CRISPRs for strain tracking and its application to microbiota transplantation data analysis

CRISPR-Cas systems are adaptive immune systems naturally found in bacteria and archaea. Bacteria and archaea use these systems to defend against invaders, including phages, plasmids and other mobile genetic elements. Relying on integration of invader sequences (protospacers) into CRISPR loci (forming spacers flanked by repeats), CRISPR-Cas systems store genetic memory of past invasions. While CRISPR-Cas systems have evolved in response to invading mobile elements, invaders have also developed mechanisms to avoid detection. As a result of arms-race between CRISPR-Cas systems and their targets, the CRISPR arrays typically undergo rapid turnover of the spacers with removal of old spacers and acquisition of new ones. Additionally, different individuals rarely share spacers amongst their microbiome. In this paper, we developed a pipeline (called CRISPRtrack) for strain tracking based on CRISPR spacer content, and applied it to fecal transplantation microbiome data to study the retention of donor strains in recipients. Our results demonstrate the potential use of CRISPRs as a simple yet effective tool for donor strain tracking in fecal transplantation, and also as a general purpose tool for quantifying microbiome similarity.