Bacteriophage Ecology Group News

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@ www.phage.org

by Stephen T. Abedon (editor)

April 1, 2005 issue (#24)

 

Beg News, the Final Quarterly Issue

Stephen T. Abedon, The Ohio State University

Bacteriophage Ecology Group News (BEG News) 24

 

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, Betty Kutter for this issue). Thanks also go to Matt Sullivan for his updates to the Cyanophage Literome, and to those many individuals who have provided me with quarterly phage images over the past six years.

 

The Bacteriophage Ecology Group will keep on going, even without a quarterly BEG News, still soliciting members—visit the BEG Bibliography for bibliography updates at www.phage.org/beg_bibliography.htm. Even BEG News may return from time to time, particularly if I receive enough submissions, editorials, or art from people to justify an issue. In other words, consider BEG News as "new and improved" rather than defunct, where publication is now driven by content rather than by calendar.

 

Thank you everybody for your ongoing support of phage.org and bacteriophage ecology.

 

Overview and History of Current

and Recurring Phage-Related Meetings

Elizabeth "Betty" Kutter, The Evergreen State College

Bacteriophage Ecology Group News (BEG News) 24

In 1945, Max Delbrnck greatly stimulated and redirected the course of phage research by organizing the first of a very long series of annual Phage Courses at Cold Spring Harbor, Long Island, drawing students and senior personnel from around the world into his project to use phage to develop an understanding of the organization and functioning of the gene and signaling the birth of molecular biology. The results were enormously successful. Phage research and funding subsequently reached its peak in about 1980, but then declined as the newly-developed phage-derived techniques enabled the explosion of molecular analyses of a variety of other organisms. Now, however, interest in phages is again exploding in new directions as we become aware of phage ecology and its worldwide roles, the possibilities of phage therapy, potentials phage offer for understanding microbial physiology and genomics, the application of phage in display technologies and in nanotechnology, and the uses of the rapidly-growing families of phage-encoded proteins in a variety of technologies.

There are 3 important, complementary phage-related meetings this summer, all of which grew out of the associated annual Cold Spring Harbor phage meeting and the changes that have happened in that meeting since it started over 50 years ago:

►The XVIX Phage/Virus Assembly Conference (June 7th – 12th) will be held in Winter Park, Colorado this year. Bob Edgar, Bill Wood and Fred Eiserling began this series of conferences in 1968 at a time when the Cold Spring Harbor meeting was primarily focusing on such phenomena as gene regulation and lysogeny; held different places each year, it has developed a good balance between phage and other viruses (www.phagevirusassembly.org).

►The Molecular Genetics of Bacteria and Phages Meeting (Aug. 2nd – 7th) now alternates between Cold Spring Harbor and Madison, Wisconsin, where it will be held this year. Its main focus is on microbial transcription mechanisms, regulatory phenomena, bacterial cell biology, genomics, and microbial pathogenesis, but it also will have a session on "bacteriophage development and host interactions" (www.union.wisc.edu/conferenceservices/phages/index.html).

►The 16th Evergreen International Phage Biology Meeting (Aug. 7th – 12th) will be held in Olympia, Washington. The only current meeting devoted exclusively to phages, it is a particularly good place to build collaborations.  It started in 1975 as a west coast phage meeting, reflecting the fact that the Cold Spring Harbor meeting had evolved into a broader yet narrower Phage and Microbial Genetics meeting and had become very expensive, particularly for students. With the help of many – particularly Bruce Alberts, Chris Mathews, Gisela Mosig, Fumio Arisaka, Jan Drake, Eleanor Spicer, Peter Gauss, Steve Abedon, Wolfgang Rueger, Vadim Mesyanzhinov, and Jim Karam – it quickly grew into a worldwide meeting for T4 and other large lytic phages and was the birthplace of the T4 genome project and the 1983 and 1994 ASM Bacteriophage T4 books. With encouragement from Ian Molineux, Rich Calendar, Mike DuBow and others, it grew into a more general phage biology meeting, emphasizing phage therapy, phage ecology and genomics along with regulation, biochemistry and assembly. Planned sessions this year include Phage Genomics, Phage Regulatory Systems; Molecular Mechanisms; Phage Ecology; The Real-world Phage Infection Process; Human Phage Therapy; Phages In agriculture and Food Safety; Dairy Phages; Innovative Applications of Phage and Their Products; Phage Structure and Function -- and a special tribute to Eduard Kellenberger and Wolfram Zillig. We are in the process of selecting a pair of chair people for each session; about half the spots are still being decided, and suggestions are welcome. The session order and lengths will be determined by the number of related abstracts we receive For more info go to www.evergreen.edu/phage.

 

Much is also now happening in broader meetings to reflect the widespread resurgence of interest in phage biology and applications.

►The American Society for Microbiology 105th General Meeting (June 5th – 9th) in Atlanta Georgia, will have sessions on Phage Therapy: New Life for an Old Idea, Getting your DNA Inside, Taking Over RNA Polymerase, and Phage Genomics and Beyond. (www.asm.org/Meetings/index.asp?bid=697). Last August, their "New Phage Biology Meeting" pulled together all of the various areas of phage interest for a "Phage Summit" in Miami which drew 350 participants with 250 posters (!!).

►The International Union of Microbiological Societies triennial meeting (July 23rd – 28th) in San Francisco, "Microbes in a Changing World" will have sessions on Bacteriophage Life Cycles and Phage Evolution and Genomics (www.iums2005.org).

►The British Society for General Microbiology 156th Meeting (April 4rd – 7th) in Edinburgh, Scotland just had 2 full days of talks on various aspects of phage biology: Phage Genomics and Evolution; Phage Ecology and Phage-Host Response; Phages and Virulence; and Phage Therapy (www.socgenmicrobiol.org.uk/meetings/mtgpages/hw.cfm).

 

 

-- The following is an advertisement --

 

 

 

T-shirts with this design are available at www.thebacteriophages.com/sales.htm

 

Help Save the G. Eliava Bacteriophage Institute

(in Tblisi, Republic of Georgia)

 

The George Eliava Institute for Bacteriophage, Microbiology and Virology (GEIBMV) in Tbilisi, Republic of Georgia, was founded in 1923 and has researched and developed bacteriophage medicines for over seventy years. These medicines formed a key element of the treatment of a wide range of bacterial infections during the Soviet era and the GEIBMV supplied the whole of the former USSR with bacteriophage therapeutics. The Institute survived the murder of Dr. Eliava, the first Head of the Institute, in 1937, and the civil war that followed the break-up of the Soviet Union in 1991.

 

Bacteriophage therapy is rapidly emerging as an important alternative to conventional chemotherapy for the treatment of bacterial infections at a time when antibiotic drug resistance threatens our continued ability to combat serious infections in our hospitals and in our communities, and at a time when the pharmaceutical industry is drastically scaling down its development of the new antibiotics that we so badly need. The GEIBMV has amassed a unique and extensive collection of medically important bacteriophages and the scientists and technicians within the Institute have unparalleled experience in research, development and clinical use of bacteriophage medicines.

