Organisms evolve in concert with a system of competitors, co-operators, predators and parasites. In the microbial world, these pressures have led to useful chemistries such as fermentation; the concomitant ingestion of carbon and excretion of acids or alcohol. Large-scale fermentation operations, such as cheese production, remain susceptible to parasites like bacteriophages. These tiny bacterium-specific viruses are brought in with raw materials and can evolve rapidly. Bacteriophage infection is the single most costly issue facing modern large-scale dairy production nationally and internationally.
Today, complete genome sequencing allows us not only to obtain a complete list of all of the genes that a bacterium has but through comparison at different time points we can identify changes that have allowed it to survive. This powerful genomic insight has yet to be applied to the fermentative bacteria used in the New Zealand dairy industry. At Fonterra microbiologists have maintained a repository of dairy fermenting bacteria and the bacteriophage parasites that have infected them for over 80 years. This collection is a rich resource of genetic material on both sides of the co-evolutionary battle between bacteria and their parasites, the bacteriophages. By investing in genomic sequencing of two bacterial strains and five bacteriophages that they have evolved resistance against we can gain unprecedented insight into two important questions:
1) How do dairy bacteria evolve resistance to the bacteriophages they encounter?
2) How do dairy bacteriophages overcome the resistance mechanisms of bacteria?