Siqi Sun

Xianglilan Zhang

Frontiers in Microbiology

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TYPE CorrectionPUBLISHED 18 September 2023DOI 10.3389/fmicb.2023.1273462OPEN ACCESSAPPROVED BYJesus L. Romalde,University of Santiago de Compostela, Spain*CORRESPONDENCEXianglilan Zhangzhangxianglilan@gmail.comRECEIVED 06 August 2023ACCEPTED 04 September 2023PUBLISHED 18 September 2023CITATIONSun S and Zhang X (2023) Corrigendum:Genetic characteristics and integrationspecificity of Salmonella enterica temperatephages. Front. Microbiol. 14:1273462.doi: 10.3389/fmicb.2023.1273462COPYRIGHT© 2023 Sun and Zhang. This is an open-accessarticle distributed under the terms of theCreative Commons Attribution License (CC BY).The use, distribution or reproduction in otherforums is permitted, provided the originalauthor(s) and the copyright owner(s) arecredited and that the original publication in thisjournal is cited, in accordance with acceptedacademic practice. No use, distribution orreproduction is permitted which does notcomply with these terms.Corrigendum: Geneticcharacteristics and integrationspecificity of Salmonella entericatemperate phagesSiqi Sun1,2 and Xianglilan Zhang1*1State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology,Beijing, China, 2Department of Life Sciences and Technology, Beijing University of Chemical Technology,Chaoyang, Beijing, ChinaKEYWORDStemperate phage, Salmonella enterica, integrase, attachment site, correlation analysis,phylogenetic analysis, taxonomic classificationA corrigendum onGenetic characteristics and integration specificity of Salmonella entericatemperate phagesby Sun, S., and Zhang, X. (2023). Front. Microbiol. 14:1199843. doi: 10.3389/fmicb.2023.1199843In the published article, (Zhang et al., 2022) was not cited in Section 2.1 and the legendof Figure 3.The citation has now been inserted in 2.1. Identification of integrase sequence,paragraph 1 and should read:“In the previous study, we first used FastQC (Babraham Bioinformatics, 2010) andTrimmomatic (Bolger et al., 2014) for quality control and NGS reads filtering, followed bythe steps of prophage detection and temperate phage detection (Zhang et al., 2022).”The citation has now been inserted in the legend of Figure 3 and should read:“These temperate phage genome sequences are from the database we generated in aprevious study (Zhang et al., 2022).”In the published article, (Bin Jang et al., 2019) was not cited in Section 3.4.The citation has now been inserted in 3.4. Taxonomic classification of Salmonellaenterica temperate phages, paragraph 1 and should read:“In particular, we used vContact2 (Bin Jang et al., 2019) to cluster the temperate phagegenome sequences with the reference virus genomes. . . ”In the published article, there was an error in the legend for Figure 5 as published. Thesquare brackets should be absolute values. The corrected legend appears below.Figure 5.Distribution of distances between integrase sequences and attachment site coreregion sequences. Distance (integrase, core region) = |Position (integrase) – Position (coreregion)|/Length (temperate phage).In the published article, there was an error in the keywords. The keyword “attachment”should be revised to “attachment site.”In Section 2.4. Phylogenetic analysis of temperate phage and integrase entries,paragraph 1, there was an error. The phrase “a neighbor-joining (NJ) tree” has been correctedto “the neighbor-joining trees”.Frontiers inMicrobiology 01 frontiersin.orgSun and Zhang 10.3389/fmicb.2023.1273462In Section 3.5. Salmonella enterica serotypes infected bythe Salmonella enterica temperate phage genome sequences,paragraphs 2 & 3, there were errors. The locations of mostphages/integrases/core regions within the ranges were incorrectlystated. These paragraphs previously stated:“Regarding the sequence length and GC content, we observeda relatively narrow range for S. enteritidis temperate phages,integrases, and core regions (Figure 9A; Supplementary Table 9).Most temperate phages had lengths between 39,267 and 39,280 bp,integrases ranged from 1,275 to 1,305 bp, and core regions spanned81 to 87 bp. Similarly, their GC content exhibited a narrow range,with temperate phages ranging from 41.1% to 41.3% GC