The oldest spacers (spacers found at the trailer end) are conserved for at least 5 years, and 12% of these retain perfect or near-perfect matches to proto-spacer targets.

The majority of proto-spacer regions contain an AAG proto-spacer adjacent motif (PAM).

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The biology of natural ecosystems is shaped by interactions between microorganisms and their phage (Chibani-Chennoufi et al., 2004).

However, cultivation has usually been required to determine phage host range and to study the interaction dynamics (Hyman and Abedon, 2010).

Second, assuming that hosts only incorporate spacer sequences from phage that infect them, CRISPR spacer sequences can be used to define the host range (Andersson and Banfield, 2008).

Metagenomic datasets are a powerful way to approach these tasks because they simultaneously sample host CRISPR loci and the mobile elements they target.

When applied to time series samples, these methods may also be able to constrain the rates of evolutionary processes (Denef and Banfield, 2012).

Many bacterial and archaeal genomes encode one or more CRISPR loci, named for the clustered regularly interspaced short palindromic repeats that separate spacer sequences that are transcribed and processed into small interfering RNAs (cr RNAs) to confer immunity to phage, plasmids and transposons (reviewed extensively in Horvath and Barrangou, 2010; Sorek et al., 2013; Barrangou and Marraffini, 2014; van der Oost et al., 2014; Westra et al., 2014).

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Bacterial CRISPR-Cas systems provide insight into recent population history because they rapidly incorporate, in a unidirectional manner, short fragments (spacers) from coexisting infective virus populations into host chromosomes.

However, studies in a certain type of CRISPR-Cas system have shown that mutations in the proto-spacer, nearest the PAM, allows the phage to escape, whereas mutations in other regions of the proto-spacer have no impact on immunity (Deveau et al., 2008; Semenova et al., 2011; Wiedenheft et al., 2011; Sun et al., 2012).

An important challenge in ecological studies is to detect and recover genome sequences from uncultivated phage and to link phage to their hosts.

Importantly, the spacer complements of loci from coexisting individuals can be compared in a position-specific way to provide insight into population history.