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Updated: Jan 8, 2026

Phage-Mediated Genetic Manipulation of the Lyme Disease Spirochete Borrelia burgdorferi
Published on: September 28, 2022
Prophage border curation reveals horizontal transfer of lysogeny-related elements between filamentous and double
1College of Civil and Transportation Engineering, Shenzhen University, Shenzhen, China. ruijiema92@gmail.com.
Abstract:
While tailed bacteriophages dominate contemporary models of phage biology, non-tailed phages-particularly filamentous inoviruses and double jelly-roll (DJR) capsid phages-remain poorly understood, despite their environmental ubiquity and ecological importance. Here, we identify 515 inoviruses and 258 DJR prophages from 688 Vibrio spp. genomes and precisely annotate prophage-bacterium junctions. This curated dataset enables us to systematically classify genomic variations and characterize lysogeny-related elements for each prophage subtype. We discover a conserved lysogeny module shared by specific inoviral and DJR subtypes, which represents an evolutionary strategy where phylogenetically distinct phages use horizontal gene transfer to co-opt host mechanisms for integration. Comparative genomics reveal that phage-encoded hypervariable regions (pHVRs) are hotspots for weaponized genetic innovation, such as anti-phage systems and virulence factors. The significantly higher prevalence of pHVR-encoding prophages compared to their pHVR-deficient counterparts across Vibrio species indicates that acquiring these adaptive genes promotes prophage persistence through mutualistic fitness benefits. Because these non-tailed elements frequently form tandem arrays and existing tools struggle with their accurate characterization, we establish a refined methodology to enhance predictive accuracy.
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