with the in-crowd before it becomes cool to do so.

Ry Young
Former Chair, Division M (Bacteriophage), ASM
Professor Emeritus, Department of Biochemistry and Biophysics, Texas A&M University

Bacteriophage Ecology Group News, or BEG News, was published mostly quarterly as an online newsletter for a total of 26 issues, starting July 1, 1999 and continuing through December 31, 2007. As follows is a reprint of the editorial from the newsletter, authored by Hans-Wolfgang Ackermann and Stephen T. Abedon. Also included in issues were lists of new members to the Bacteriophage Ecology Group, an introduction to new website features, a list of upcoming meetings, phage images found on the web (remember, this was 2001, so effectively pre-Google), etc., but most of all, a listing of new phage ecology-related publications. The newsletter was modelled after T4 News, which was a printed newsletter distributed earlier in the 1990s. The newsletter's successors are the ongoing Phage.org website, phage-therapy.org, and the Bacteriophage Ecology Group Facebook page.

The first bacteriophage known to science was the Bacteriophagum intestinale described by Félix d'Hérelle (3), an enterobacterial phage or a mixture of phages that was considered by d'Hérelle as a single virus with many races. In 1961 Eisenstark published the first list of phages, which included 111 phages with tailed, cubic or filamentous morphology (4). A second phage list, published by Fraenkel-Conrat in 1974, included 411 bacterial viruses and the dimensions and physicochemical properties of many of them (5). Unfortunately, phage names with Greek letter ϕ were reported without this letter. At present, over 5000 bacteriophages have been studied by electron microscopy and can be attributed to 11 virus families.

During 80 years, phage names have been constructed in the absence of any system and usually reflect little more than their author's imagination (or lack thereof). Phage nomenclature is therefore in a primitive and confusing state. Phage names may:

1. Be single letters or numerals in any combination, even names of individuals or cities.
2. Include Greek letter ϕ or the Latin letter P to indicate phage status.
3. Include special types (superscript or infrascript characters, dots, dashes).
4. Vary between authors, studies, even printer conventions.

As a result, (i) phage names do not reflect basic phage properties, (ii) synonyms and homonyms abound, and (iii) some designations are unduly complicated and a printer's nightmare. Certain synonyms of enterobacterial phages are even willful creations of investigators who published one and the same virus up to six times under different designations. Further ambiguities are created by the identity of some Roman letters and numerals (I, V), or are the product of odd printer conventions (witness, for the latter, the ambiguous numeral subscript status of the original T phages of Escherichia coli B; 2). However, one notes that quite numerous phage names have been constructed from host names and therefore reflect host ranges, and that names of temperate phages often comprise two elements, one for the phage and another for the host strain.

Eighty years after the discovery of phages, it is clearly too late to construct a nomenclature system that reflects basic phage properties such as nucleic acid or particle shape. The most that can be done is to limit the amount of synonyms and homonyms. The practice of constructing phage names from host names should be continued as it gives at least a clue to the phage. We suggest the following:

1. To use the first two letters of the host genus and the host species names, respectively (e.g., Esco for Escherichia coli).
2. To complement the above constructs with any letters or numerals (e.g., Esco1).
3. To avoid the over-used letters ϕ and P.
4. To avoid superscript or infrascript characters, parentheses, or dashes.
5. To check phage-name lists (e.g., "Bacteriophage Names 2000") for naming precedent.
6. To avoid the invention of new names for old phages.
7. For a description of ICTV nomenclature rules.
8. To obtain rules on virus genera and families see Van Regenmortel, M.H.V., Fauquet, C.M., Bishop, D.H.L. (eds.-in-chief). 2000. Virus Taxonomy. Classification and Nomenclature of Viruses. Seventh Report of the International Committee on Taxonomy of Viruses. Academic Press, San Diego, pp. 1065-1069. The latest ICTV taxonomy report is available at ICTV taxonomy.

For reference, see "Bacteriophage Names 2000", which presents these names alphanumerically, by phage family, and by host genera.

Hans-Wolfgang Ackermann
Félix d'Hérelle Reference Center for Bacterial Viruses, Laval University, Quebec, Canada

Stephen T. Abedon
Department of Microbiology, The Ohio State University, Mansfield, Ohio

References

1.  Ackermann, H.-W. 2001. Bacteriophage descriptions in the year 2000. Archives of Virology 146:843-857. 10.1007/s007050170120
2.  Demerec, M., and Fano, U. 1945. Bacteriophage-resistant mutants in Escherichia coli. Genetics 30:119-136.
3.  D'Hérelle, F. 1918. Technique de la recherche du microbe filtrant bactériophage (Bacteriophagum intestinale). C.R. Soc. Biol. 81:1160-1162.
4.  Eisenstark, A. 1967. Bacteriophage techniques. In: Maramorosch, K., Koprowski, H. (eds.), Methods in Virology, vol. 1. Academic Press, New York, pp. 449-525.
5.  Fraenkel-Conrat, H. 1974. Descriptive catalogue of viruses. In: Fraenkel-Conrat, H., Wagner, R.R. (eds.), Comprehensive Virology, vol. 1. Plenum Press, New York, pp. 121-156.

See Also

https://namecheck.phage.org/ — a tool for checking bacteriophage name availability and precedent.

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 10. The newsletter’s successors are the ongoing Phage.org website, phage-therapy.org, and the Bacteriophage Ecology Group Facebook page.

At the level of individual infections, our molecular understanding of phages integrates with our ecological understanding within a framework that I call phage organismal ecology. The details of the phage growth cycle impact on phage ecology and, ultimately, phage evolution. The relevant parameters include the latent period, the rise period, the burst size, adsorption kinetics, virion inactivation rates, and whether the phage displays a lytic, lysogenic, or chronic infection cycle.

The rise period is typically defined as that period of the one-step growth experiment during which extracellular phage titers increase from the burst of the first-infected bacterial cell to the burst of the last-infected cell. During the rise, phage progeny are being released from host cells, accumulating extracellularly until the last infected cell lyses.

The rise period has a duration equal to the standard deviation of the latent period. A short rise period means infected cells are all bursting at approximately the same time. A long rise period means greater variation in when individual infected cells burst.

From an ecological standpoint, a short rise period concentrates the release of phage progeny to a particular moment in time, making large numbers of free phage simultaneously available to adsorb to new host cells. A longer rise period spreads out progeny release, potentially allowing individual released progeny to infect new hosts before later-released progeny have even been released.

The rise period also impacts phage-mediated bacterial population dynamics. A shorter rise period means bursts more likely occur simultaneously, exposing bacteria to abrupt increases in phage densities. A longer rise period means a more gradual release of progeny phages and consequently more gradual phage-mediated bacterial mortality.

Thus the rise period is yet another aspect of the phage growth cycle with broader ecological and evolutionary implications.

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References

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 11. The newsletter’s successors are the ongoing Phage.org website, phage-therapy.org, and the Bacteriophage Ecology Group Facebook page.