 

All this is now under threat. The Georgian Academy of Sciences have revealed plans to merge the GEIBMV with five other Institutes in Georgia as a simple cost cutting exercise, and plan to disperse the resources and expertise that currently resides under one roof in Tbilisi. Such a move will spell the end of this unique microbiological institution, with all that entails for the future development of unconventional but effective anti-infective medicines.  The proposal to merge the Institute has serious implications for the future, in particular:

 

+         Loss of commercial funding opportunities

+         Loss of key staff members

+         Loss of external assistance in technical and commercial fields

+         Disruption of collaboration agreements already in place

+         Loss of new opportunities to develop commercial/joint ventures

+         Potential repayment of some grants owing to changed management and ownership

 

Under this scenario the proposed move will result NOT in cost savings, but instead in additional costs and the lost opportunities for Georgia in biotechnology on the world stage.  No decision should be taken about the future merging of the Eliava Institute until a proper study is undertaken of all the economic, technical and financial implications.

 

Help to ensure that this does not happen – sign this petition and you will send a message to the Georgian Academy of Sciences that the loss of GEIBMV would be a blow not only to science in Georgia but also will significantly impoverish the global fight against the ravages of infectious disease.

 

The Petition: We the undersigned hereby urge the Georgian Government to recognize the strategic  importance of the G. Eliava Institute of Bacteriophage, Microbiology and Virology to the future of the people of Georgia, and it's extraordinary impact in the development of anti- infective biomedicine worldwide, by establishing the Institute as an independent public institution – the Eliava National Institute – within the Ministry of Education and Science of Georgia.

 

To sign the petition, please visit www.phage.org/GEIBMV_petition.pdf.  Please print out this one-page document, fill it out as completely as you can, sign and date it, and then either scan the completed document to email to Nino Chanishvili (n_chanish.ibmv@caucasus.net) or send it by snail mail send it to Kazbegi street, 41, VERA region, 380079, Tbilisi, Georgia.

 

 

The Entrance to the G. Eliave Bacteriophage, Virology and Microbiology Institute.

 

 

Two views of Tbilisi: from above the city at Turtle Lake and a view of Metekhi, built in the 12th century.

 

Phage Art Show at ASM in Atlanta

 

 

 

 

Dear fellow microbiologists and phage enthusiasts,

We are excited to announce "The Art of Phage: An Exhibition", which will be held at the ASM meeting in Atlanta, Georgia. The main art show will be held at the Division H,M,S,K and T Mixer on Tuesday, June 7 at the Omni Hotel. Slide shows will be presented in selected sessions and colloquia of Division M and Division H.

Pieces of art will be for sale and any inquires can be communicated with Neilan Kuntz throughout the meeting at 970-309-0410 and/or kuntzn@rohan.sdsu.edu We look forward to sharing the vision and creativity of thse bacteriophage-inspired artists. Artist information, art gallery and automated slide show of some of the selected art can also be seen at the following link: http://phage.sdsu.edu/imagery/gallery/images/artshow.php.

Sincerely,

Dr. Forest Rohwer (San Diego State University)
Dr. Anca Segall (San Diego State University)
Neilan Kuntz (Polymerlinks.org)
Dr. Stephen Abedon (Ohio State University)

 

 

Supported by the NSF BioComplexity Program and San Diego State University

 

 

 

Raettig Punch Cards!

 

 

 

Shown is a piece of phage history.  Hansjnrgen Raettig (1911-1997) assembled and published in 1958, and again in 1967, the definitive phage bibliographies, containing a total of approximately 11,405 references.  To assemble and index these references he employed early computer punch cards, such as the one shown above.

 

Thank you to Hans Ackermann, who acquired and scanned the card you are viewing, and to Dr. H. Gelderblom who provided the cards.  Click the following links to view full-sized scans of this card and a second (or here and here to view reduced, grayscale versions).

 

 

New BEG Members

 

go to www.phage.org/beg_join.htm for joining information

 

name
(home page links)

status

address/research interests

Anna Ivanova

PI

Department of Physics, Tbilisi State University, 3, Chavchavadze str., 0128, Tbilisi, Georgia

interests:

Physico-chemical properties of bacteriophages and their receptors (for example, thermal and hydrodynamical properties); also phage DNA ejection in a model system consisting of phages, bacterial membrane fragments, and receptors. (contents | BEG members | top of page)

Jeffrey B. Jones

PI

University of Florida, Plant Pathology Dept., Gainesville, FL 32611

interests:

Integrated approach to controlling bacterial diseases of plants. We are using phage therapy for this IPM approach. (contents | BEG members | top of page)

Leonard Peruski

PI

Associate Professor, Microbiology and Immunology, Indiana University School of Medicine, Northwest Center, 3400 Broadway, Gary, Indiana 46408-1197

interests:

Evolution of bacteriophage that infect the Bacillus cereus genetic group, with special emphasis on lytic and temperate phage of B. anthracis. (contents | BEG members | top of page)

Manan Sharma

PI

USDA-ARS, ANRI, Food Technology and Safety Lab, Bldg. 201, BARC-East, 10300 Baltimore Ave., Beltsville, MD 20705

interests:

Food safety, specifically post-harvest interventions that may be applied to reduce microbial pathogens and spoilage organisms. (contents | BEG members | top of page)

Juan E. Suárez

PI

Area de Microbiologia, Facultad de Medicina, Julian Claveria 6, E-33006 Oviedo, Spain Telephone: +34 985103559

interests:

We work with phages that infect lactic acid bacteria, mainly those active on industrial starters but also on those affecting probiotic bacteria. We are starting a new line on phage therapeutics, taking advantage of our location in a Faculty of Medicine that has an adjunct hospital. (contents | BEG members | top of page)

 

 

 

Bacteriophages:

Biology and Applications

 


Elizabeth Kutter & Alexander Sulakvelidze (eds)

 

CRC Press, Boca Raton, Florida

 

ª 2004

 

ISBN: 0849313368

 

510 pages

 

 

Forward

by Bruce Alberts

Chapter 1:

Introduction by Elizabeth Kutter and Alexander Sulakvelidze

Chapter 2:

Bacteriophage Research: Early Research by William C. Summers

Chapter 3:

Basic Phage Biology by Burton Buttman, Raul Raya, and Elizabeth Kutter

Box 1:

Antigenicity of Phages by Ketevan Gachechiladze

Chapter 4:

Bacteriophage Classification by Hans-W. Ackermann

Chapter 5:

Genomics and Evolution of Tailed Phages by Harald Brnssow and E. Kutter

Chapter 6:

Phage Ecology by Harald Brnssow and E. Kutter

Chapter 7:

Molecular Mechanisms of Phage Infection by Elizabeth Kutter, Raul Raya, and Karin Carlson

Chapter 8:

Bacteriophages and Bacterial Virulence by E. Fidelma Boyd

Chapter 9:

Phage for the Detection of Pathogenic Bacteria by Catherine E. D. Rees and Martin J. Loessner

Chapter 10:

Control of Bacteriophages in Industrial Ferments by Sylvain Moineau and CTline LTvesque

Chapter 11:

Phage as Vectors and as Targeted Delivery Vehicles by Caroline Westwater and David A. Schofield

Chapter 12:

The Use of Phage Lytic Enzymes to Control Bacterial Infections by Vincent A. Fischetti

Chapter 13:

Phage Therapy in Animals and Agribusiness by Alexander Sulakvelidze and Paul Barrow

Chapter 14:

Bacteriophage Therapy in Humans by Alexander Sulakvelidze and Elizabeth Kutter

Appendix:

Working with Bacteriophages: Common Techniques and Methodological Methods by Karin Carlson

Box 2:

Electron Microscopy by Hans-W. Ackermann

 

 

Reprint of Forward from Kutter and Sulakvelidze, 2004

Bruce Alberts, President, National Academy of Sciences; Washington, DC

Bacteriophage Ecology Group News (BEG News) 24

It is a privilege for me to have this opportunity to provide a brief foreword to Bacteriophages: Biology and Applications by Elizabeth Kutter and Alexander Sulakvelidze. I was one of many who first became fascinated with the romance of science by reading the book Arrowsmith as a teenager. In that novel written by Sinclair Lewis in 1925, an attempt to develop phage therapies against bacterial diseases played a central role. But by the early 1950s, when I read the book, the widespread success of newly introduced antibiotics had seemed to make this alternative approach to the selective killing of bacteria unnecessary.

