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CRISPR-Cas (clustered regularly interspaced short palindromic repeats—CRISPR-associated proteins) systems are adaptive immune systems commonly found in prokaryotes that provide sequence-specific defense against invading mobile genetic elements (MGEs). The memory of these immunological encounters are stored in CRISPR arrays, where spacer sequences record the identity and history of past invaders. Analyzing such CRISPR arrays provide insights into the dynamics of CRISPR-Cas systems and the adaptation of their host bacteria to rapidly changing environments such as the human gut.

In this study, we utilized 601 publicly availableBacteroides fragilisgenome isolates from 12 healthy individuals, 6 of which include longitudinal observations, and 222 availableB. fragilisreference genomes to update the understanding ofB. fragilisCRISPR-Cas dynamics and their differential activities. Analysis of longitudinal genomic data showed that some CRISPR array structures remained relatively stable over time whereas others involved radical spacer acquisition during some periods, and diverse CRISPR arrays (associated with multiple isolates) co-existed in the same individuals with some persisted over time. Furthermore, features of CRISPR adaptation, evolution, and microdynamics were highlighted through an analysis of host-MGE network, such as modules of multiple MGEs and hosts, reflecting complex interactions betweenB. fragilisand its invaders mediated through the CRISPR-Cas systems.

We made available of all annotated CRISPR-Cas systems and their target MGEs, and their interaction network as a web resource athttps://omics.informatics.indiana.edu/CRISPRone/Bfragilis. We anticipate it will become an important resource for studying ofB. fragilis, its CRISPR-Cas systems, and its interaction with mobile genetic elements providing insights into evolutionary dynamics that may shape the species virulence and lead to its pathogenicity.