Microbiologists are not a terribly mathematically inclined bunch. If we were, we probably wouldn’t be microbiologists. Indeed, microbiology is difficult enough without having to worry about mathematics. Nevertheless, some math is unavoidable, particularly if one is interested in the population-level or ecological behavior of microorganisms. This short piece is a brief introduction to three mathematical concepts that arise regularly in phage ecology: exponential growth, Poisson statistics, and dimensional analysis.

Exponential Growth

Exponential growth occurs when the rate of growth of a quantity is proportional to the current size of that quantity. For bacteria and phages growing in favorable conditions, this is the normal mode of population growth. The key parameter is the doubling time — the time it takes a population to double. Phage populations can have remarkably short doubling times, sometimes on the order of minutes.

The mathematics of exponential growth: N(t) = N₀ × e^(rt), where N(t) is the population size at time t, N₀ is the initial size, r is the intrinsic rate of increase, and e ≈ 2.718. Understanding exponential growth is essential for predicting how quickly a phage population can expand within a bacterial culture and for interpreting one-step growth experiments.

Poisson Statistics

The Poisson distribution describes the probability of discrete events occurring independently within a fixed interval. In phage biology it underlies the calculation of multiplicity of infection (MOI) and the interpretation of plaque assays. When phages are mixed with bacteria, the number of phages that adsorb to any given bacterium follows a Poisson distribution. At an average MOI of one, approximately 37% of bacteria receive no phages, 37% receive exactly one, and 26% receive two or more.

Dimensional Analysis

Dimensional analysis is the practice of tracking units of measurement through a calculation to ensure the result makes physical sense. For phage ecologists working with adsorption rates, phage densities, and bacterial growth rates, keeping track of units — per milliliter, per minute, per cell — is essential. A phage adsorption rate constant has units of mL/min; multiplying by a phage titer (phages/mL) and bacterial density (bacteria/mL) yields encounters per minute per bacterium.

These three tools — exponential growth, Poisson statistics, and dimensional analysis — form much of the quantitative foundation of phage ecology.

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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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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 an article from Volume 14. The newsletter’s successors are the ongoing Phage.org website, phage-therapy.org, and the Bacteriophage Ecology Group Facebook page.

by Hans-Wolfgang Ackermann During the last 50 years the terms "bacteriophage" and "phage" had a plural in the English-language scientific literature. As usual, it was indicated by -s: bacteriophages, phages. Similar plurals exist in other major scientific languages such as German, French, and Russian. Japanese is an exception because it has no plurals.

This happy situation seems to be over. Suddenly one notices in recent papers or manuscripts that some authors are using "bacteriophage" and "phage" as invariable nouns: one bacteriophage, two bacteriophage rather than one bacteriophage, two bacteriophages . These authors are generally raw newcomers to the field of virology. Where did they get their terminology from? What is correct? Presumably not from dictionaries or usage books. Dictionaries use singular forms of nouns and do not indicate plurals. Usage books do not even mention "bacteriophage" and "phage."

We love (or hate) bacterial viruses. We owe them our salaries and livelihood. We write papers on them (or are supposed to). We should strive to use optimal language. We thus should give the matter some thought. To do this, we shall go back to the history of the terms "bacteriophage" and "phage" and seek help in the books of Raettig [9, 10], which are indispensable guides to the older literature.

The terms "bacteriophage" and "phage" were coined by Félix d'Hérelle in 1918 [6]. He believed that there was only one bacteriophage with many races (hence no need for a plural) though he was convinced of the corpuscular, viral nature of his agents (which, of course, would suggest a need). d'Hérelle's ideas and terminology became widely known and almost universally accepted, partly because his two most important books were translated into English in 1922 and 1926, respectively [7, 8]. However, already in 1923 an outsider put the word "bacteriophage" into plural [5].

The plural form was truly introduced in 1929, when Burnet and McKie [1] proved that viruses of staphylococci were indeed heterogeneous and could not be considered as a single entity. By the fifties the plural form became generalized, for example in the publications of Delbrück, Dulbecco, Elford, Jacob, Luria, Lwoff, Nicolle, Ruska, and Wyckoff. Some people, using "bacteriophage" as variable or invariable nouns in different papers, had it both ways. In the sixties, the variable form (one bacteriophage, two bacteriophages) was almost universally accepted, although use of the singular form (two bacteriophage) lingered on.

Now, after 50 years of relative peace, the old invariable form is returning to the literature. We now have two usages: Bacteriophage(s) and phage(s). The noun is variable. The singular denotes an individual virus particle, a phage species, or a phage strain. The plural designates a population of phage particles, several phage species or strains, and the sum of all bacterial viruses: two types of phages or the sum of all phages. Bacteriophage and phage. The noun is invariable. Singulars and plurals are indicated by pronouns or modifiers (it, this, these, few) and verb forms: these phage, those phage, and a few phage as well as two phage and the sum of all phages, rather than "phages" for each of the above examples. Differentiation is generally impossible in the past tense. Invariable nouns are infrequent in the English language and fall into several categories [2, 3, 4]. Nouns used only in the singular (e.g., physics). Nouns used only in the plural (e.g., clothes or arms). Nouns used in the singular or plural according to context: Collective or groups nouns, in which the singular form (without terminal -s) can take either a singular or plural verb (army, committee, family, majority). The choice depends on whether the group is considered as a single unit or a collection of individuals [2]. Oddities without plural endings (e.g., sheep, aircraft, offspring, series, species, French, Japanese, Swiss). Ethnic names with facultative -s terminals (e.g., Haussa, Yoruba). The choice depends on the whim of the writer. Pidgins (e.g., "two book are" in Jamaican Creole) [4]. The invariable variety of the noun "bacteriophage" originated as a term without a plural and then became a group name. It is thus grammatically correct to say "bacteriophage is" and "bacteriophage was." The question is rather: is there any advantage to this? I see only one, of sorts, that it recalls an old misinterpretation. The disadvantages are many. In particular, invariable nouns are: Relatively unusual. Relatively rigid and unclear; indeed, they promote muddled writing. Unwarranted and generally useless if there are plurals in good standing. In particular, "the bacteriophages" is an excellent collective name and there is no need for an invariable form. Virtually nonexistent elsewhere in microbiology. I noticed indeed a title in an old paper that read "destruction of bacterial virus", but this would be inacceptable today. Reminiscent of Pidgin English. Finally, the invariable term "bacteriophage" is at variance with the use of this word in other scientific languages and the use of "-phage" in related compound words (e.g., anthropophage, macrophage, sarcophage). Thus, I do not understand when the old invariable term was resurrected and I side, definitely, in favor of pluralization and "bacteriophages and phages."

