Rapid loss of CRISPR-mediated herd immunity from bacterial populations
CRISPR-Cas is a prokaryotic defence system against phages and mobile genetic elements. Although substantial research has focused on the mechanism of CRISPR function, much less is understood about the evolutionary ecology of this defence system. For example, the distribution of CRISPR across the bacterial phylogeny is patchy, suggesting environmental drivers may play an important role in the maintenance or loss of such defence systems. We use experimental evolution and genomic analyses to explore the effect of ecological factors on CRISPR evolution. We then use amplicon sequencing to track the frequencies of thousands of bacterial genotypes under varying infection regimes.
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