Instead, a small set of bacteriophages had begun to attract attention as "model organisms" – prime systems for probing the basic chemistry of life. These phages were attractive to scientists, because they were much easier to study with the then-available tools than were more complex life forms such as bacterial or human cells. They had relatively small genomes and multiplied rapidly, making them unusually amenable to genetic analyses that aimed at obtaining multiple mutants in each bacteriophage gene. To enable the essential genes for viral multiplication to be genetically identified, screening techniques were developed that focused on conditional lethal mutations – for example, through the identification of "temperature-sensitive" phage mutants that would grow at low but not high temperatures. Moreover, because large amounts of infected cells were easy and inexpensive to obtain, biochemical approaches could be readily employed, so that the products of the genes identified by genetic screens could be isolated and characterized in cell-free systems.

The model organism approach worked better than anyone had had a right to expect, in part because the mechanisms that are used to control gene expression and to recombine and replicate DNA genomes turned out to be much more highly conserved across life forms than anyone had suspected. Much of the work was concentrated on several viruses that infect the bacterium E. coli – most notably the bacteriophages lambda, T4 and T7. The findings made in multiple laboratories could thereby be combined, yielding results that were immensely important in developing the field of molecular biology, as reviewed in the early chapters of this book.

To give a personal example, for 30 years beginning in 1965, my own laboratory would exploit the combined genetic and biochemical advantages of the T4 virus for study of fundamental DNA replication mechanisms. In the end, the "protein machine" mechanisms revealed at the replication fork through bacteriophage studies turned out to be highly similar to those used to move the replication forks of higher organisms, including that of humans (Alberts 2003).

In the 1960s and 1970s, many advances were made in a wide range of laboratories studying both bacteriophages and the bacterial cells themselves. The new knowledge of biological mechanisms that resulted soon allowed the development of more powerful research tools (such as DNA cloning). With these new tools, researchers could begin to unravel the molecular mechanisms in more complex cells and organisms. As a result, by the 1980s most of the action and excitement in molecular biology had moved away from simpler organisms to investigations of mammalian cells.

For several unrelated reasons, we may have come full circle over the course of the last 80 years. First of all, there is an urgent need for new types of antibacterial therapies. We now live in an evermore crowded, more interconnected world in which resistant strains of microorganisms spread with amazing rapidity. Modern science has increased our ability to design countermeasures to these diseases of humans and animals; the standard countermeasures have been new drug and vaccine developments. But producing a new drug is an enormously expensive endeavor. In addition, market failures have discouraged the development of new vaccines in the private sector. As a result, the world now faces a serious challenge in dealing with a host of microbial threats that were once thought to be defeated rather easily by antibiotics (Institute of Medicine, 2003). As described in Chapters 12 to 14, there is therefore every reason to reintroduce bacteriophage therapies as an additional tool in the war against bacterial diseases.

A second feature of modern biology that is reawakening interest in bacteriophages is our new ability to obtain the DNA sequences of large number of organisms inexpensively. From this DNA sequence information, we can determine the relatedness of organisms and attempt to retrace the past history of life on the Earth. The sequencing of bacteriophages is only just beginning. Not only are there immense numbers of novel proteins yet to be discovered among what could be 100 million different bacteriophages in the environment, the vast majority not yet known (the genomes of only about 400 have thus far been completely sequenced), but it is now suspected that some of the lytic phages carry genes that trace back in evolutionary history to the common ancestor of eukaryotic and prokaryotic cells (see Chapter 5). In summary, bacteriophages represent a huge untapped genetic reservoir that can be productively mined -- both by those interested in proteomics and by those who are trying to decipher the mysterious nature of the early cells that predated the split between the three families of cells that are alive today: the archaea, the bacteria, and eukaryotes.

Now that we have access to the complete molecular anatomy of a cell, a third reason for a new focus on bacteriophages stems from the realization – sobering to scientists like myself -- that biological systems are so complex that they can not be understood without new methods of analyzing and conceptualizing them. Thus, for example, the nearly 500 different protein molecules that are encoded by the genome of the simplest known living cell, the small bacterium Mycoplasma genitalium, interact with each other and with substrates in an enormous number of ways. Even if we had a complete catalog of all of these interactions and their rate constants, information we are far from achieving today, we could not claim to understand this cell in any deep sense – that is, in the sense of being able to explain how it is able to grow and reproduce itself as a chemical system. Living systems are made possible by a huge web of networked chemical reactions, and we presently lack the tools to decipher what is most significant within such complexity. This realization, new to most molecular biologists, raises the question of whether it might be productive to focus once again on one or a few bacterial viruses that could serve as model organisms – far simpler than any free-living cell -- for developing new types of complexity analyses. If so, which viruses should be targeted and through what types of experimental strategies?

Finally, the increasingly large role that science and technology will play in driving societal changes in the 21st century argues strongly for a new type of science education in our schools. Beginning with 5 year olds, what is needed is an education that allows students to explore the world around them using evidence and logic, so that they leave school learning to solve problems the way that scientists do. They also need to understand what science is and why it represents a special way of knowing about the natural world, if they are to respect its judgments concerning the many important issues that they will need to decide in their lifetimes – such as whether they should avoid exposures to substances that could adversely affect their health in the future, or whether their nation should make sacrifices to reduce the release of greenhouse gases into the atmosphere.

The National Science Education Standards call for a revolutionary change in science teaching, with an emphasis on teaching science as inquiry (National Research Council, 1996). As the ultimate step in such an education effort, it should be possible for a select group of students to participate in a real scientific investigation in their upper years of high school. It is thus encouraging to find high school students appearing as coauthors of a major publication from the University of Pittsburgh, in which a diverse set of novel bacteriophages that infect mycobacteria have been identified and sequenced (Pedulla, et al. 2003).

 

The National Academy of Sciences has just published the results of an unusual workshop in which 25 leading scientists outside the field were exposed to the biology of the smallpox virus and challenged with the task of suggesting new approaches to antiviral therapies (Harrison, et al. 2004). As this exercise made clear, we badly need a new infusion of talent and energy into the field of virology, where there is an enormous opportunity for scientific breakthroughs whose results will be of great practical benefit to human health (Alberts and Fineberg 2004). What better way to recruit outstanding young people into such fields than to expose them as teenagers to a scientific exploration of the wonderfully rich and diverse world of bacteriophages?

I would like to end by congratulating both the coauthors and the many contributors to this volume for their dogged persistence in sticking to bacteriophage research over many decades. They have survived their years in the shadows, and now we can all appreciate the strong platform their work has established for the many exciting years of research ahead.

 

REFERENCES

1.       Alberts, B. M., 2003, DNA replication and recombination. Nature 421: 431-435.

2.       Alberts, B. M. and Fineberg, H. V., 2004 Harnessing new science is vital for biodefense and global health. Proc Natl Acad Sci U S A 101: 11177.