content,integrases from 48.9% to 49.0%, and core regions from 49.3% to50.0% (Figure 9B; Supplementary Table 9).For S. typhimurium temperate phages, their sequence lengthsprimarily fell within the 42,100 to 42,594 range, integrases rangedfrom 1,170 to 1,227, and core regions from 18 to 58 (Figure 10A;Supplementary Table 10). The GC contents of temperate phagegenomes, integrases, and core regions were mainly between 50.0%to 50.2%, 46.7% to 48.5%, and 39.1% to 55.6%, respectively (Figure10B; Supplementary Table 10).”The corrected paragraphs appear below:“Regarding the sequence length and GC content, we observeda relatively narrow range for S. enteritidis temperate phages,integrases, and core regions (Figure 9; Supplementary Table 9).Most temperate phages had lengths between 39,267 bp and 39,279bp, integrases had a length of 1,275 bp, and core regions had alength of 81 bp (Figure 9A; Supplementary Table 9). Similarly,their GC content exhibited a narrow range, with most temperatephages ranging from 41.32% to 41.33% GC content, integrases at49.02%, and core regions at 49.38% (Figure 9B; SupplementaryTable 9).For S. typhimurium temperate phages, their sequence lengthsprimarily fell within the 38,866 bp to 42,575 bp, integrasesranged from 1,173 bp to 1,227 bp, and core regions from 18bp to 58 bp (Figure 10A; Supplementary Table 10). The GCcontents of temperate phage genomes, integrases, and core regionswere mainly between 50.05% to 50.23%, 46.70% to 51.18%,and 39.13% to 55.56%, respectively (Figure 10B; SupplementaryTable 10).”In Section 4. Discussion, paragraph 6, there was an error.The percentages of different integrase types were incorrect. Thesentence previously stated:“Our analysis identified 3,857 unique S. enterica temperatephage sequences with integrases from three categories: intA(11.9%, 1,047/3,857), intS (31.9%, 2,801/8,777), and phiRv2(0.1%, 9/3,857).”The corrected sentence appears below:“Our analysis identified 3,857 unique S. enterica temperatephage sequences with integrases from three categories: intA(27.15%, 1,047/3,857), intS (72.62%, 2,801/3,857), and phiRv2(0.23%, 9/3,857).”In the Section 3.4. Taxonomic classification of Salmonellaenterica temperate phages, paragraph 3, the last sentence has beendeleted, because it is identical to the title of the following section.The corrected sentence appears below:“The taxonomic results show that from the aspect of integrasetypes, some temperate phages with intA and intS integrases weretaxonomically clustered, respectively (Figure 7, the two clusterson the right; Supplementary Tables 6, 7); while some phageswith different integrase types were taxonomically mixed together(Figure 7, left and middle; Supplementary Tables 6, 7). Weconducted an analysis of the nucleic acid sequences of the coreregions of attP and attB sites (Figure 8; Supplementary Table1). The findings reveal that temperate phages with intA integraseexhibit consistent core regions at positions 18 to 21 (TGAG), whilethose with intS integrase show conservation at starting positionswith AAT, ending positions with TA, and middle positions from19 to 24 (TGCAGG). Furthermore, phages with phiRv2 integrasedisplay consistency at all positions. These results highlight acorrelation between the core region sequences and the integrasetypes, as evidenced by distinct conserved positions for differentintegrase types.”The authors apologize for these errors and state that these donot change the scientific conclusions of the article in any way. Theoriginal article has been updated.Publisher’s noteAll claims expressed in this article are solely those of theauthors and do not necessarily represent those of their affiliatedorganizations, or those of the publisher, the editors and thereviewers. Any product that may be evaluated in this article, orclaim that may be made by its manufacturer, is not guaranteed orendorsed by the publisher.Frontiers inMicrobiology 02 frontiersin.org

Corrigendum: Genetic characteristics and integration specificity of Salmonella enterica temperate phages

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Corrigendum: Genetic characteristics and integration specificity of Salmonella enterica temperate phages

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