{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T11:57:18Z","timestamp":1790769438748,"version":"4.1.0"},"reference-count":49,"publisher":"American Association for the Advancement of Science (AAAS)","issue":"1","funder":[{"name":"Grant of Key Research Items from the Ministry of Science and Technology of China","award":["2023YFC2307100"],"award-info":[{"award-number":["2023YFC2307100"]}],"id":[{"id":"https:\/\/ror.org\/02kv4zf79","id-type":"ROR","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100019540","name":"Science Fund for Distinguished Young Scholars of Zhejiang Province","doi-asserted-by":"publisher","award":["LZY24H150003"],"award-info":[{"award-number":["LZY24H150003"]}],"id":[{"id":"10.13039\/501100019540","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003185","name":"Fraunhofer-Gesellschaft","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003185","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["spj.science.org"],"crossmark-restriction":true},"short-container-title":["Comput Struct Biotechnol J"],"published-print":{"date-parts":[[2026,3,1]]},"abstract":"<jats:p>\n                    Tailocins are phage tail-like bacteriocins derived from prophages that have lost the ability to package viral genomes while retaining bactericidal activity against related bacterial strains. In\n                    <jats:italic toggle=\"yes\">Pseudomonas aeruginosa<\/jats:italic>\n                    , these elements are referred to as pyocins and contribute to ecological fitness and antimicrobial applications. Despite lacking essential phage components, pyocin-encoding gene clusters share substantial sequence homology with phage tail genes, creating a major challenge for genome annotation. Current prophage prediction tools, which rely on phage gene homology, can frequently misclassify pyocins as prophages, potentially confounding genomic analyses and downstream experimental design. Here, we present TattleTail, a rule-based bioinformatic pipeline for identifying canonical pyocin-encoding gene clusters in\n                    <jats:italic toggle=\"yes\">P. aeruginosa<\/jats:italic>\n                    . The current implementation targets the characteristic\n                    <jats:italic toggle=\"yes\">trpE<\/jats:italic>\n                    \u2013\n                    <jats:italic toggle=\"yes\">trpG<\/jats:italic>\n                    -associated genomic architecture of these loci and integrates the detection of conserved pyocin-associated genes with the exclusion of canonical phage features, enabling discrimination between pyocin-encoding gene clusters and prophage regions. Evaluation across manually curated and independently selected\n                    <jats:italic toggle=\"yes\">P. aeruginosa<\/jats:italic>\n                    genomes, together with\n                    <jats:italic toggle=\"yes\">P. aeruginosa<\/jats:italic>\n                    genomes computationally depleted of their pyocin loci and non-\n                    <jats:italic toggle=\"yes\">P. aeruginosa<\/jats:italic>\n                    controls, demonstrated accurate identification of canonical pyocin loci without false-positive predictions. Application to clinical isolates identified representative pyocin clusters, which were experimentally validated by mitomycin C induction, transmission electron microscopy, and bactericidal activity assays, supporting that predicted loci in these isolates correspond to functional pyocin particles. TattleTail complements existing prophage prediction tools and supports accurate annotation of phage-derived elements.\n                  <\/jats:p>","DOI":"10.34133\/csbj.0230","type":"journal-article","created":{"date-parts":[[2026,9,14]],"date-time":"2026-09-14T07:46:34Z","timestamp":1789371994000},"update-policy":"https:\/\/doi.org\/10.34133\/aaas_crossmark_01","source":"Crossref","is-referenced-by-count":0,"title":["TattleTail: A Rule-Based Tool for Identifying Canonical Pyocin-Encoding Gene Clusters in\n                    <i>Pseudomonas aeruginosa<\/i>"],"prefix":"10.34133","volume":"35","author":[{"ORCID":"https:\/\/orcid.org\/0009-0008-9901-8062","authenticated-orcid":false,"given":"Rayhaan Gerard","family":"Pais","sequence":"first","affiliation":[{"name":"Department of Infection Research and Diagnostics, \rFraunhofer Institute for Cell Therapy &amp; Immunology, Leipzig, Saxony 04103, Germany."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-2185-7802","authenticated-orcid":false,"given":"Weilian","family":"Chen","sequence":"additional","affiliation":[{"name":"School of Life Sciences, \rZhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, China."},{"name":"Department of Infectious Diseases, \rSir Run Run Shaw Hospital, Hangzhou, Zhejiang 310053, China."