Bacteriophage Discovery and Genomics

Bacteriophage particles are the majority of all biological entities in the biosphere.  In addition to being vast, the phage population is both dynamic and old.  Not surprisingly, phages are also highly diverse genetically, and we are interested in defining this diversity and exploring the evolutionary mechanisms that generate it.  We have focused on the comparative genomic analysis of phages that infect the host Mycobacterium smegmatis mc(2)155, and over 850 complete genome sequences are available (as of July 2015).

The Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science

The large collection of mycobacteriophages and their sequenced genomes was established by the Phage Hunters Integrating Research and Education (PHIRE) program at the University of Pittsburgh, and the Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Sciences (SEA-PHAGES) program.  Both use a phage discovery and genomics platform, with PHIRE being local to the Hatfull lab, and  SEA-PHAGES as a broadly implemented program that includes almost 100 institutions and over 2,600 undergraduates - primarily first year students – involved each year. More information on the phages is available at and on the SEA-PHAGES program at and at      

A phage toolbox for tuberculosis genetics

Bacteriophages are wonderful toolboxes developing clinical and genetic tools.  A subset of the phages isolated on M. smegmatis also infect Mycobacterium tuberculosis and these can be used for efficient delivery of transposons, reporter genes, and allelic exchange substrates.  Numerous genetic modules can also be exploited for mycobacterial genetics, including integration-proficient vectors, non-antibiotic selectable markers, and recombineering systems. 

Site-specific recombination

Bacteriophage integration provides numerous examples of different types of site-specific recombination systems using both tyrosine- and serine-integrases.  We have studied both at the mechanistic level with a primary focus on the control of directionality, as well as developing integration-proficient vectors for tuberculosis genetics.