3.       Harrison, S. C., Alberts, B. M., Ehrenfeld, E., Enquist, L., Fineberg, H. V., Mcknight, S. L., Moss, B., et al., 2004 Discovery of antivirals against smallpox. Proc Natl Acad Sci U S A 101: 11178-11192.

4.       Institute of Medicine, 2003. Microbial Threats to Health: Emergence, Detection, and Response. Mark S. Smolinski, Margaret A. Hamburg, and Joshua Lederberg, Editors. Natl. Acad. Press, Washington, D. C.

5.       National Research Council, 1996. National Science Education Standards. Natl. Acad. Press, Washington, D. C.

6.       Pedulla, M. L., Ford, M. E., Houtz, J. M., Karthikeyan, T., Wadsworth, C., Lewis, J. A., Jacobs-Sera, D., et al., 2003 Origins of highly mosaic mycobacteriophage genomes. Cell 113: 171-182.

 

 

Reprinted with Permission

 

 

 

Bruce Alberts, President, National Academy of Sciences; Washington, DC 20037, Professor of Biochemistry and Biophysics, University of California, San Francisco; San Francisco, CA 94143

 

 

New Bacteriophage-Ecology References

 

Anonymous 2004. Renaissance phage. Nature Reviews Microbiology 2:922. Abstract: In today's culture of spin, 'renaissance' is a term that is often applied undeservingly to particular areas of science. In the case of current phage research, however, its use is easily justified.

 

Allwood, P. B., Y. S. Malik, S. Maherchandani, K. Vought, L. A. Johnson, C. Braymen, C. W. Hedberg, and S. M. Goyal. 2004. Occurrence of Escherichia coli, noroviruses, and F-specific coliphages in fresh market-ready produce. J. Food Prot.67:2387-2390. Abstract: Forty samples of fresh produce collected from retail food establishments were examined to determine the occurrence of Escherichia coli, F-specific coliphages, and noroviruses. An additional six samples were collected from a restaurant undergoing investigation for a norovirus outbreak. Nineteen (48%) of the retail samples and all outbreak samples were preprocessed (cut, shredded, chopped, or peeled) at or before the point of purchase. Reverse transcription-PCR, with the use of primers JV 12 and JV 13, failed to detect norovirus RNA in any of the samples. All six outbreak samples and 13 (33%) retail samples were positive for F-specific coliphages (odds ratio undefined, P = 0.003). Processed retail samples appeared more likely to contain F-specific coliphages than unprocessed samples (odds ratio 3.8; 95% confidence interval 0.8 to 20.0). Only two (5.0%) retail samples were positive for E. coli; outbreak samples were not tested for E. coli. The results of this preliminary survey suggest that F-specific coliphages could be useful conservative indicators of fecal contamination of produce and its associated virological risks. Large-scale surveys should be conducted to confirm these findings.

 

Avery, S. M., L. D. Walters, and M. L. Hutchison. 2005. Fate of Escherichia coli O157 and detection of stx phage during fermentation of maize, an animal feedstuff. Lett. Appl. Microbiol. 40:99-105. Abstract: AIMS: The fate of inoculated Escherichia coli O157, stx phages and the physico-chemical properties of maize were studied during laboratory-scale fermentation by naturally occurring lactic acid bacteria. METHODS AND RESULTS: Before fermentation, chopped maize was inoculated with 6.2 log(10) CFU g-1 of a five-isolate mixture of E. coli O157. After fermentation, the silage contained 70.6 g kg-1 dry matter (DM) lactic acid and 12.8 g kg-1 DM acetic acid and was pH 4.0. Levels of E. coli O157 fell rapidly, and none of the five isolates could be recovered from the fermenting maize after 8 days. Using a resuscitation step did not consistently enhance recovery of E. coli O157. Stx phages were not isolated from the fermenting maize at any time. Pulsed-field gel electrophoresis (PFGE) genotyping showed that E. coli O157 2975 and 64a/01 survived better than the other three isolates studied. Escherichia coli O157 isolate 1474/00 was particularly sensitive to the laboratory procedures used to harvest the inocula and contaminate the maize. Some colonies recovered during the fermentation had one to three band alterations compared with the initial PFGE genotypes. SIGNIFICANCE AND IMPACT OF THE STUDY: None of the five different E. coli O157 genotypes survived maize fermentation. Fermentation of maize produces an animal feedstuff that is unlikely to contain E. coli O157 or stx phages.

 

Bailey, S., M. R. J. Clokie, A. Millard, and N. H. Mann. 2004. Cyanophage infection and photoinhibition in marine cyanobacteria. Res. Microbiol. 155:720-725. Abstract: Members of two cyanobacterial genera, Synechococcus and Prochlorococcus, are dominant within the prokaryotic component of the picophytoplankton and contribute significantly to global photosynthetic productivity. These organisms are known to be susceptible to infection by bacteriophages (viruses that infect bacteria) and it is believed that phage infection in the oceans has exerted selective pressures on the evolution of both phage and host and continues to influence community structure. Understanding of the processes of host-phage interaction within the marine environment is limited; however, new insights have arisen from sequence analysis of the genome of the bacteriophage S-PM2, which infects Synechococcus strains. The phage was found to encode homologs of the key photosystem II reaction center core polypeptides, D1 and D2. These reaction center polypeptides are known to be rapidly turned over in uninfected cells in a repair cycle that helps to protect oxygenic phototrophs against photoinhibition. This finding suggests that bacteriophages infecting marine cyanobacteria may play an active role in protecting their hosts against photoinhibition, thereby ensuring an energy supply for replication by preventing the deleterious effects on host cell integrity seen during acute photoinhibition.

 

Balogh, B., Jones, J. B., Momol, M. T., Olson, S. M., Obradovic, A., Jackson, L. E. 2003. Improved Efficacy of Newly Formulated Bacteriophages for Management of Bacterial Spot on Tomato. Plant Disease 87:949-954. Abstract: Bacteriophages are currently used as an alternative method for controlling bacterial spot disease on tomato incited by Xanthomonas campestris pv. vesicatoria. However, the efficacy of phage is greatly reduced due to its short residual activity on plant foliage. Three formulations that significantly increased phage longevity on the plant surface were tested in field and greenhouse trials: (i) PCF, 0.5% pregelatinized corn flour (PCF) + 0.5% sucrose; (ii) Casecrete, 0.5% Casecrete NH-400 + 0.5% sucrose + 0.25% PCF; and (iii) skim milk, 0.75% powdered skim milk + 0.5% sucrose. In greenhouse experiments, the nonformulated, PCF-, Casecrete-, and skim milk- formulated phage mixtures reduced disease severity on plants compared with the control by 1, 30, 51, and 62%, respectively. In three consecutive field trials, nonformulated phage caused 15, 20, and 9% reduction in disease on treated plants compared with untreated control plants, whereas plants treated with PCF- and Casecrete-formulated phage had 27, 32, and 12% and 30, 43, and 24% disease reduction, respectively. Plants receiving copper-mancozeb treatments were included in two field trials and had a 20% decrease in disease in the first trial and a 13% increase in the second one. Skim milk-formulated phage was tested only once and caused an 18% disease reduction. PCF-formulated phage was more effective when applied in the evening than in the morning, reducing disease on plants by 27 and 13%, respectively. The Casecrete formulated phage populations were over 1,000-fold higher than the nonformulated phage populations 36 h after phage application.