REFERENCES Burnet, F.M., McKie, M. 1929. Type differences amongst staphylococcal bacteriophages. Austr. J. Exp. Biol. Med. Sci. 6, 21. Chalker, S., Weiner, E. 1994. The Oxford Dictionary of English Grammar. Clarendon Press, Oxford, 1994, pp. 69, 180, 301. Clark, J.O.E. 1990. Harrap's Dictionary of English Usage. Harrap, London, p. 317. Crystal, D. 1995. The Cambridge Encyclopedia of the English Language. Cambridge University Press, Cambridge, p. 200. Doerr, R. 1922. Die Bakteriophagen (Phänomen von Twort und d'Hérelle). Klin. Wschr. 1922, 1489 and 1537. d'Hérelle, F. 1918. Sur le rôle du microbe filtrant bacteriophage dans la dysenterie bacillaire. C.R. Acad. Sci. 167, 970. d'Hérelle, F. 1922. The bacteriophage; its role in immunity. Baltimore, Williams & Wilkins. d'Hérelle, F. 1926. The bacteriophage and its behavior. Baltimore, Williams & Wilkins. Raettig, H. 1958. Bakteriophagie 1917 bis 1956, part II. Gustav Fischer, Stuttgart. Raettig, H. 1968. Bakteriophagie 1957-1965, part II. Gustav Fischer, Stuttgart. Editor's Note: Though I will make no claims to consistency, nevertheless when in doubt I substitute "horse" for "phage" in my writing. If the resulting construct seems to call for "horses" rather than "horse," then I use "phages" rather than "phage," i.e., one horse, two horses, many horses, those horses, etc.

Hans-Wolfgang Ackermann
Félix d'Hérelle Reference Center for Bacterial Viruses, Laval University, Québec, Canada

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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 an article from Volume 15. The newsletter’s successors are the ongoing Phage.org website, phage-therapy.org, and the Bacteriophage Ecology Group Facebook page.

It is critical that NIH and NSF develop plans for a major expansion of research in phage biology.

Bacteriophages areKey factors in microbial pathogenesis,Major tools in biotechnology,Integral components in global ecology, and, potentially, Powerful weapons against the rising tide of drug-resistant bacterial pathogens and microbial bioweapons. Unfortunately, there are few laboratories ready to engage any of these issues. Classical phage biology, supported by many NIH and NSF grants, dominated molecular biology into the 1970's and generated much of its core knowledge base. Now support for phage biology has been reduced to a mere handful of grants, mostly to principal investigators already late in their careers. The scheduled extinction of the NIH study section responsible for most phage biology grant proposals merely puts a end to an era of unabated decline in bacteriophage research.

Many factors contributed to this decline, including the highly visible exodus from the field of many prominent scientists who viewed phage as powerful experimental tools and means to an end, rather than an intrinsically important component of modern microbiology. In any case, there are very few young scientists with training in phage biology, and fewer still being trained, especially in the United States. Thus, although the general scientific community thinks that phage biology is a mature field, the reality is that very little is known about any bacteriophages outside of a few classic systems. In a real sense, the new phage biology that is needed for progress in such diverse areas as bacterial genomics, marine ecology, microbial pathogenesis and phage-based therapeutics lacks a fundamental base, because we do not know that our detailed knowledge of the classic coliphages can be extended to phages of other bacteria. In fact, recent results suggest otherwise:A Bordetella phage was described which apparently uses an HIV-type reverse transcriptase to mutagenize its own tail fiber gene (Science 295:2091).

Classically, filamentous phages were thought to be exclusively virulent until it was shown that active cholera derives from the induction of an M13-like prophage of V. cholerae (Science 272:5270).

The shiga-like toxin of hemorrhagic E. coli turns out to be a phage protein and its release is caused by phage lysis (Molec. Microbiol. 44:957).These and other developments suggest that our knowledge of bacteriophages is an inch wide and a mile deep.

The NIH, NSF and other national funding agencies are the only forces capable of attracting young scientists to phage biology, which is in a kind of potentially still-born infancy. Concrete steps would be to Promulgate RFAs in aspects of phage biology of many different bacterial genera and to assign the responsibility for research proposals in bacteriophage biology to new peer review entities with appropriate expertise. Failure to take action will cause serious delays in developing a component of modern microbiology critical to our understand of bacterial pathogenesis and ecology. Moreover, public perception is primed to appreciate bacteriophage as an ally, and a natural one at that, in the struggle against bacterial disease and bioterrorism. Phage biology, once a great American intellectual province, should languish no more. Please Help by Signing our Phage Manifesto On-Line Petition View List of Supporters of Phage-Biology Research

Ry Young
Professor Emeritus, Department of Biochemistry and Biophysics, Texas A&M University

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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 an obituary from Volume 15. The newsletter’s successors are the ongoing Phage.org website, phage-therapy.org, and the Bacteriophage Ecology Group Facebook page.

Gisela Mosig, 72, a pioneering genetic researcher and distinguished faculty member, died Jan. 12 at Alive Hospice. She had been undergoing cancer treatment for two years.

Mosig, a researcher and teacher at Vanderbilt for the past 38 years, was a central figure in understanding the role that DNA recombination plays in the replication of DNA and in the evolution of genomes. She had well over 100 publications in scientific journals.

One of the few women scientists of her era in molecular biology, she blazed the trail for others who followed. Mosig was a professor in the Department of Molecular Biology, which recently became the Biological Sciences Department. She was named professor emerita in May 2002.

Born in the Saxony region of Germany, Mosig grew up on a farm, where she first became interested in biology and genetics. After World War II, her home fell under East German rule.

In high school, she got a strange introduction to how ideology can affect the scientific quest for truth. Overnight her instructors stopped teaching Mendel's scientifically accepted rules of genetic inheritance and switched to a theory, espoused by Stalin's chief agronomist, T.D. Lysenko, that environment could change genes.

This difficult atmosphere helped her decide to escape East Germany. In 1948, when she was just 18, she managed to cross by bicycle into West Germany, carrying only the possessions that would fit on her bike.

In West Germany, she began her university studies. She did her undergraduate work at the University of Bonn and her graduate work, studying plant genetics, at the University of Cologne, where she was awarded her doctorate in 1959.

At Cologne, Mosig met Gus Doermann, a distinguished Vanderbilt biologist. He inspired her to study the genetics of a virus, bacteriophage T4, and recruited her to take a postdoctoral fellowship working in his lab at Vanderbilt. Studies with bacteriophage T4 led various labs to make some of the groundbreaking discoveries in understanding how genes function.

From 1962 to 1965, Mosig was a research associate at the Carnegie Institution Laboratory in Cold Spring Harbor, N.Y., where she worked with Nobel laureate Alfred Hershey. With Hershey's approval and support, she challenged lab dogma about the way the T4 virus's DNA recombined.

This zest for re-examining and challenging scientific dogma continued when Mosig became an independent scientist and faculty member at Vanderbilt in 1965. She shared her philosophy with the many students she taught and inspired over the years.

Mosig's achievements earned her many honors. She recently gave an invited lecture to a National Academy of Sciences colloquium, published in the Proceedings of the National Academy of Sciences USA. In recognition of her many contributions, her colleagues elected her a fellow of the American Society of Microbiology in 1994.

At Vanderbilt, she was honored for both her research and her teaching, winning the Earl Sutherland Prize for Achievement in Research in 1995 and the Outstanding Graduate Teaching Award in 1989.

