Horvath and his team provided key details of the extremely complex mechanisms involved in CRISPR's function as an immune system for bacteria against bacteriophages. Analogous to Pasteur's heroic role in saving the French wine industry 150 years earlier, Drs. Horvath and Barrangou were called upon by a high-tech food company that was using the bacterium Streptococcus thermophilus in the production of yogurt, mozzarella cheese and other dairy products, commandeering a mine of Strep cultures worth more than 40 billion dollars. This collection of cultures was under attack from bacteriophages, and at eminent risk from being wiped out.

To solve this problem Horvath and colleagues explored sections in the bacterial genome with clustered regularly interspaced short palindromic repeats (CRISPR). The CRISPR system in the strep had highly variable 'space' sequences that would vary in between different strep strains. The researchers obtained two of the principal attacking bacteriophages and mixed them with the strep in test tubes. They found that although the highly efficient killing bacteriophage machines killed about 99.9% of the bacteria, evolution intervened and created a few rare spontaneous mutant strains that were immune to phage attack. They then looked closely at the CRISPR sequences in the immune mutants, and found that they differed from the killed bacterial strains. Those bacterial sequences had acquired new snipets of DNA spliced between the CRISPR repeats, and now matched genome sections of the DNA of the killer phages, thus binding to the phage nucleic acid, and inactivating it using an inherent nuclease cutting tool that could remove a predetermined nucleic acid sequence. This tool, embedded into the CRISPR system is called the "Cas" /Cas9 system. Furthermore, since these "new" sequences were in the bacterial DNA they were being passed on automatically in a genetic manner to following generations.

(Thanks to Juan Weiss for this reference and its interpretation.)