Stern et al. use a tailored algorithm to exploit the presence of the bacterial CRISPR (clustered regularly interspaced short palindromic repeat) immune system to detect bacteriophages that prey on human gut bacteria. The CRISPR system integrates fragments of incoming viral or plasmid DNA into the bacterial genome to form CRISPR loci (barcodes of mobile elements that have infected a bacterium), then packages transcribed CRISPR mRNA sequences into a protein complex that patrols the cell and degrades incoming matching foreign DNA. Stern et al. extract CRISPR barcodes from the MetaHIT data set (>500 million bp of microbiome genes from 124 people) and use these barcodes to pull out almost 1,000 phage genomes from MetaHIT contigs. By scanning several human gut microbiome data sets, they show that almost 80% of these phages are shared by individuals around the world. They also used the CRISPR sequences to match gut phages to the bacterial species they infect, based on the presence of CRISPR barcodes in individually sequenced human gut bacteria. Finally, they identify individuals with high and low phage abundance. Although we cannot yet link phage-mediated modulation of gut microbiota composition to health or disease, this analysis is a step in the right direction. (Genome Res. advance online publication, doi:10.1101/gr.138297.112, 25 June 2012)