Recently, an interview with Mosig was included as a chapter in a textbook on genetics. Asked how she maintained her enthusiasm for science for so long, she said, "I have been so privileged to work on and teach something that interests me most. It far exceeded any expectation that I had when I grew up. Is it surprising that I am enthusiastic about it?"

Mosig's interests extended far beyond science. She was a patron of the arts and environmental causes, and her adventurous spirit led her to travel around the world.

Mosig is survived by a large family in Germany: three brothers and four sisters, 16 nieces and nephews and 22 grandnieces and grandnephews.

Over the years Mosig hosted four of the younger generation of her family as they spent a semester or more studying in Nashville. Her niece, Kristina Mosig, studied at Belmont University. Nephews Ruediger and Axel Mosig attended the University School of Nashville. Her grandniece, Julianne Schubert, attended the University School just last year.

Mosig is also remembered by the many scientists whom she taught by example to love science and revere the truth.

Burial will be private. A memorial service will be held later in Nashville. In lieu of flowers, donations can be made to Alive Hospice of Nashville, the Nashville Symphony or the Tennessee Conservation League.

reprinted with permission from The Daily Register, The paper of record for the Vanderbilt University Community

We would like to collect more on Gisela for our next issue of BEG News. Colleagues, former grad students, friends, relatives, Please send any and all photos and reminiscences to microdude+@osu.edu or by snail-mail to Stephen T. Abedon, The Ohio State University, 1680 University Dr., Mansfield, OH 44906. Many thanks. Please also pass on this request to any interested parties that you may be aware of: http://www.phage.org/bgnws015.htm#gisela_mosig

Note: This obituary was reprinted in BEG News from an external source, in honor of Gisela Mosig’s contributions to bacteriophage biology. The original source has since been taken offline. It is reproduced here to honor her memory and her foundational work on bacteriophage T4.

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Bacteriophage Ecology Group News, or BEG News, was published mostly quarterly as an online newsletter for a total of 26 issues, starting July 1, 1999 and continuing through December 31, 2007. As follows is a reprint of an article from the newsletter, authored by Hans-Wolfgang Ackermann. Also included in issues were lists of new members to the Bacteriophage Ecology Group, an introduction to new website features, a list of upcoming meetings, phage images found on the web (remember, this was 2003, so effectively pre-Google), etc., but most of all, a listing of new phage ecology-related publications. The newsletter was modelled after T4 News, which was a printed newsletter distributed earlier in the 1990s. The newsletter's successors are the ongoing Phage.org website, phage-therapy.org, and the Bacteriophage Ecology Group Facebook page.

The "Félix d'Hérelle Reference Center for Bacterial Viruses" was founded in 1982 by Dr. Hans-W. Ackermann, M.D., as a repository for type viruses of bacteriophage species (1). It was initially funded by grants of the National Research Council for Science and Engineering (NSERC) of Canada. Since 1995, after a funding crisis in Canadian Science, the Center has to rely on fees to cover its costs.

The Félix d'Hérelle Center is an instrument of the ICTV (International Committee on Taxonomy of Viruses). It collects and preserves type viruses of phage species and phages with interesting applications (typing, teaching, industrial) or properties (e.g., capsule-specificity or large DNA size). The collection contains about 430 bacteriophages and as many bacterial hosts belonging to over 50 genera. It is the largest phage collection in the world. Most phages are for acinetobacters, enterobacteria, bacilli, pseudomonads, rhizobia, and vibrios.

The Center seeks out interesting phages in the literature and requests deposits from the original investigators. Phages are examined in the electron microscope and depositors receive a complimentary micrograph. Phages are preserved (i) as lysates at +4°C and (ii) in 50% glycerol at −80°C and in liquid nitrogen. Host bacteria are preserved in 15% glycerol at −80°C and in liquid nitrogen. Phages are available without restrictions to any scientist. The Center has a collection of approximately 6000 books or articles, provides expertises, and accepts visitors for training.

Dr. Ackermann retired about two years ago. The new curator is Dr. Sylvain Moineau, Ph.D., of the Faculty of Science. He is a specialist of phages of lactic acid bacteria. Dr. Ackermann is staying on for advice and electron microscopy.

The Center, located for a long time at the Medical Faculty of Laval University, was recently moved to the Faculty of Science. Its new address is the Department of Biochemistry and Microbiology, Faculty of Science, Laval University, Quebec, Qc, Canada G1K 7P4, tel. (418) 656-2131, ext. 3112; fax (418) 656-2861 (collection.phages@bcm.ulaval.ca).

1. Ackermann, H.-W., Martin, M., Vieu, J.-F., Nicolle, P. Félix d'Hérelle: his life and work and the foundation of a bacteriophage reference center. ASM News, 48:346-348, 1982.

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 an article from Volume 17. The newsletter’s successors are the ongoing Phage.org website, phage-therapy.org, and the Bacteriophage Ecology Group Facebook page.

Bacteriophages are extremely diverse in the range of microbial hosts that they infect and the chemical nature, size and geometry of their genetic materials. As the most abundant organisms on Earth [1], they contribute substantially to overall diversity of the gene pool in the microbial world. It is no surprise then that they have become prominent in the ongoing discussion on microbial diversity [2-4]. The interactions of phages with their hosts are not only important for maintenance of the ecological balance, they may also constitute a major component of the network for lateral transfer of genes among microorganisms. This notion is based on studies with all types of archived phages, which of course represent only a minute fraction of the estimated number of unique phage genomes in nature. Nevertheless, the extent to which phage may contribute to microbial diversity is becoming better appreciated because of an ongoing expansion of sequence databases for all types of organisms, including phage. In the US, funding agencies have teamed together to coordinate a significant increase in support for microbial genome sequencing projects, with a great deal of emphasis being placed on speed and economy of generating, assembling, annotating, and sharing sequence data. It is anticipated that the microbial genome database will continue to expand at a fast pace in the foreseeable future.

The most commonly used approach for sequencing a microbial genome involves genomic library construction (usually from randomly sheared genomic DNA), sequencing a large number of library clones (high-throughput sequencing), computer-assisted assembly of sequence data into contiguous segments (contigs), and carrying out more sequencing and data assembly to close gaps between contigs. The high-throughput stage is expected to yield data from overlapping clones for better accuracy of sequence reads and length of assembled contigs. In principle, the approach is straightforward and has the clearly defined goal of producing an accurate single contiguous sequence of the genome. In practice, it is riddled with bottlenecks that can be different for different genomes, depending on their sizes, states of modification, content of sequences that cannot be cloned and other factors. Personnel training and quality of operations in general are also critical factors to consider in such projects. It is very common for projects to use commercial outfits or collaborations with well-funded research institutes for operations that are impractical to support locally. Usually progress is very rapid during the early stages of a project, but gets bogged down in later stages. Some genomes remain 80-90% finished for months or years, but can still be mined for useful information, provided that this information is released to the scientific community. The technology continues to improve on several fronts, and we can expect that alternate approaches, e.g., circumventing cloning and more powerful computer programming, will cut down the time and expense required to produce a finished genome sequence and allow the sequencing of several genomes concurrently by the same team.

