Bacteriophages

Discovery of phages In 1896, Ernest Hanbury Hankin discovered large differences in the concentration of cholera bacteria at different points of the Ganges river Following filtration, the water was still capable of killing cholera bacteria People bathing in the Ganges River at Calcutta

Discovery of phages French-Canadian microbiologist Félix d'Hérelle was working in Paris during WWI Discovered "an invisible, antagonistic microbe of the dysentery bacillus". Filtered culture was able to kill dysentery-causing bacteria He also recorded a dramatic account of a man suffering from dysentery that the bacteriophages cured.

History of phages First complete genome sequence was fX174 genome (Sanger et al., Nature 1977) First complete shotgun genome sequence was lambda phage (Sanger et al. J. Mol. Biol. 1982) Courtesy of nlm.gov

Phages Bacteriophages are viruses of bacteria Phages are specific to particular bacterial hosts Estimated 1031 bacteriophages on Earth Population is extremely dynamic: 1025 infections/sec Phages are the largest reservoir of unexplored genetic information 5

Do phage cause human disease? Only one good example: Shiga toxin (Stx2) is a gene present in a phage which infects Escherichia coli O157:H7. The toxin leads to disease in humans. More often they are beneficial: http://discovermagazine.com/2014/march/9-bacteria-killing-phages-could-be-an-alternative-to-antibiotics http://www.nature.com/news/phage-therapy-gets-revitalized-1.15348

What do phages do? 7

What about the phages we’re working with? Infect M. smegmatis bacteria a fast-growing (~3hr doubling time) bacteria not a pathogen, but rather a soil bacterium Phage can be isolated from soil, compost etc. Look for plaque formers on lawns of M. smegmatis bacteria Safety- - must not be immunosuppressed, talk to me if you have concerns No food in lab Wash hands, clean spills

Mycobacteriophages ~250 of them have completely sequenced genomes Average genome size: ~72kbp Average number of genes: 88/genome High genetic diversity Most genes of unknown function

How can we learn more about phages? Single nucleotide changes Small insertions and deletions Deletions of whole genes Rearranging gene order Combining different phages together Codon optimization Maximal difference in codons