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<p>Bacteriophages are highly diverse and infect essentially all microbes on earth. Their genomes encode products that have been useful for biotechnology applications including food safety diagnostics, antibiotic resistant strain therapeutics, DNA delivery vehicles, strain construction and many more relevant technologies. This project addresses the biology and biotechnological applications of bacteriophages, starting from total genome sequence to specific gene function, process and application. The major goals of this project are: </p>
<p>1) isolation and genomic sequencing of new bacteriophages infecting Mycobacterium spp. (soil hydrocarbon bioremediation bacteria), Aeromonas spp. (opportunistic fish pathogen), Paenibacillus larvae (honeybee pathogen), Salmonella spp., Xanthomonas spp. (plant pathogen) and others; </p>
<p>2) annotation of sequenced genomes for accurate gene prediction and function; </p>
<p>3) confirmation of encoded gene product function through expression analysis, RNA or protein studies, and enzyme activity assays; and </p>
<p>4) derivation of biotechnologically relevant applications from phage genomes for food safety, environmental, plant and animal health issues.</p>
<p>NON-TECHNICAL SUMMARY:<br/> Bacteriophages (viruses that infect bacteria) are the most abundant life form on earth, infecting every type of bacterium in every known environment. These phages, due to their ability to infect one cell and then infect another cell, play an important role in moving genes from one bacterium to another and in maintaining population numbers of bacteria. Study of bacteriophages provides insights to genome evolution, bacterial adaptation to new conditions, how DNA is expressed and copied, and potentially provides new biotechnology products. Phage products can be used in food safety for diagnostics and therapeutics, in plant and animal gene transfer methods, and in developing anti-bacterial reagents against infectious bacteria, to name a few. Because of the vast number of bacteriophages extant, and the even larger number of unexplored genes that they
carry, additional research is needed to fully understand and benefit from the biology and biotechnology of phages. The methods and approaches used, that of DNA sequencing, bioinformatics analysis, and gene function study, are procedures used in contemporary genomics research and to train the next generation of scientists, educators and industry employees. Some of the bacteria targeted for study with bacteriophage genomics include Mycobacterium (useful for environmental bioremediation), Aeromonas (a fish pathogen impacting aquaculture), Xanthomonas (a pathogen of fruit trees), and Salmonella (a pathogen found in poultry products). Phages infect all of these organisms of agricultural importance and study of their biology and biotechnologically useful gene products have the potential to improve food safety and agricultural yields.
<p>APPROACH:<br/> Efforts on the project focus on phage isolation, DNA purification, genomic sequencing, genome annotation using bioinformatics tools, and experimental laboratory work to confirm the function and activities of discovered gene products. Phage-host interactions are studied to derive new biological insights and potential new applications. Phages and their genomic DNA are isolated by relatively standard methods, although different host systems require different media, growth conditions, etc. Genome sequencing is now conducted by a few different "next generation sequencing" procedures, with each NGS approach requiring its own reagent set. Bioinformatics uses commercial or online web processing tools. Students and researchers in the lab and in the classroom learn these approaches to become prepared scientists for research careers, educators or industry employees.
Evaluation of the project is through a variety of means: 1) publication of peer-reviewed manuscripts in international journals; 2) comparative genomics of phage sequences, relative to other work and genomes in the public database (i.e., Genbank); 3) efficacy of cloned gene products as anti-bacterial or other potential application in biotechnology; and 4) performance of students in classroom assessments and / or quality of scientific presentations at regional and international meetings. Therefore, essential milestones include publication of results, scientific meeting presentations, and advancement of potential new technology. The intended audiences are the scientific community, classroom peers and technology transfer professionals at the university and in the commercial sector.