Phage oriented projects have so far completed the sequences of ~150 genomes (GenBank). In some cases, several members of the same phage family (Siphoviridae, Myoviridae or Podoviridae; ICTV nonenclature) are included in databases. Collectively, the data suggest that despite their vast differences in genetic composition, all dsDNA phages share similar genome architecture. The typical dsDNA phage genome consist of a mosaic of gene sets that are shared with other members of the same phage "genus" and gene sets that are unique to each genome and interspersed with the genus-specific sets. That is, dsDNA phage genomes seem to evolve by gathering genes from different sources, including genes that qualify the phages for membership in their particular genera. In some instances, lateral DNA transfer (by homologous or nonhomologous recombination) is suspected to be responsible for mosaic patterns that appear inside some phage genes. Since gene evolution by mutation (vertical change) and genome evolution by lateral DNA transfer probably occur independently of each other, it is difficult to relate whole genomes belonging to the same genus to one another in chronological order. Such timelines are more meaningful when sequences of shared (homologous) genes or gene clusters (or their protein products) are compared, e.g., divergence of an essential gene/protein within a phage genus. The framework represented by genomes of the T4-like phages is an excellent example of how vertical and horizontal evolution may drive diversity in a dsDNA phage genome type. The T4 genome type is large by viral standards and carries many genes that one usually finds in cellular rather than viral genomes. Among these are genes for some enzymes of intermediary metabolism, a multi-component DNA replisome, extensive machinery for genetic recombination, and certain types of mobile DNA elements (including homing endonuclease genes) that can move themselves and flanking DNA unidirectionally [5, 6]. There is also a well-studied prototype, phage T4 [7, 8], than can be used as reference when comparing nucleotide sequences and genome organization of different T4-like phages.

In a collaborative project with Henry Krisch (CNRS, Toulouse, France), we have been sequencing the genomes of a number of T4-like Myoviridae that diverge in host range and/or other characteristics, as determined by preliminary genetic and genomic scanning. Thanks to the efforts of Hans Ackermann, a number of these phages that infect bacterial hosts other than E. coli have been archived at LaValle University (Quebec, CA) and made available for our studies. The sequences of 2 Aeromonas phages, Aeh1 (A. hydrophila) and 44RR2.8t (A. salmonicida) and 2 coliphages RB69 and RB49 are now posted on a publicly accessible web site (http://phage.bioc.tulane.edu) and are in the process of being submitted to GenBank. Although the available data probably represent only a very tiny sampling of what must exist in nature for this type of phage genome, certain predictions can already be made with regards to the kind of diversity one may encounter if a much more extensive collection of T4-like phages is analyzed. For example, whereas genome size appears to be rather fixed for some dsDNA phages, T4-like genomes can vary in length over a wide range. Currently, the observed range is ~164Kbp (for phage RB49) to ~233Kbp (for phage Aeh1). So it appears that genomes of the T4 kind can recruit variable amounts of DNA to go with a certain core that is common to all. Reversible gain and loss of genes and homologues may occur depending on composition of the gene pool where exchanges take place. Based on what we know from T4 studies, the highly recombinogenic character of this genetic system may allow it to be an effective scavenger of DNA from microbial hosts. . The Aeh1 genome carries 23 tRNA genes (19 amino-acid specificities), which is one indication of DNA acquisition from cellular sources. Matches to bacterial sequences in databases account for 2-5% of the predicted ORFs for any of the genomes sequenced so far. This is probably a vast underestimate of the contribution of bacterial DNA to T4-like genomes. More likely, much of the other nonT4-like DNA we observe for these phages has its matches in microorganisms that have yet to be discovered. The combinatorial potential of the genome framework acquired by the T4-like phages might underlie a potential for these phages to cross species barriers between bacteria. If this is happening in nature, then the T4-like population and unrelated phage populations with similar potential [4] could be dynamically affecting microbial diversity on a global scale.

It is still unclear what constitutes the "core" DNA of a T4-like genome. It could be >100 ORFs. Because morphological criteria have figured significantly in the classification of phages into families and genera, it has not been surprising to find homologues of the T4 morphogenesis genes in all the genomes examined so far in the "T4-Like Genome Project" (http://phage.bioc.tulane.edu). On the other hand, homologues of the T4 DNA replication/recombination gene clusters are consistently being observed to coexist with the morphogenesis clusters. Functional coupling between replication and morphogenesis has been documented in T4 studies, and could conceivably be required for natural selection of this type of phage genome. It remains to be seen if phages of the T4 morphotype exist in nature which utilize a different mode of replication from the T4 paradigm, or vice versa. To find out, one would have to utilize specific probes to access a much larger set of genomes than exists today in laboratory archives. It is particularly important to be able to screen environmental sources for genomes of phages that cannot be isolated through traditional plaque assays. T4-like phages that have significantly larger genomes than T4 and those that grow on bacterial hosts other than E. coli (or the enterobacteria in general) are underrepresented in laboratory collections [9]. Also, no phages of this genus have been reported whose heads/genomes are much smaller than T4. Finding more of T4's relatives in a variety of environmental niches and sequencing them would boost our understanding of the pathways leading to microbial diversity. In addition, such phages/genomes would constitute a treasure chest of genes and proteins for all types of studies in basic and applied molecular biology. I beg the BEG to undertake the search for more T4-like phages.

Wommack, K. E., and Colwell, R. R. (2000). Virioplankton: viruses in aquatic ecosystems. Microbiol Mol Biol Rev 64, 69-114.

Hendrix, R. W., Smith, M. C., Burns, R. N., Ford, M. E., and Hatfull, G. F. (1999). Evolutionary relationships among diverse bacteriophages and prophages: all the world's a phage. Proc Natl Acad Sci U S A 96, 2192-2197.

Brussow, H., and Hendrix, R. W. (2002). Phage genomics: small is beautiful. Cell 108, 13-16.

Pedulla, P. L., Ford, M.E., Houtz, J.M., Karthikeyan, T., Wadsworth, C., Lewis, J.A., Jacobs-Sera, D., Falbo, J., Gross, J., Pannunzio, N.R., Brucker, W., Kumar, V., Kandasamy, J., Keenan, L., Bardarov, S., Kriakov, J., Lawrence, J.G., Jacobs jr., W.R., Hendrix, R.W., Hatfull, G.F. (2003) Origins of highly mosaic Mycobacteriophage genomes. Cell 113: 171-182.

Belle, A., Landthaler, M., and Shub, D. A. (2002). Intronless homing: site-specific endonuclease SegF of bacteriophage T4 mediates localized marker exclusion analogous to homing endonucleases of group I introns. Genes Dev 16, 351-362.

Edgell, D. R. (2002). Selfish DNA: New Abode for Homing Endonucleases. Curr Biol 12, R276-278.

Miller, E. S., Kutter, E., Mosig, G., Arisaka, F., Kunisawa, T., and Ruger, W. (2003). Bacteriophage T4 Genome. Microbiol Mol Biol Rev 67, 86-156.

Karam et al Eds., Molecular Biology of Bacteriophage T4. ASM Press, 1994.