},{"name":"Hangzhou Digital-Micro Biotech Co., Ltd.","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4847-4622","authenticated-orcid":false,"given":"Sebastian","family":"Leptihn","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, \rUniversity of Southern Denmark, Odense, Funen 5230, Denmark."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8215-916X","authenticated-orcid":true,"given":"Xiaoting","family":"Hua","sequence":"additional","affiliation":[{"name":"Department of Infectious Diseases, \rSir Run Run Shaw Hospital, Hangzhou, Zhejiang 310053, China."},{"name":"Zhejiang Provincial Engineering Research Center of Innovative Instruments for Precise Pathogen Detection","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1364-6911","authenticated-orcid":true,"given":"Belinda","family":"Loh","sequence":"additional","affiliation":[{"name":"Department of Infection Research and Diagnostics, \rFraunhofer Institute for Cell Therapy &amp; Immunology, Leipzig, Saxony 04103, Germany."}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"221","published-online":{"date-parts":[[2026,9,30]]},"reference":[{"key":"e_1_3_4_2_2","doi-asserted-by":"publisher","DOI":"10.4161\/viru.24498"},{"key":"e_1_3_4_3_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2024.05.006"},{"issue":"1","key":"e_1_3_4_4_2","doi-asserted-by":"crossref","first-page":"46","DOI":"10.1038\/s41522-025-00674-1","article-title":"Prophages in the infant gut are pervasively induced and may modulate the functionality of their hosts","volume":"11","author":"Redgwell TA","year":"2025","unstructured":"Redgwell TA, Thorsen J, Petit M-A, Deng L, Vestergaard G, Russel J, Chawes B, B\u00f8nnelykke K, Bisgaard H, Nielsen DS, et al. Prophages in the infant gut are pervasively induced and may modulate the functionality of their hosts. NPJ Biofilms Microbiomes. 2025;11(1):46.","journal-title":"NPJ Biofilms Microbiomes"},{"issue":"12","key":"e_1_3_4_5_2","doi-asserted-by":"crossref","first-page":"2854","DOI":"10.1038\/ismej.2016.79","article-title":"Prophages mediate defense against phage infection through diverse mechanisms","volume":"10","author":"Bondy-Denomy J","year":"2016","unstructured":"Bondy-Denomy J, Qian J, Westra ER, Buckling A, Guttman DS, Davidson AR, Maxwell KL. Prophages mediate defense against phage infection through diverse mechanisms. ISME J. 2016;10(12):2854\u20132866.","journal-title":"ISME J"},{"key":"e_1_3_4_6_2","doi-asserted-by":"publisher","DOI":"10.1038\/ismej.2017.16"},{"issue":"5","key":"e_1_3_4_7_2","doi-asserted-by":"crossref","first-page":"639","DOI":"10.3390\/microorganisms8050639","article-title":"Bacteriocins, antimicrobial peptides from bacterial origin: Overview of their biology and their impact against multidrug-resistant bacteria","volume":"8","author":"Simons A","year":"2020","unstructured":"Simons A, Alhanout K, Duval RE. Bacteriocins, antimicrobial peptides from bacterial origin: Overview of their biology and their impact against multidrug-resistant bacteria. Microorganisms. 2020;8(5):639.","journal-title":"Microorganisms"},{"issue":"6701","key":"e_1_3_4_8_2","doi-asserted-by":"crossref","DOI":"10.1126\/science.ado0713","article-title":"A phage tail-like bacteriocin suppresses competitors in metapopulations of pathogenic bacteria","volume":"384","author":"Backman T","year":"2024","unstructured":"Backman T, Latorre SM, Symeonidi E, Muszy\u0144ski A, Bleak E, Eads L, Martinez-Koury PI, Som S, Hawks A, Gloss AD, et al. A phage tail-like bacteriocin suppresses competitors in metapopulations of pathogenic bacteria. 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Mol Microbiol. 2000;38(2):213\u2013231.","journal-title":"Mol Microbiol"},{"issue":"1","key":"e_1_3_4_12_2","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1038\/s41598-022-27341-1","article-title":"Study of 32 new phage tail-like bacteriocins (pyocins) from a clinical collection of Pseudomonas aeruginosa and of their potential use as typing markers and antimicrobial agents","volume":"13","author":"Blasco L","year":"2023","unstructured":"Blasco L, de Aledo MG, Ortiz-Cartagena C, Bl\u00e9riot I, Pacios O, L\u00f3pez M, Fern\u00e1ndez-Garc\u00eda L, Barrio-Pujante A, Hern\u00e1ndez-Garcia M, Cant\u00f3n R. et al. Study of 32 new phage tail-like bacteriocins (pyocins) from a clinical collection of Pseudomonas aeruginosa and of their potential use as typing markers and antimicrobial agents, Sci Rep. 2023;13(1)117.","journal-title":"Sci Rep"},{"issue":"6","key":"e_1_3_4_13_2","doi-asserted-by":"crossref","DOI":"10.1128\/jb.00029-23","article-title":"F-type pyocins are diverse noncontractile phage tail-like weapons for killing Pseudomonas aeruginosa","volume":"205","author":"Saha S","year":"2023","unstructured":"Saha S, Ojobor CD, Li ASC, Mackinnon E, North OI, Bondy-Denomy J, Lam JS, Ensminger AW, Maxwell KL, Davidson AR. F-type pyocins are diverse noncontractile phage tail-like weapons for killing Pseudomonas aeruginosa. 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