It is also not entirely clear how to reconcile phage–bacteria
infection–resistance interactions through the CRISPR system with
the apparent abundance of lysogenic phages in the gut, which this
study also supports. This suggests there may be some form of
protection of the bacterial genome (harboring the prophage) from
the CRISPR system (Stern et al. 2010). A recent study (Edgar and
Qimron 2010) has shown that acquisition of spacers against a lysogenized
phage can lead to bacterial cell death but may also prevent
prophage induction and subsequent cell lysis to the benefit of
bacteria under certain circumstances. Spacers against a phage not
yet integrated were shown to prevent lysogenization (Edgar and
Qimron 2010). This study and our findings suggest the CRISPR
system may have important roles in regulating phage–bacteria
interactions even when they are not primarily lytic.