Unveiling Hidden Allies: In Silico Discovery of Prophages in Species

Overview

Journal Antibiotics (Basel)

Specialty Pharmacology

Date 2025 Jan 8

PMID 39766574

Authors

Carolina Ramirez

Jaime Romero

Affiliations

Soon will be listed here.

Abstract

Methods: We assessed the presence of prophages in 212 genomes/assemblies available in the NCBI repository, comprising several species and global locations, using the PHASTEST program. Then, we focused on those regions classified as intact, evaluating the most common phages found using VICTOR. The protein of interest discovered in the prophages was evaluated using the ProtParam, DeepTMHMM, InterPro, and Phyre2 tools. In addition, we evaluated the presence of antiphage defense systems in those genomes with intact prophages using the DefenseFinder tool.

Results: We identified 25 phage elements in 24 out of the 212 genomes/assemblies analyzed, with 11% of the assemblies containing phage elements. These were concentrated in and , which harbored 10 and 7 prophage regions, respectively. Of the identified elements, six were classified as intact, including four in , with the most common phages belonging to the and families. Bioinformatic analysis showed that the putative endolysin is a stable protein of 432 amino acids and 49.8 kDa, with three transmembrane helices and a CHAP domain, structurally similar to the CHAP lytic domain of bacteriophage K.

Conclusions: Key prophage elements in , especially in , show promise for phage therapy against tenacibaculosis, supporting sustainable, antibiotic-free treatments in aquaculture.

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