Ackermann, H. W., and Krisch, H. M. (1997). A catalogue of T4-type bacteriophages. Arch Virol 142, 2329-2345.

Jim D. Karam
Department of Biochemistry, Tulane University Health Sciences Center, New Orleans, Louisiana

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References

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 an article from Volume 18. The newsletter’s successors are the ongoing Phage.org website, phage-therapy.org, and the Bacteriophage Ecology Group Facebook page.

Coliphage T1, one of the original seven T phages suggested by Max Delbrück (3, 4) for concentrated study by the bacteriophage community, has been sequenced. This phage, which the International Council for the Taxonomy of Viruses (ICTV) has treated as a species within the "T1-like viruses" genus (family Siphoviridae), possesses a polyhedral head approximately 60 nm in diameter with a characteristically long (150 nm) flexible noncontractile tail. Other phages which may be part of this genus are: UC-1 (11), D20, Hi, 102, 103, 150, 168, and 174 (7). To this we can now add the TolC-specific phage TLS - previously known as U3 in many laboratories (5).

Initially made famous by its use as the selective agent in the famous fluctuation test conducted by Salvador Luria and Max Delbrück (12)A, T1 gained notoriety because of its resistance to desiccation and its virulence. Unsubstantiated horror stories exist about its effect on industrial laboratories employing fermentations involving Escherichia coliB. Furthermore, while its potential impact was long appreciated by the phage community, the increase in molecular studies by biologists/biochemists unaware of its virulence has often resulted in unwanted infections. Today many biotech firms market T1-resistant competent cells (i.e. strains carrying a tonA marker; e.g. Cambio, Epicentre, Invitrogen).

Unfortunately research on this interesting and important virus largely languished after the mid 1980s, and prior to the current project the only T1 sequence data to be found in GenBank is for two genes one of which encodes a DNA N-6-adenine-methyltransferase (dam) (19). [We have found that this sequence (GenBank Accession No. BAA94133) contains an internal inframe deletion]. T1 sequence data has also inadvertently ended up in GenBank. A sequence reported to encode a European squid (Loligo forbesi) neurofilament-like protein (X66695) is, in fact, T1 sequence. The sequence of T1 has now been completed (18) revealing many of the secrets of this interesting virus. In addition, Drs. Gregory German and Rajeev Misra (Department of Microbiology, Arizona State University) have completed the sequence of phage TLS (6). In the following paragraphs I will briefly summarize some of the common properties of these two viruses. The Phage T1 Genome

Previous studies on T1 DNA indicated that the genome size was in the order of 48.5 kb with a terminal redundancy of approximately 2800 bp (13). Sequencing has actually shown that the T1 genome size is 50.7 kb with terminal repeats of 1.9 kb. Phage TLS is about the same size (50.9 kb) but possesses shorter (1 kb) terminal repeats. While these two phages differ somewhat in their overall base composition: T1 is 45.6 mol%G+C while TLS is 42.7 G+C their genomes show considerable overall sequence similarity as illustrated by the following Dotplot. Major differences in sequence and genes occur at the ends of the two genomes.

It has long been known that T1 DNA is insensitive to EcoBI [TGA(N8)TGCT] and EcoKI [AAC(N6)GTGC] type I restriction endonucleases. The reason for this has been revealed to be a complete lack of these site in the DNA. Phage TLS DNA has 13 EcoBI sites and a single EcoKI site. While it is unknown how this phage responds to these restriction endonucleases, German and Misra have evidence that TLS encodes a protein which inhibits type I restriction enzymes.

The T1 genome harbours 77 ORFs while that of TLS has 86. As suggested by the Dotplot results and confirmed by protein alignments many of the genes are similar. One significant difference is the finding that TLS encodes both a Dam and a Dcm (N-5-cytosine methyltransferase) methylase.

The work of Bourque and Christensen (2), employing host temperature-sensitive DNA replication mutants, showed that DNA polymerase III, DNA primase (DnaG) and clamp-loading protein (DnaX) were required for T1 replication, while replisome-organizer protein DnaA, helicase-loading protein DnaC and replicative DNA helicase DnaB were not. Sequencing has revealed the T1/TLS encode their own helicases, primases and single-stranded DNA-binding proteins. The origin for replication occurs, as it does in Salmonella phage P22, within the helicase gene. In addition, both phages contain RecE and Erf homologs which are part, in the case of T1, of a general recombination system termed "grn."

In coliphage early transcription involves host holo-RNA polymerase recognition of promoters which contain variants of the canonical hexamers (-35 TTGACA; -10 TATAAT) separated by 15-19 bp (15). While T1 contains many incidences of this type of promoter sequence its molecular approach to transcription is unusual, particularly within the morphogenesis genes. The late region is divided up into a series of transcriptional modules (transcriptons; Figure below) containing RpoD-dependent promoters�and perhaps enhancers�and is flanked by rho-independent terminators. The latter differ from those of coliphage T4 by lacking a UUCG or GNRA loop sequence (16).

Both T1 and TLS possess numerous 21 nt direct repeats located in the intergenic regions or overlapping the translational terminators of the preceding genes. While their high AT content is reminiscent of UP-elements in E. coli (10), their position suggests that they may function in a manner equivalent to eukaryotic enhancers. This transcriptional model differs fundamentally from that displayed by coliphage HK022 (Q-mediated transcriptional read-through) (8) or T7 (multiple phage RNA polymerases-specific promoters) and may account for the short latent period of 13 minutes observed with coliphage T1 (1, 3, 17).

Excluding the genes for the terminase subunits phage T1 has 23 genes which are most probably involved in morphogenesis. SDS-PAGE analysis has shown that the T1 virion is composed of 13-15 structural proteins (14, 20, 21) while TLS preparations contains fewer structural proteins. As part of the analysis of coliphage T1, Dr. Nancy Martin (Queen's University) analyzed the T1 proteome by two-dimensional gel electrophoresis/mass spectrometry. [She would be most interested in discussing potential collaborative phage proteomic projects with interested members of the phage community]. Packaging occurs in a headful manner from pac sites which have been localized in TLS to a 60 bp region which contains six tandem repeats of GATT(T/r) [G. German, personal communication (6)]. The analogous packaging site in T1 contains five adjacent repeats of ATATA.

With a couple of exceptions T1/TLS proteins display low sequence similarity to other phage proteins in the databases. The exceptions are the lysis proteins which possess 40% amino acid identity with lysozymes of Escherichia coli prophage CP-933K, and Salmonella typhimurium PS119 and PS34; and, the tail assembly genes. The latter, T1 genes 38 to 31, are homologous to N15 genes 16 to 23. In addition, both phages code for Cor homologs! Within this cluster are four proteins encoded by linked genes which have been implicated in tail cone assembly (9). The latter are related to similar genes in other members of the Siphoviridae infecting, or carried by, members of the class gamma-Proteobacteria including Burkholderia thailandensis phage phiE125 (22), and coliphages HK97, HK022, N15 and phi80. All of the latter phages are classified as lambda-like viruses at NCBI Taxonomy Browser (http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/) suggesting that, at a higher phylogenetic level, phages T1 and TLS might be said to be part of the order lambda within the Siphoviridae.

