{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,14]],"date-time":"2026-09-14T20:02:47Z","timestamp":1789416167701,"version":"build-2803163510"},"reference-count":40,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2023,8,1]],"date-time":"2023-08-01T00:00:00Z","timestamp":1690848000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:sec><jats:title>Introduction<\/jats:title><jats:p>Temperate phages can engage in the horizontal transfer of functional genes to their bacterial hosts. Thus, their genetic material becomes an intimate part of bacterial genomes and plays essential roles in bacterial mutation and evolution. Specifically, temperate phages can naturally transmit genes by integrating their genomes into the bacterial host genomes via integrases. Our previous study showed that <jats:italic>Salmonella enterica<\/jats:italic> contains the largest number of temperate phages among all publicly available bacterial species. <jats:italic>S. enterica<\/jats:italic> is an important pathogen that can cause serious systemic infections and even fatalities.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>Initially, we extracted all <jats:italic>S. enterica<\/jats:italic> temperate phages from the extensively developed temperate phage database established in our previous study. Subsequently, we conducted an in-depth analysis of the genetic characteristics and integration specificity exhibited by these <jats:italic>S. enterica<\/jats:italic> temperate phages.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Here we identified 8,777 <jats:italic>S. enterica<\/jats:italic> temperate phages, all of which have integrases in their genomes. We found 491 non-redundant <jats:italic>S. enterica<\/jats:italic> temperate phage integrases (integrase entries). <jats:italic>S. enterica<\/jats:italic> temperate phage integrases were classified into three types: intA, intS, and phiRv2. Correlation analysis showed that the sequence lengths of <jats:italic>S. enterica<\/jats:italic> integrase and core regions of <jats:italic>attB<\/jats:italic> and <jats:italic>attP<\/jats:italic> were strongly correlated. Further phylogenetic analysis and taxonomic classification indicated that both the <jats:italic>S. enterica<\/jats:italic> temperate phage genomes and the integrase gene sequences were of high diversities.<\/jats:p><\/jats:sec><jats:sec><jats:title>Discussion<\/jats:title><jats:p>Our work provides insight into the essential integration specificity and genetic diversity of <jats:italic>S. enterica<\/jats:italic> temperate phages. This study paves the way for a better understanding of the interactions between phages and <jats:italic>S. enterica<\/jats:italic>. By analyzing a large number of <jats:italic>S. enterica<\/jats:italic> temperate phages and their integrases, we provide valuable insights into the genetic diversity and prevalence of these elements. This knowledge has important implications for developing targeted therapeutic interventions, such as phage therapy, to combat <jats:italic>S. enterica<\/jats:italic> infections. By harnessing the lytic capabilities of temperate phages, they can be engineered or utilized in phage cocktails to specifically target and eradicate <jats:italic>S. enterica<\/jats:italic> strains, offering an alternative or complementary approach to traditional antibiotic treatments. Our study has implications for public health and holds potential significance in combating clinical infections caused by <jats:italic>S. enterica<\/jats:italic>.<\/jats:p><\/jats:sec>","DOI":"10.3389\/fmicb.2023.1199843","type":"journal-article","created":{"date-parts":[[2023,8,1]],"date-time":"2023-08-01T15:00:38Z","timestamp":1690902038000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":3,"title":["Genetic characteristics and integration specificity of Salmonella enterica temperate phages"],"prefix":"10.3389","volume":"14","author":[{"given":"Siqi","family":"Sun","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xianglilan","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2023,8,1]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"912","DOI":"10.3390\/v15040912","article-title":"The Lytic Activity of Bacteriophage ZCSE9 against Salmonella enterica and Its Synergistic Effects with Kanamycin","volume":"15","author":"Abdelsattar","year":"2023","journal-title":"Viruses"},{"key":"ref2","article-title":"FastQC A Quality Control tool for High Throughput Sequence Data","year":"2010"},{"key":"ref3","doi-asserted-by":"publisher","first-page":"1515","DOI":"10.1046\/j.1365-2958.2002.03130.x","article-title":"Integration and excision of the Mycobacterium tuberculosis prophage-like element, \u03c6Rv1: Integration and excision of \u03c6Rv1","volume":"45","author":"Bibb","year":"2002","journal-title":"Mol. 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