{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,8]],"date-time":"2026-10-08T04:42:26Z","timestamp":1791434546685,"version":"4.3.3"},"reference-count":66,"publisher":"Microbiology Society","issue":"9","license":[{"start":{"date-parts":[[2026,9,11]],"date-time":"2026-09-11T00:00:00Z","timestamp":1789084800000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Investissement d'avenir","award":["ANR-10-INBS-09"],"award-info":[{"award-number":["ANR-10-INBS-09"]}]},{"DOI":"10.13039\/501100001665","name":"Agence Nationale de la Recherche","doi-asserted-by":"crossref","award":["ANR-19-CE35-0016"],"award-info":[{"award-number":["ANR-19-CE35-0016"]}],"id":[{"id":"10.13039\/501100001665","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,9,11]]},"abstract":"<jats:p>\n                    Transposon sequencing (Tn-seq) is a powerful technique for defining the essential genes required for bacterial survival. However, gene essentiality can vary significantly across taxonomic levels, and comparing large Tn-seq datasets from multiple strains presents considerable analytical challenges. To address this, we developed TNSEEK, a fully automated bioinformatics pipeline for the systematic and comparative analysis of Tn-seq experiments. We applied TNSEEK to analyse newly generated data for six soft rot\n                    <jats:italic>Pectobacteriaceae<\/jats:italic>\n                    strains, encompassing species from the\n                    <jats:italic>Dickeya<\/jats:italic>\n                    and\n                    <jats:italic>Pectobacterium<\/jats:italic>\n                    genera, grown in a rich medium. This approach identified a core essentialome of 225 genes, primarily involved in fundamental cellular maintenance, conserved across all 6 strains, a set comparable in size to that of the neighbouring\n                    <jats:italic>Enterobacteriaceae<\/jats:italic>\n                    family. Only a few genus-specific essential genes were found, highlighting interesting distinct metabolic capabilities between\n                    <jats:italic>Dickeya<\/jats:italic>\n                    and\n                    <jats:italic>Pectobacterium<\/jats:italic>\n                    genera. In striking contrast, we discovered a large variable essentialome comprising 181 strain-specific genes, many of which are of unknown function. A portion of these strain-specific essential genes are components of defence systems and prophage genomic regions. The unexpected essentiality of selected components of these modules is consistent with cellular dependency on cognate toxic, restriction or immunity functions encoded by defence-associated loci under the tested growth condition. Furthermore, a comparison with the\n                    <jats:italic>Escherichia coli<\/jats:italic>\n                    essentialome demonstrates that discrepancies in gene essentiality can often be attributed to differences in growth conditions, particularly temperature, as well as variations in genetic redundancy. In conclusion, the TNSEEK pipeline provides a reproducible framework for comparative analysis of mariner\/Himar1 Tn-seq datasets across multiple strains.\n                  <\/jats:p>","DOI":"10.1099\/mgen.0.001762","type":"journal-article","created":{"date-parts":[[2026,9,11]],"date-time":"2026-09-11T15:16:33Z","timestamp":1789139793000},"source":"Crossref","is-referenced-by-count":1,"title":["Comparative essentialome analysis of six Pectobacteriaceae strains using the TNSEEK pipeline identifies conserved and strain-specific fitness determinants"],"prefix":"10.1099","volume":"12","author":[{"given":"Julie","family":"Baltenneck","sequence":"first","affiliation":[{"name":"Univ Lyon, Universit\u00e9 Lyon 1, INSA de Lyon, CNRS UMR 5240 Microbiologie Adaptation et Pathog\u00e9nie, Villeurbanne, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lo\u00efc","family":"Couderc","sequence":"additional","affiliation":[{"name":"Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, Lille, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jacques","family":"P\u00e9dron","sequence":"additional","affiliation":[{"name":"Sorbonne Universit\u00e9, INRAE, Institut d'\u00c9cologie et des Sciences de l'Environnement de Paris, Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guillemette","family":"Marot","sequence":"additional","affiliation":[{"name":"Univ. Lille, CHU Lille, Inria, ULR2694 \u2013 Metrics - Datavers, Lille, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-4309-2803","authenticated-orcid":false,"given":"Areski","family":"Flissi","sequence":"additional","affiliation":[{"name":"Univ. 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