 

Blanch, A. R., L. Belanche-Munoz, X. Bonjoch, J. Ebdon, C. Gantzer, F. Lucena, J. Ottoson, C. Kourtis, A. Iversen, I. Kuhn, L. Moce, M. Muniesa, J. Schwartzbrod, S. Skraber, G. Papageorgiou, H. D. Taylor, J. Wallis, and J. Jofre. 2004. Tracking the origin of faecal pollution in surface water: an ongoing project within the European Union research programme. Journal of water and health 2:249-260. Abstract: The objectives of this study are to generate knowledge about methods to track the sources of faecal pollution in surface waters, with the aim of having one or a few easy procedures applicable to different geographic areas in Europe. For this, a first field study using already proposed methods (genotypes of F-specific RNA bacteriophages, bacteriophages infecting Bacteroides fragilis, phenotypes of faecal coliforms and enterococci, and sterols) has been done in five areas representing a wide array of conditions in Europe. The present faecal indicators (faecal coliforms, enterococci, sulfite reducing clostridia and somatic coliphages) have also been included in this first field study. At the same time some emerging methods have been settled or adapted to water samples and assayed in a limited number of samples. The results of this first field study indicate that no single parameter alone is able to discriminate the sources, human or non-human, of faecal pollution, but that a 'basket' of 4 or 5 parameters, which includes one of the present faecal indicators, will do so. In addition, numerical analysis of the data shows that this 'basket' will allow the successful building of predictive models. Both the statistical analyses and the studied predictive models indicate that genotype II of F-specific RNA bacteriophages, the coprostanol and the ratio coprostanol: coprostanol+epicoprostanol are, out of the studied parameters, those with a greater discriminating power. Either because unsuccessful adaptation of the methods to water samples or because the preliminary assays in water samples indicated low discriminating capability, only three (sorbitol-fermenting bifidobacteria, some species of bifidobacteria detected by PCR with specific primers and phages infecting Bacteroides tethaiotaomicron) of the newly assayed methods have been considered for a second field study, which is currently underway. Expectations are that these new tools will minimize the number of parameters in the 'basket', or at least minimize the difficulty in assaying them.

 

Borchardt, M. A., N. L. Haas, and R. J. Hunt. 2004. Vulnerability of drinking-water wells in La Crosse, Wisconsin, to enteric-virus contamination from surface water contributions. Appl. Environ. Microbiol. 70:5937-5946. Abstract: Human enteric viruses can contaminate municipal drinking-water wells, but few studies have examined the routes by which viruses enter these wells. In the present study, the objective was to monitor the municipal wells of La Crosse, Wisconsin, for enteric viruses and determine whether the amount of Mississippi River water infiltrating the wells was related to the frequency of virus detection. From March 2001 to February 2002, one river water site and four wells predicted by hydrogeological modeling to have variable degrees of surface water contributions were sampled monthly for enteric viruses, microbial indicators of sanitary quality, and oxygen and hydrogen isotopes. 18O/16O and 2H/1H ratios were used to determine the level of surface water contributions. All samples were collected prior to chlorination at the wellhead. By reverse transcription-PCR (RT-PCR), 24 of 48 municipal well water samples (50%) were positive for enteric viruses, including enteroviruses, rotavirus, hepatitis A virus (HAV), and noroviruses. Of 12 river water samples, 10 (83%) were virus positive by RT-PCR. Viable enteroviruses were not detected by cell culture in the well samples, although three well samples were positive for culturable HAV. Enteroviruses detected in the wells by RT-PCR were identified as several serotypes of echoviruses and group A and group B coxsackieviruses. None of the well water samples was positive for indicators of sanitary quality, namely male-specific and somatic coliphages, total coliform bacteria, Escherichia coli, and fecal enterococci. Contrary to expectations, viruses were found in all wells regardless of the level of surface water contributions. This result suggests that there were other unidentified sources, in addition to surface water, responsible for the contamination.

 

Bordenstein, S. R. and J. J. Wernegreen. 2004. Bacteriophage Flux in Endosymbionts (Wolbachia): Infection Frequency, Lateral Transfer, and Recombination Rates. Mol. Biol. Evol. 21:1981-1991. Abstract: The highly specialized genomes of bacterial endosymbionts typically lack one of the major contributors of genomic flux in the free-living microbial world-bacteriophages. This study yields three results that show bacteriophages have, to the contrary, been influential in the genome evolution of the most prevalent bacterial endosymbiont of invertebrates, Wolbachia. First, we show that bacteriophage WO is more widespread in Wolbachia than previously recognized, ccurring in at least 89% (35/39) of the sampled genomes. Second, we show through several phylogenetic approaches that bacteriophage WO underwent recent lateral transfers between Wolbachia bacteria that coinfect host cells in the dipteran Drosophila simulans and the hymenopteran Nasonia vitripennis. These two cases, along with a previous report in the lepidopteran Ephestia cautella, support a general mechanism for genetic exchange in endosymbionts-the ''intracellular arena'' hypothesis-in which genetic material moves horizontally between bacteria that coinfect the same intracellular environment. Third, we show recombination in this bacteriophage; in the region encoding a putative capsid protein, the recombination rate is faster than that of any known recombining genes in the endosymbiont genome. The combination of these three lines of genetic evidence indicates that this bacteriophage is a widespread source of genomic instability in the intracellular bacterium Wolbachia and potentially the invertebrate host. More generally, it is the first bacteriophage implicated in frequent lateral transfer between the genomes of bacterial endosymbionts. Gene transfer by bacteriophages could drive significant evolutionary change in the genomes of intracellular bacteria that are typically considered highly stable and prone to genomic degradation.

 

Brion, G. M., N. B. O'Banion, and G. L. Marchin. 2004. Comparison of bacteriophages for use in iodine inactivation: batch and continuous flow studies. Journal of water and health 2:261-266. Abstract: Inactivation rates in batch studies for four commonly used surrogate bacteriophages were measured in stable aqueous iodine solutions for the purpose of determining which was the most suited to evaluate iodine disinfection efficacy in batch and continuous flow conditions. Two types of group Leviviridae bacteriophages were used, Type I (MS2) and Type II (GA), along with group Microviridae, FX174, and group Tectiviridae, PRD1. Inactivation was compared at iodine doses of 1.0-1.5 mg l2/l. MS2 was the most susceptible to iodine inactivation of the four phages tested. Inactivation of naked, icosahedral bacteriophages, MS2 and FX174 demonstrated removals to below detection limits (>99. 99%) in less than 10 min. Lipid-containing PRD1 and F+ssRNA GA bacteriophages demonstrated the greatest iodine resistance in batch experiments with an average of 1.82 logs of inactivation (98.5%) after 60 min and 1.05 logs of inactivation (91.1%) after 30 min respectively. Similarly, in continuous flow studies through pentaiodide quaternary ammonium strong base resin, MS2, GA and FX174 were more strongly inactivated than PRD1. The lipid component of PRD1 is thought to enhance resistance to iodine over non-lipid-containing bacteriophages by protecting easily oxidized groups on the protein capsid, but further research is needed before proving this hypothesis. The results from this research may provide a surrogate standard for more rigorous and developed research into the mode of iodine disinfection and its inactivation kinetics.

