It's not every day we get to see an arms race in action. Every gory detail is laid out by Paez-Espino et al in the March/April issue of mBio*. The authors use deep DNA sequencing to track CRISPR acquisition in the bacterium Streptococcus thermophilus when challenged with Streptococcus phage 2972 (a phage featured in Life in Our Phage World). 

As S. thermophilus evolved in the presence of 2972, its CRISPR loci acquired new spacers employed to recognize future invasions of 2972 phage DNA, thereby foiling future attacks by that phage. At least 160,000 spacer acquisitions were observed in the three experiments that each lasted 250 days. The bacteria didn't waste any time, but they did make mistakes. On average 0.02% of spacer acquisitions did not match phage DNA, they matched host DNA. A costly mistake, as that hapless host would recognize its own DNA as foreign and chop it up. Instant death. 

The phage had its own strategy for escaping the host's recognition of its DNA: mutation. The phage's mutation rate was on the order of ~10^-6 per nucleotide per host generation, roughly 1000-fold higher than the mutation rate in the host. These mutations were clustered in the genomic regions that matched spacers acquired in the host, enabling the phage to briefly get one step ahead of the host. But once again, the host would counter with another spacer acquisition, and boom, no more invading phage. 

At this point it looked like the host might win. In one experiment the phage was undetectable by day 35. In the other two experiments, the phage survived longer, over 200 days. Extended survival may have been possible with a little help from a phage friend, Streptococcus phage 2766. Although this phage was not intentionally included in the experiment, it "migrated" into the cultures and offered genomic fragments to 2972, saving its life and promoting escape from the host's CRISPR recognition system. 

Phages, too, get by with a little help from their phriends. 

*disclaimer: I take full responsibility for any conclusions in this post that are over the top.