Prospecção e classificação de profagos em genomas de bactérias do gênero Proteus

Abstract

Bacteriophages are viruses that infect bacteria. During their replication process phages can be integrated with bacterial genomes and thus influence the bacterial evolutionary process. Phages are present in different environments and play several relevant roles in different ecosystems, in addition to being involved in some processes of interest to the medical industry, such as the use of phages as antibacterial agents. One of the most used approaches for the study of bacteriophages is through its prospection in bacterial genomes, through computational bioinformatics tools. However, this approach still has limitations regarding a taxonomic and complete classification of the genomes found. Proteus bacteria are opportunistic pathogens that infect the urinary tract and catheters, and can even form biofilm and clog medical equipment. Although treatments that use bacteriophages already exist to mitigate the occurrence of proliferation and biofilm formation, the genomes of bacteria of the the genomes of bacteria of the genus Proteus have great need of systematically and massively search of prophages. In this work, we seek to explore genomes of bacteria of the Proteus genus in search of prophages and classify them in relation to taxonomy and completeness, in a systematic, automated and reproducible way. For this, we analyzed the genomes available in GenBank with VirSorter2, we classified the viral elements in relation to their completion using CheckV. We sought to taxonomically classify viral elements that have more than 90% exploited completeness based on protein content, with vContact2 and VipTree; based on the presence of genes in the pangenome, with Roary; and on genomic similarity, with VIRIDIC. 3907 viral elements were found, of which, after a trimming process, 1106 were classified as complete or high-quality genomes. Our result proposes the creation of two new subfamilies, Bcepmuvirinae and Menelausvirinae, 20 new genera and 47 new viral species within the Myoviridae family. The methodology used allows for a greater systematization of the completeness check in future works and allows us to quantitatively compare future methodologies.