Cryptic Prophages: The Gift that Keeps on Giving

Ben Caulfield

Program: Master’s Program in Bioinformatics and Medical Informatics
Date: Wednesday, June 10, 2026
Time: 1:00pm
Location: Life Sciences North (LSN)
Zoom: https://sdsu.zoom.us/j/81220181089

Abstract

Bacteriophages, or phages, are viruses that infect bacteria. Many phages are temperate, meaning they regulate their lifestyle in response to environmental and physiological conditions. Temperate phages can either begin producing new phage particles shortly after infecting a bacterial host, or they postpone virion production and enter lysogeny. During lysogeny, the phage genome is maintained within the host, often by integrating into the bacterial chromosome as a prophage. Once integrated, prophages replicate as part of the host chromosome and may remain there indefinitely unless environmental signals, such as DNA damage or starvation, induce the prophage to return to the lytic cycle. Integrated prophages can benefit their bacterial hosts by protecting them from infection by related phages and by encoding gene products that improve survival under adverse conditions, e.g. by contributing to resistance against host-associated stresses such as reactive oxygen or nitrogen species produced during infection of animals.

However, prophages also create an endogenous danger for the lysogen, killing it if induced to re-enter the lytic cycle. This risk selects for prophages to lose genes involved in induction, excision, replication, virion assembly, or lysis. Over time, this process can produce cryptic prophages, which are degraded prophage regions that are no longer able to complete the lytic life cycle. If prophage genes are functionally neutral, then they should be lost, by becoming pseudogenes or being deleted, more or less randomly as prophage regions degrade. However, if some prophage genes are retained more often than the surrounding prophage background, such a pattern suggests that gene loss is not entirely random. These retained genes provide candidates for prophage-derived functions that may benefit the bacterial host.

This study investigated whether genes associated with four well-characterized Salmonella prophages, Gifsy-1, Gifsy-2, Fels-1 and Fels-2, are lost randomly or retained in structured patterns. To this end, 4,974 Salmonella genomes were downloaded from NCBI and analyzed in a custom scaffold-based workflow to determine the presence, absence, and relative length of genes located within these prophage regions. These data were converted into binary presence/absence matrices and gene length-aware matrices, then analyzed using gene retention tests, prophage prevalence and co-occurrence analysis, random forest models, and host-prophage phylogenetic comparisons. The resulting models and statistical tests showed a difference in prophage gene occurrence and resistance to degradation, with certain particularly resistant genes having products that could be beneficial to the host if expressed. Our research points to certain genes of interest for in vitro testing in addition to building a framework to apply to other prophage.