Our findings also imply that CRISPR spacers are actively acquired
in response to phages in the human gut. First, the large
number of unique phage-matching spacers we detected is suggestive
of the numerous events in which such interactions have occurred.
Second, we have identified cases in which the most recently
acquired spacers in the rapidly evolving CRISPR array
perfectly match a phage co-occurring in the same gut, at apparently
depressed levels (e.g., Fig. 3), as well as absolutely no conservation
of the most recently acquired spacer in a particular array
across individuals (Supplemental Table S3). Finally, our data suggest
that CRISPR spacers usually successfully exclude targeted
phages, while showing positive correlation of highly matching
spacers (thus also likely to be recently acquired) with targeted
phages about to be completely excluded. Combined, this evidence
suggests that there is an ongoing ‘‘immune’’ interaction between
phages and their bacterial hosts within the gut microbial community,
whose potential effect remains to be fully characterized. It
is possible that the rapid nature of this dynamic is what has made it
so difficult to capture in previous studies. Notably, although the
typical ecological manifestations of predatory interactions were
observed in numerous niches, past studies did not report on such
dynamics in the gut, and this study was not suited to examine it
directly due to the lack of time-series data.