 

Canchaya, C., G. Fournous, and H. Brussow. 2004. The impact of prophages on bacterial chromosomes. Mol. Microbiol. 53:9-18. Abstract: Prophages were automatically localized in sequenced bacterial genomes by a simple semantic script leading to the identification of 190 prophages in 115 investigated genomes. The distribution of prophages with respect to presence or absence in a given bacterial species, the location and orientation of the prophages on the replichore was not homogeneous. In bacterial pathogens, prophages are particularly prominent. They frequently encoded virulence genes and were major contributors to the genetic individuality of the strains. However, some commensal and free-living bacteria also showed prominent prophage contributions to the bacterial genomes. Lysogens containing multiple sequence-related prophages can experience rearrangements of the bacterial genome across prophages, leading to prophages with new gene constellations. Transfer RNA genes are the preferred chromosomal integration sites, and a number of prophages also carry tRNA genes. Prophage integration into protein coding sequences can lead to either gene disruption or new proteins. The phage repressor, immunity and lysogenic conversion genes are frequently transcribed from the prophage. The expression of the latter is sometimes integrated into control circuits linking prophages, the lysogenic bacterium and its animal host. Prophages are apparently as easily acquired as they are lost from the bacterial chromosome. Fixation of prophage genes seems to be restricted to those with functions that have been co-opted by the bacterial host.

 

Chibani-Chennoufi, S., J. Sidoti, A. Bruttin, M. L. Dillmann, E. Kutter, F. Qadri, S. A. Sarker, and H. Brnssow. 2004. Isolation of Escherichia coli bacteriophages from the stool of pediatric diarrhea patients in Bangladesh. J. Bacteriol. 186:8287-8294. Abstract: A 3-week coliphage survey was conducted in stool samples from 140 Bangladeshi children hospitalized with severe diarrhea. On the Escherichia coli indicator strain K803, all but one phage isolate had 170-kb genomes and the morphology of T4 phage. In spot tests, the individual T4-like phages infected up to 27 out of 40 diarrhea-associated E. coli, representing 22 O serotypes and various virulence factors; only five of them were not infected by any of these new phages. A combination of diagnostic PCR based on g32 (DNA binding) and g23 (major capsid protein) and Southern hybridization revealed that half were T-even phages sensu strictu, while the other half were pseudo-T-even or even more distantly related T4-like phages that failed to cross-hybridize with T4 or between each other. Nineteen percent of the acute stool samples yielded T4-like phages, and the prevalence was lower in convalescent stool samples. T4-like phages were also isolated from environmental and sewage water, but with low frequency and low titers. On the enteropathogenic E. coli strain O127:K63, 14% of the patients yielded phage, all of which were members of the phage family Siphoviridae with 50-kb genomes, showing the morphology of Jersey- and beta-4 like phages and narrow lytic patterns on E. coli O serotypes. Three siphovirus types could be differentiated by lack of cross-hybridization. Only a few stool samples were positive on both indicator strains. Phages with closely related restriction patterns and, in the case of T4-like phages, identical g23 gene sequences were isolated from different patients, suggesting epidemiological links between the patients.

 

Dabrowska, K., A. Opolski, J. Wietrzyk, K. Switala-Jelen, J. Godlewska, J. Boratynski, D. Syper, B. Weber-Dabrowska, and A. Gorski. 2004. Anticancer activity of bacteriophage T4 and its mutant HAP1 in mouse experimental tumour models. Anticancer research 24:3991-3995. Abstract: BACKGROUND: Previously, we have shown the ability of the bacteriophage T4 and its substrain HAP1 (selected for a higher affinity to melanoma cells) to reveal antimetastatic activity in a mouse melanoma model. Here, we investigated the potential phage anticancer activity in primary tumour models. MATERIALS AND METHODS: Mice were inoculated subcutaneously with B16 or LLC cells (collected from in vitro culture). Bacteriophages T4 and HAP1 were injected intraperitoneally daily (8 x 108pfu/mouse, except the experiment concerning the dose-dependence). RESULTS: Treatment with purified preparations of bacteriophage T4 resulted in significant reduction of tumour size, the effect being dose-dependent. HAP1 was more effective than T4 and its activity was also dose-dependent. Parallel experiments with non-purified bacteriophage lysates resulted in significant stimulation of tumour growth. CONCLUSION: These data suggest that purified bacteriophages may inhibit tumour growth, a phenomenon with potentially important clinical implications in oncology.

 

Danovaro, R., E. Manini, and A. Dell'Anno. 2002. Higher abundance of bacteria than of viruses in deep mediterranean sediments. Appl. Environ. Microbiol. 68:1468-1472. Abstract: The interactions between viral abundance and bacterial density, biomass, and production were investigated along a longitudinal transect consisting of nine deep-sea stations encompassing the entire Mediterranean basin. The numbers of viruses were very low (range, 3.6 x 107 to 12.0 x 107 viruses g-1) and decreased eastward. The virus-to-bacterium ratio was always < 1.0, indicating that the deep-sea sediments of the Mediterranean Sea are the first example of a marine ecosystem not numerically dominated by viruses. The lowest virus numbers were found where the lowest bacterial metabolism and turnover rates and the largest cell size were observed, suggesting that bacterial doubling time might play an important role in benthic virus development.

 

Daubin, V. and H. Ochman. 2004. Start-up entities in the origin of new genes. Cur. Opin. Gen. Devel. 14:616-619. Abstract: The remarkable diversity in the contents of genomes raises questions about how new genes and new functions originate. Recent evidence indicates that parasitism, particularly the molecular interactions between phage and their bacterial hosts, is a likely mechanism for generating new genes. This invention of such novel functions seems to be founded on a strategy that secures the short-term survival of parasitic elements and thereby contributes to the renovation of gene repertoires in their host.

 

Debattista, J. 2004. Phage therapy: where East meets West. Exp. Rev. Anti-Infect. Ther. 2:815-819.

 

Dennehy, P. P. and P. E. Turner. 2004. Reduced fecundity is the cost of cheating in RNA virus f6. Proc. R. oc. Lond. B Biol. Sci. 271:2275-2282. Abstract: Co-infection by multiple viruses affords opportunities for the evolution of cheating strategies to use intracellular resources. Cheating may be costly, however, when viruses infect cells alone. We previously allowed the RNA bacteriophage f6 to evolve for 250 generations in replicated environments allowing coinfection of Pseudomonas phaseolicola bacteria. Derived genotypes showed great capacity to compete during co-infection, but suffered reduced performance in solo infections. Thus, the evolved viruses appear to be cheaters that sacrifice between-host fitness for within-host fitness. It is unknown, however, which stage of the lytic growth cycle is linked to the cost of cheating. Here, we examine the cost through burst assays, where lytic infection can be separated into three discrete phases (analogous to phage life history): dispersal stage, latent period (juvenile stage), and burst (adult stage). We compared growth of a representative cheater and its ancestor in environments where the cost occurs. The cost of cheating was shown to be reduced fecundity, because cheaters feature a significantly smaller burst size (progeny produced per infected cell) when infecting on their own. Interestingly, latent period (average burst time) of the evolved virus was much longer than that of the ancestor, indicating the cost does not follow a life history trade-off between timing of reproduction and lifetime fecundity. Our data suggest that interference competition allows high fitness of derived cheaters in mixed infections, and we discuss preferential encapsidation as one possible mechanism.

