Uncovering novel phage defense systems through genomic island analysis in Streptococcus thermophilus
Year: 2026
Type: preprint
Abstract: Bacteria encode diverse antiviral defense systems, yet the evolutionary reservoirs that generate this immune innovation remain poorly defined. Although genomic context has been instrumental in discovering defense systems, genomic islands (GIs), variable chromosomal regions enriched in defense genes and proteins of unknown function, have not been systematically explored as sources of new bacterial immunity. Here, using comparative genomics of Streptococcus thermophilus, we identified 30 defense-associated GIs displaying extensive accessory gene diversity. Investigation of candidate loci from three GIs uncovered 15 previously uncharacterized antiviral systems, including 10 with novel architectures or features, revealing the potential within even a small subset of GIs. Several systems were not located near known defense genes, highlighting that GI-based discovery complements the traditional guilt-by-association approach, revealing systems that would otherwise remain undetected. Together, our findings establish GIs as reservoirs of antiviral innovation and provide a framework for uncovering the diversity of bacterial immune systems.
Institution: Université Laval
Language: English
Subfield: Virology
Field: Immunology and Microbiology
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W7220472893