Phages, the most prevalent bacterial predators, represent a great challenge in fermented food industry such as cheese production. Using various CRISPR detection tools, we analysed the diversity of the different CRISPR components in selected bacterial assemblies and various cheese metagenomes. Phage defence mechanisms and CRISPR-Cas systems in particular, are highly diverse in cheese related bacteria. CRISPR spacers are clearly strain specific however, we currently only explain a small fraction of the spacers and protospacer diversity observed in the microbial communities of cheese. Active spacers, the ones with a matching protospacer in the sample, show a Piggyback-The-Winner distribution, predicting that phages integrate their hosts genomes as prophages when microbial abundance and growth rate are high. The understanding of the CRISPR systems extent and temporal scale is an important factor for stable and efficient microbial communities in cheese making.