 

Fischer, C. R., M. Yoichi, H. Unno, and Y. Tanji. 2005. The coexistence of Escherichia coli serotype O157:H7 and its specific bacteriophage in continuous culture. FEMS Microbiol. Lett. 241:171-177. Abstract: For the development of phage therapy, systematic understanding mechanisms of bacteriophage resistance will be required. We describe a new strain of Escherichia coli O157:H7, named MuL, which stably co-exists with the O157:H7-specific lytic bacteriophage PP01. Chemostat cultures of E. coli O157:H7 infected with PP01 showed unchanging cell concentration, but phage concentrations which increased by 108 PFU mL-1. However, the latent period, burst size, and growth rate of MuL were the same as in a PP01-susceptible strain. The binding rate of PP01 to the cell surface was diminished 8.5-fold in MuL. By observation of the binding of fluorescently labeled O157:H7-specific phage to individual MuL cells, we found that clonal MuL cultures were heterogeneous in their ability to bind bacteriophage. 15% of the MuL population was completely resistant to PP01 infection. MuL also co-existed with bacteriophages unrelated to PP01. Broad-range phage resistance by clonal heterogeneity represents a new class of bacteria-phage interactions.

 

Froissart, R., C. O. Wilke, R. Montville, S. K. Remold, L. Chao, and P. E. Turner. 2004. Co-infection weakens selection against epistatic mutations in RNA viruses. Genetics 168:9-19. Abstract: Co-infection may be beneficial in large populations of viruses because it permits sexual exchange between viruses that is useful in combating the mutational load. This advantage of sex should be especially substantial when mutations interact through negative epistasis. In contrast, co-infection may be detrimental because it allows virus complementation, where inferior genotypes profit from superior virus products available within the cell. The RNA bacteriophage phi6 features a genome divided into three segments. Co-infection by multiple phi6 genotypes produces hybrids containing reassorted mixtures of the parental segments. We imposed a mutational load on phi6 populations by mixing the wild-type virus with three single mutants, each harboring a deleterious mutation on a different one of the three virus segments. We then contrasted the speed at which these epistatic mutations were removed from virus populations in the presence and absence of co-infection. If sex is a stronger force, we predicted that the load should be purged faster in the presence of co-infection. In contrast, if complementation is more important we hypothesized that mutations would be eliminated faster in the absence of co-infection. We found that the load was purged faster in the absence of co-infection, which suggests that the disadvantages of complementation can outweigh the benefits of sex, even in the presence of negative epistasis. We discuss our results in light of virus disease management and the evolutionary advantage of haploidy in biological populations.

 

Gamage, S. D., A. K. Patton, J. F. Hanson, and A. A. Weiss. 2004. Diversity and host range of Shiga toxin-encoding phage. Infect. Immun. 72:7131-7139. Abstract: Shiga toxin 2 (Stx2) from the foodborne pathogen Escherichia coli O157:H7 is encoded on a temperate bacteriophage. Toxin-encoding phages from C600::933W and from six clinical E. coli O157:H7 isolates were characterized for PCR polymorphisms, phage morphology, toxin production, and lytic and lysogenic infection profiles on O157 and non-O157 serotype E. coli. The phages were found to be highly variable, and even phages isolated from strains with identical pulsed-field gel electrophoresis profiles differed. Examination of cross-plaquing and lysogeny profiles further substantiated that each phage is distinct; reciprocal patterns of susceptibility and resistance were not observed and it was not possible to define immunity groups. The interaction between Shiga toxin-encoding phage and intestinal E. coli was examined. Lytic infection was assessed by examining Shiga toxin production following overnight incubation with phage. While not common, lytic infection was observed, with a more-than-1,000-fold increase in Stx2 seen in one case, demonstrating that commensal E. coli cells can amplify Shiga toxin if they are susceptible to infection by the Shiga toxin-encoding phages. Antibiotic-resistant derivatives of the Stx2-encoding phages were used to examine lysogeny. Different phages were found to lysogenize different strains of intestinal E. coli. Lysogeny was found to occur more commonly than lytic infection. The presence of a diverse population of Shiga toxin-encoding phages may increase the pathogenic fitness of E. coli O157:H7

 

Glud, R. N. and M. Middelboe. 2004. Virus and bacteria dynamics of a coastal sediment: Implication for benthic carbon cycling. Limnol. Oceanogr. 49:2073-2081. Abstract: We measured microbial heterotrophic activity, bacteria, and virus-like particle (VLP) abundance in homogenized, undiluted, and anoxic enclosures of sediment collected at a coastal station. The bacterial growth rate and VLP net production increased along with the respiratory activity in response to temperature. This suggests that VLPs represent a dynamic component of benthic microbial communities and that the net production of viriobenthos is regulated by the metabolic activity of bacteria. The abundance, net production, and decay rate of VLPs were significantly higher than those encountered in most pelagic systems. However, the rates were lower than the very few available potential rates (three studies) of viriobenthic activity, which all were obtained applying different slurry approaches. Our measurements support the general observation that virus abundance and production correlate with the trophic status of the environment and show that microbial activity can regulate the viriobenthic production in undiluted, homogenized marine sediments. The virus-induced bacterial mortality corresponded to similar to 20% of bacterial net production and similar to 2% h-1 of the total bacterial population. This is moderate compared with the results of most pelagic studies, and the associated leakage of lysates (dissolved organic carbon) only amounted to 4-8% of the produced dissolved inorganic carbon. Despite high standing stocks and relatively high turnover rates, VLP-induced bacterial lysis represented only a minor shunt in the benthic carbon cycle at the investigated site.

 

Goh, S., B. J. Chang, and T. V. Riley. 2005. Effect of phage infection on toxin production by Clostridium difficile. J. Med. Microbiol. 54:129-135. Abstract: Infection with Clostridium difficile and subsequent production of toxins A and B may result in C. difficile-associated diarrhoea and pseudomembranous colitis in hospital patients. The effect of four temperate phages, obtained by induction of clinical C. difficile isolates, on toxin production by C. difficile was determined. None of these phages converted a lysogenized non-toxigenic C. difficile strain to toxin production. One of the accessory toxin genes, tcdE, was detected in three phages, fC2, fC6 and fC8; however, the non-repeating regions of tcdA and tcdB encoding the enzymic domains were not carried on phage DNA. Phage infection of toxigenic strains increased toxin B production in four of six lysogens, although the level of tcdB transcription as determined by real-time RT-PCR was not significantly altered. However, levels of toxin A transcription in two lysogens were significantly altered without any corresponding differences in toxin A production.

 

Goodridge, L. D. 2004. Bacteriophage biocontrol of plant pathogens: fact or fiction? Trends in Biotechnology 22:384-385. Abstract: Bacterial resistance due to the misuse of antibiotics has become a global issue and alternative methods are being developed that might decrease the use of antimicrobials in agricultural settings. Bacteriophage therapy represents a novel way to control the growth of plant-based bacterial pathogens. Although this method shows promise, a recent paper by Gill and Abedon has shown that the complex bacteriophage-host interactions in the plant environment must be investigated further.

 

Gorski, A. and B. Weber-Dabrowska. 2005. The potential role of endogenous bacteriophages in controlling invading pathogens. Cell Mol. Life Sci. 62:511-519. Abstract: Bacteriophages (phages) are omnipresent in our environment, and recent studies highlight their potential impact on the microbial world. Phages can also be present in mammalian organisms, including man (intestines, oral cavity, urine, sputum and serum). Data are available which suggest that those endogenous phages could play an important role in eliminating bacteria and regulating the body ecosystem. Furthermore, our most recent findings suggest that phages can exert immunosuppressive action in the gut, helping control local inflammatory and autoimmune reactions, and demonstrate anticancer activity. We hypothesize that phages could act in concert with the immune system in immunosurveillance against bacteria, viruses and cancer.