While many of the mysteries of T1 have been revealed through analysis of its genome sequence there are still many unanswered questions. Research contemplated or in progress will analyze of the temporal expression of the T1 genome, its regulation, and the role of the 21 nt direct repeats. How the host genome is degraded remains a mystery, and in light of the number of proteins potentially involved in morphogenesis the latter deserves further experimentation. Lastly, we have the universal phage genome question: what is the function of the 53% of the ORFs which failed to result in a BLAST hit?

For those who would like a preview look at the annotated T1 sequence data please visit: http://microimm.queensu.ca/Phage/. References

Borchert, L. D. and H. Drexler. 1980. T1 genes which affect transduction. Journal of Virology 33:1122-1128.

Bourque, L. W. and J. R. Christensen. 1980. The synthesis of coliphage T1 DNA: requirement for host dna genes involved in elongation. Virology 102:310-316.

Delbrück, M. 1945. The burst size distribution in the growth of bacterial viruses. Journal of Bacteriology 50:131-135.

Delbrück, M. and S. E. Luria . 1942. Interference between bacterial viruses. I. Interference between two bacterial viruses acting upon the same host, and the mechanism of virus growth. Archives of Biochemistry 1:111-114.

German, G. J. and R. Misra. 2001. The TolC protein of Escherichia coli serves as a cell-surface receptor for the newly characterized TLS bacteriophage. Journal of Molecular Biology 308:579-585.

German, G. J. and R. Misra. 2003. The T1-like TolC- and lipopolysaccharide-specific (TLS) bacteriophage genome and the evolution of virulent phages. Journal of Molecular Biology (submitted).

Hug, H., R. Hausmann, J. Liebeschuetz, and D. A. Ritchie. 1986. In vitro packaging of foreign DNA into heads of bacteriophage T1. Journal of General Virology 67:333-343.

Juhala, R. J., M. E. Ford, R. L. Duda, A. Youlton, G. F. Hatfull, and R. W. Hendrix. 2000. Genetic sequences of bacteriophages HK97 and HK022: Pervasive genetic mosaicism in the lambdoid bacteriophages. Journal of Molecular Biology 299:27-51.

Katsura, I. 2003. Tail assembly and injection, p. 331-346. In R. W. Hendrix, J. W. Roberts, F. W. Stahl, and R. A. Weisberg (eds.), Lambda II. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.

Kolasa, I. K., T. Lozinski, and K. L. Wierzchowski. 2002. Effect of An tracts within the UP element proximal subsite of a model promoter on kinetics of open complex formation by Escherichia coli RNA polymerase. Acta Biochimica Polonica 49:659-669.

Lundrigan, M. D., J. H. Lancaster, and C. F. Earhart. 1983. UC-1, a new bacteriophage that uses the tonA polypeptide as its receptor. Journal of Virology 45:700-707.

Luria, S. and M. Delbrück. 1943. Mutations of bacteria from virus sensitivity to virus resistance. Genetics 2:491-511.

MacHattie, L. A., M. Rhoades, and C. A. J. Thomas. 1972. Large repetition in the non-permuted nucleotide sequence of bacteriophage T1 DNA. Journal of Molecular Biology 72:645-656.

Martin, D. T., C. A. Adair, and D. A. Ritchie. 1976. Polypeptides specified by bacteriophage T1. Journal of General Virology 33:309-319.

McLean, B. W., S. L. Wiseman, and A. M. Kropinski. 1997. Functional analysis of sigma-70 consensus promoters in Pseudomonas aeruginosa and Escherichia coli. Canadian Journal of Microbiology 43 :981-985.

Miller, E. C., E. Kutter, G. Mosig, F. Arisaka, T. Kunisawa, and W. R�ger. 2003. Bacteriophage T4 genome. Microbiology and Molecular Biology Reviews 67:86-156.

Roberts, M. D. and H. Drexler. 1981. T1 mutants with increased transduction frequency are defective in host chromosome degradation. Virology 112:670-677.

Roberts, M. D., N. L. Martin, and A. M. Kropinski. 2003. The genome and proteome of coliphage T1. Virology (in press).

Schneider-Scherzer, E., B. Auer, E. J. de Groot, and M. Schweiger. 1990. Primary structure of a DNA (N6-adenine)-methyltransferase from Escherichia coli virus T1. DNA sequence, genomic organization, and comparative analysis. Journal of Biological Chemistry 265:6086-6091.

Toni, M., G. Conti, and G. C. Schito. 1976. Viral protein synthesis during replication of bacteriophage T1. Biochemical & Biophysical Research Communications 68:545-552.

Wagner, E. F., H. Ponta, and M. Schweiger. 1977. Development of E. coli virus T1: The pattern of gene expression. Molecular and General Genetics 150:21-28.

Woods, D. E., J. A. Jeddeloh, D. L. Fritz, and D. DeShazer. 2002. Burkholderia thailandensis E125 harbors a temperate bacteriophage specific for Burkholderia mallei. Journal of Bacteriology 184:4003-4017.

AAt the time known as phage a. See pp. 482 and 483 of Abedon (2000) for a brief history of the original T set of coliphages.

BKnowledge of phage T1�s desiccation resistance likely forms the basis of the famous "Phage in a Letter" urban legend, which apparently has since morphed into "Phage M13 in a letter." M13 is also a desiccation-resistant phage, but one which few have rejected from their laboratories perhaps because M13 is relatively avirulent and otherwise popular as a platform for protein display. See: http://www.panix.com/~iayork/phage.shtml or http://www.urbanlegends.com/science/phage.html for popular discussion of the "Phage in a Letter" urban legend.

Andrew M. Kropinski
Department of Microbiology, University of Guelph, Guelph, Ontario, Canada

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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 an article from Volume 21. The newsletter’s successors are the ongoing Phage.org website, phage-therapy.org, and the Bacteriophage Ecology Group Facebook page.

Declining Electron Microscopy

Twenty years ago there were many electron microscopes and microscopists. My medical school alone had four Philips EM 300 microscopes. There is now only one, mine. Two others, though in perfect order, were dismantled. The fourth EM was sold to the U.S.A., which says a lot about the budget cuts that Canadian science has been subjected to. The general situation is that both electron microcopes (EM) and electron microscopists are endangered species.

A Huge Drop in Quality

It also used to be that phage papers included reasonably good micrographs. No longer. In the last 10 years standards have plunged and scores of terrible pictures, graced with improbable dimensions or no dimensions at all, have been published. Gone are such fine electron microscopists as D.E. Bradley in Canada, E. Kellenberger in Switzerland, or A.S. Tikhonenko in Russia, who led by example and kept standards up. Many (most?) phage pictures in the present literature are vastly inferior to those published in 1959 by Brenner and Horne, the fathers of negative staining (1).