 

Griffith, J. F., S. B. Weisberg, and C. D. McGee. 2003. Evaluation of microbial source tracking methods using mixed fecal sources in aqueous test samples. Journal of water and health 1:141-151. Abstract: Microbiological source tracking (MST) methods are increasingly being used to identify fecal contamination sources in surface waters, but these methods have been subjected to limited comparative testing. In this study, 22 researchers employing 12 different methods were provided sets of identically prepared blind water samples. Each sample contained one to three of five possible fecal sources (human, dog, cattle, seagull or sewage). Researchers were also provided with portions of the fecal material used to inoculate the blind water samples for use as library material. No MST method that was tested predicted the source material in the blind samples perfectly. Host-specific PCR performed best at differentiating between human and non-human sources, but primers are not yet available for differentiating between all of the non-human sources. Virus and F+ coliphage methods reliably identified sewage, but were unable to identify fecal contamination from individual humans. Library-based isolate methods correctly identified the dominant source in most samples, but also had frequent false positives in which fecal sources not in the samples were incorrectly identified as being present. Among the library-based methods, genotypic methods generally performed better than phenotypic methods.

 

Hagens, S., A. Habel, U. von Ahsen, A. von Gabain, and U. BlSsi. 2004. Therapy of experimental pseudomonas infections with a nonreplicating genetically modified phage. Antimicrob. Agents Chemother. 48:3817-3822. Abstract: Bacteriophage therapy of bacterial infections has received renewed attention owing to the increasing prevalence of antibiotic-resistant pathogens. A side effect of many antibiotics as well as of phage therapy with lytic phage is the release of cell wall components, e.g., endotoxins of gram-negative bacteria, which mediate the general pathological aspects of septicemia. Here we explored an alternative strategy by using genetically engineered nonreplicating, nonlytic phage to combat an experimental Pseudomonas aeruginosa infection. An export protein gene of the P. aeruginosa filamentous phage Pf3 was replaced with a restriction endonuclease gene. This rendered the Pf3 variant (Pf3R) nonreplicative and concomitantly prevented the release of the therapeutic agent from the target cell. The Pf3R phage efficiently killed a wild-type host in vitro, while endotoxin release was kept to a minimum. Treatment of P. aeruginosa infections of mice with Pf3R or with a replicating lytic phage resulted in comparable survival rates upon challenge with a minimal lethal dose of 3. However, the survival rate after phage therapy with Pf3R was significantly higher than that with the lytic phage upon challenge with a minimal lethal dose of 5. This higher survival rate correlated with a reduced inflammatory response elicited by Pf3R treatment relative to that with the lytic phage. Therefore, this study suggests that the increased survival rate of Pf3R-treated mice could result from reduced endotoxin release. Thus, the use of a nonreplicating modified phage for the delivery of genes encoding proteins toxic to bacterial pathogens may open up a new avenue in antimicrobial therapy.

 

Herold, S., H. Karch, and H. Schmidt. 2004. Shiga toxin-encoding bacteriophages—genomes in motion. Int. J. Med. Microbiol. 294:115-121. Abstract: Shiga toxins (Stx) represent a group of bacterial toxins that are involved in human and animal disease. Stx are mainly produced by Escherichia coli isolated from human and non-human sources, Shigella dysenteriae type 1, and sporadically, by Citrobacter freundii, Enterobacter cloacae and Shigella flexneri. The genes encoding Stx are encoded in the genome of heterogeneous lambdoid prophages (Stx-converting bacteriophages; Stx-phages). They are located in a similar position in the late region of the prophage genome and stx is under control of phage genes. Therefore, induction of Stx-converting prophages triggers increased production of Stx. Following induction, Stx-phages can infect other bacteria in vivo and in vitro. Stx-phages may be considered to represent highly mobile genetic elements that play an important role in the expression of Stx, in horizontal gene transfer, and hence in genome diversification.

 

Hewson, I. and J. A. Fuhrman. 2003. Viriobenthos production and virioplankton sorptive scavenging. Microb. Ecol. 46:337-347. Abstract: Virus production in oxic surface sediments and virioplankton sorption to suspended particles was estimated across three stations in the Southern California region (33. 4ÝN, 118.6ÝW). Viriobenthos production was estimated using a sterile sediment and filtered porewater dilution technique that targeted production from both attached bacteria and bacteria living free in the porewater, and attached bacteria alone. Potential virus production rates by bacteria free in the porewater ranged from 1.7 to 4.6 x 108 VLP cm-3 h-1, while attached bacteria had slower potential production rates of between 0. 4 and 1.1 x 108 VLP cm-3 h-1, suggesting turnover rates of viruses in sediments (1-5 h) which are significantly higher than those of virioplankton (similar to24-48 h). Virioplankton adsorbed to small (<150 mum) suspended sediments at stations with high ambient suspended solid concentrations. Virioplankton scavenging rates combined with published sedimentation rates demonstrate that this mechanism of virus arrival could only account for 0.01% of daily benthic virus production. Calculated mortality rates of benthic bacteria (4-14% h-1) suggest viruses may play an important role in sediment carbon cycling.

 

Hewson, I., G. A. Vargo, and J. A. Fuhrman. 2003. Bacterial diversity in shallow oligotrophic marine benthos and overlying waters: Effects of virus infection, containment, and nutrient enrichment. Microb. Ecol. 46:322-336. Abstract: Little is known of the factors shaping sediment bacterial communities, despite their high abundance and reports of high diversity. Two factors hypothesized to shape bacterial communities in the water column are nutrient (resource) availability and virus infection. The role these factors play in benthic bacterial diversity was assessed in oligotrophic carbonate-based sediments of Florida Bay (USA). Sediment-water mesocosm enclosures were made from 1-m diameter clear polycarbonate cylinders which were pushed into sediments to 201 cm sediment depth enclosing similar to 80 L of water. Mesocosms were amended each day for 14 d with 10 muM NH4+ and 1 muM PO43-. In a second experiment, viruses from a benthic flocculent layer were concentrated and added back to flocculent layer samples which were collected near the mesocosm enclosures. Photosynthesis by microalgae in virus-amended incubations was monitored by pulse-amplitude modulated (PAM) fluorescence. In both experiments, bacterial diversity was estimated using automated rRNA intergenic spacer analysis (ARISA), a high-resolution fingerprinting approach. Initial sediment bacterial operational taxonomic unit (OTU) richness (236 +/- 3) was higher than in the water column (148 +/- 9), where an OTU was detectable when its amplified DNA represented >0.09% of the total amplified DNA. Effects on bacterial diversity and operational taxonomic unit (OTU) richness in nutrient-amended mesocosms may have been masked by the effects of containment, which stimulated OTU richness in the water column, but depressed OTU richness and diversity in sediments. Nutrient addition significantly elevated virus abundance and the ratio of viruses to bacteria (p < 0.05 for both) in the sediments, concomitant with elevated bacterial diversity. However, water column bacterial diversity (in unamended controls) was not affected by nutrient amendments, which may be due to rapid nutrient uptake by sediment organisms or adsorption of P to carbonate sediments. Addition of live viruses to benthic flocculent layer samples increased bacterial OTU diversity and richness compared with heat-killed controls; however, cluster analyses showed that the community structure in the viru