This decline of EM is not seen in vertebrate and plant virology, where editorial standards are still high and poor electron micrographs and poor descriptions, as they are now frequent in phage papers, would probably be rejected. What happened? The reasons for the decline are manifold: High costs of electron microscopes. Run-away costs of EM service contracts. Shifting of research interests to molecular biology (cloning, sequencing). Retirement of experienced electron microscopists. Disappearance of EM courses. Contract research ('farming out'). Soft standards of journals: a reviewer system in disrepair.

'Farming out' of EM to other laboratories is due to the rarefaction of electron microscopes and microscopists, plus the perception of administrators that electron microscopy is a simple service. Nothing could be less true. While 'farming out' to a reputed research laboratory may be acceptable, this is not so in the case of commercial laboratories. It is just unlikely that an ordinary technician, ignorant of the project in question, lacking time and supervision, and trained in, say, pathology, is able to produce good pictures of bacterial viruses. Yet these laboratories take good money for poor service. The problem is not confined to North America. I have seen terrible examples from Australia.

Since general standards have gone down, reviewers of periodicals, even reputed ones, now frequently tolerate poor pictures. Journals of the American Society of Microbiology are no exception. The situation is particularly bad in environmental microbiology journals.

Why Electron Microscopy?

EM provides instant identification of individual phages, phage families and, very often, genera and species. It cannot be replaced by molecular probes or genome sequencing. Probes will 'catch' part of a phage genome only, the sequencing and annotation of a phage genome may take a year or more, but EM identification may take as little as 1-2 minutes. The domain of EM is the description and identification of novel phages, classification, environmental research, and purity checks and identity controls of phages with practical applications (e.g., therapeutic or typing phages). EM cannot replace molecular biology and cannot be replaced by the latter. Both techniques are complementary. An EM is an expensive precision instrument that, when properly handled, produces data close to the molecular level.

EM pictures are easily archived, directly comparable, permanent documents. In contrast, scientists change institutes, countries, and jobs, retire, or die. It is even worse with phages because, as a rule, phages described more than five years ago can no longer be obtained. Thus, EM pictures are often the only permanent results of a scientist's activity and the only records of past observations. Therefore, good EM is a must.

The Disease

It is now common to see unsharp, astigmatic, low-contrast, or scratched pictures of impure phages, without scale markers or dimensions. Some phages are barely recognizable as such, especially in environmental papers, and some papers just mention 'head-tail phages' without dimensions and micrographs. It is surprising to see such a deterioration because the literature abounds in descriptions of basic electron microscopical techniques. Clearly, this literature is not consulted. Why? Because it is not on the Net?

Staining artifacts (e.g., capsid shrinkage after positive staining with uranyl acetate) are consistently ignored. Some people present capsular slime is as a 'tailed phage,' feel the need to fix phages with glutaraldehyde (useless), or stain with uranyl acetate for 15 minutes (instead of 30 seconds). More seriously, the 'Materials' sections of phage papers are generally silent on phage purification and magnification control. Together with poor pictures, this indicates to the insider that people examined crude lysates and confided into manufacturer indications on magnification (ignoring that the magnification of electron microscopes varies with the electrical current and must be controlled or adjusted).

This kind of 'science' is useless because it produces terrible data and does not help fellow scientists. Concretely, phage workers, who isolate new phages and want to compare their viruses to those of the literature, often face the problem that data from other laboratories cannot be interpreted. It follows that an individual who practices poor EM, and produces pictures which other scientists cannot use, does a disservice to the scientific community.

Diagnosis and Cure

The principal problems seem to be examination of crude or 'dirty' lysates, absence of magnification control, and poor contrast. The first can be addressed by simple washing in a buffer. Phages must be freed from proteins and sugars of the medium. No lengthy density gradient purification is necessary; it suffices to wash the phages 1-2 times in 0.1 M ammonium acetate (best) or phosphate buffer using, for reduction of time and g forces, a medium-sized centrifuge with a fixed-angle rotor; for example, 25,000 g for 1 hour are enough for all but the smallest phages. For magnification control, one must include into each film or cassette load 1-2 pictures of an internal standard. One may use T4 tails (length 113 nm). Then: please measure your phages. It takes a few minutes only. The phages must be so described so that other people can use your descriptions. This is for posterity! The contrast problem is one of basic photography and can be solved by selecting the right photographical papers and developers.

A deadly problem arose a year ago when Kodak Company (Rochester) changed abruptly its production line. Customers were not informed and no explanation was offered. Suddenly, the excellent Ektamatic paper, which lent itself to automatic processing, was no longer available. Kodak representatives could not be contacted or did not know their own products. Fortunately, fellow electron microscopists from the Armand-Frappier Institute near Montreal suggested to me the use of Kodak Polycontrast III RC paper in conjunction with the usual Dektol or the novel Polymax T developers.

My experience is that the paper provides excellent, if sometimes too strong contrast. It allows the salvage of underexposed or underdeveloped films, but grey shades may be lost. All development must be done manually because small table-top Kodak or Ilford processors can no longer be used. The development is followed by a stop bath, fixation and washing as usual, but drying and glazing in a machine are no longer necessary because the paper is resin-coated and naturally glossy, and dries in a short while. Caution: violet smears will develop if the the Dektol developer is not totally neutralized.

(1) Brenner, S. and Horne, R.W. 1959. A negative staining method for high resolution electron microscopy of viruses. Biochim. Biophys. Acta 34:103-110.

Hans-Wolfgang Ackermann
Félix d'Hérelle Reference Center for Bacterial Viruses, Laval University, Québec, Canada

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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 24. The newsletter’s successors are the ongoing Phage.org website, phage-therapy.org, and the Bacteriophage Ecology Group Facebook page.

When I began BEG News six years ago, for a July 1, 1999 issue, I had hoped that I might keep up the pace of putting out one issue a quarter for a year or two. But one issue turned into a dozen and now to two dozen, dutifully put out each quarter by yours truly. Not always on time, mind you, but not so late as to matter. The core of the newsletter came to be an editorial and a list of new phage ecology references. Between that and entering all of the new non-members into the BEG database (particularly as subscribers to BEG News via BioMed Central), I’ve devoted something approaching one full workweek to getting each issue out.

The original intent was to do this once a quarter to inspire me to update phage.org on a regular basis. Indeed, early issues of BEG News documented those updates. Ultimately, however, the result has been that I’ve spent far more time putting together BEG News than working on the rest of phage.org. Perhaps as a consequence, www.phage.org is no longer the Google number one site for a phage search (though I suspect the real reason we’re no longer number one is that they’ve rejiggered how they score sites). Please, everybody, for the sake of the Bacteriophage Ecology Group, place a link on your web sites that points to http://www.phage.org (rather than to http://www.mansfield.ohio-state.edu/~sabedon, which goes to the same place but is not the same thing). We’re still the phage ecology and bacteriophage ecololgy number one Google hit, however, so all is not yet lost. J

I would like to thank Hans Ackermann for his endless support as well as Steve McQuinn for his tireless devotion to computer rendering of the phage T4 virion. I would like to thank those of you, in addition to Hans, who contributed editorials to BEG News: Ry Young, Jim Karam, and Andrew Kropinski (and, of course,

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