{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,14]],"date-time":"2026-09-14T06:04:01Z","timestamp":1789365841567,"version":"build-2803163510"},"reference-count":73,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,9,14]],"date-time":"2026-09-14T00:00:00Z","timestamp":1789344000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100014440","name":"Ministerio de Ciencia, Innovaci\u00f3n y Universidades","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100014440","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100031478","name":"NextGenerationEU","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100031478","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Bioinform."],"abstract":"<jats:p>\n                    Table olives are among the most important fermented vegetables in the Mediterranean region, with fermentations largely driven by\n                    <jats:italic>Lactiplantibacillus<\/jats:italic>\n                    species. While\n                    <jats:italic>Lactiplantibacillus pentosus<\/jats:italic>\n                    has been extensively studied at the genomic level, genomic information on olive-associated\n                    <jats:italic>Lactiplantibacillus plantarum<\/jats:italic>\n                    remains scarce. To expand current knowledge, three novel\n                    <jats:italic>L. plantarum<\/jats:italic>\n                    strains isolated from table olive fermentations in Spain (Lpl15 and LPT703) and Greece (B282) were subjected to whole-genome sequencing and comparative genomic analysis. Genome assemblies ranged from 3.25 to 3.50 Mb and contained 3,060\u20133,328 predicted protein-coding genes. While Illumina assemblies remained fragmented, hybrid sequencing produced a complete genome assembly for strain\n                    <jats:italic>L. plantarum<\/jats:italic>\n                    Lpl15, including a complete chromosome and three plasmids. Comparative analyses incorporating\n                    <jats:italic>L. plantarum<\/jats:italic>\n                    genomes from diverse ecological origins, including vegetable fermentations, animal-derived foods, and human-associated environments, were performed using Average Nucleotide Identity (ANI), pangenome analysis, and core-genome phylogeny. Neither ANI nor phylogenomic analyses supported the existence of a distinct lineage associated with table olive fermentations. Functional and metabolic comparisons revealed two major genomic groups linked to ecological origin. Genomes predominantly associated with vegetable fermentations lacked complete nitrogen metabolism pathways, whereas strains of animal origin generally retained these functions. In addition, vegetable-associated strains showed an enrichment of genes involved in exopolysaccharide biosynthesis. Analyses of protein families, domains, and mobilome-related elements further revealed niche-associated genomic patterns. Overall, these results indicate that\n                    <jats:italic>L. plantarum<\/jats:italic>\n                    from table olive fermentations does not constitute a distinct evolutionary lineage. Instead, adaptation appears to be reflected in functional and accessory genomic traits associated with ecological origin, providing new insights into the diversity and adaptive potential of this species across different environments.\n                  <\/jats:p>","DOI":"10.3389\/fbinf.2026.1936258","type":"journal-article","created":{"date-parts":[[2026,9,14]],"date-time":"2026-09-14T05:39:19Z","timestamp":1789364359000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Comparative functional genomic analysis of table olive-associated Lactiplantibacillus plantarum strains"],"prefix":"10.3389","volume":"6","author":[{"given":"Elio","family":"L\u00f3pez-Garc\u00eda","sequence":"first","affiliation":[{"name":"Food Biotechnology Department, Instituto de La Grasa (CSIC), Campus Universitario Pablo de Olavide","place":["Seville, Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Antonio","family":"Ben\u00edtez-Cabello","sequence":"additional","affiliation":[{"name":"Food Biotechnology Department, Instituto de La Grasa (CSIC), Campus Universitario Pablo de Olavide","place":["Seville, Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Efstathios Z.","family":"Panagou","sequence":"additional","affiliation":[{"name":"Laboratory of Microbiology and Biotechnology of Foods, Department of Food Science and Human Nutrition, School of Food and Nutritional Sciences, Agricultural University of Athens","place":["Athens, Greece"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jos\u00e9 Luis","family":"Ruiz-Barba","sequence":"additional","affiliation":[{"name":"Food Biotechnology Department, Instituto de La Grasa (CSIC), Campus Universitario Pablo de Olavide","place":["Seville, Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Francisco No\u00e9","family":"Arroyo-L\u00f3pez","sequence":"additional","affiliation":[{"name":"Food Biotechnology Department, Instituto de La Grasa (CSIC), Campus Universitario Pablo de Olavide","place":["Seville, Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,9,14]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1371\/journal.pone.0176801","article-title":"In silico genomic insights into aspects of food safety and defense mechanisms of a potentially probiotic Lactobacillus pentosus MP-10 isolated from brines of naturally fermented alore\u00f1a green table olives","volume":"12","author":"Abriouel","year":"2017","journal-title":"PLoS ONE"},{"key":"B2","doi-asserted-by":"publisher","first-page":"D517","DOI":"10.1093\/nar\/gkz935","article-title":"CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database","volume":"48","author":"Alcock","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"B3","doi-asserted-by":"publisher","first-page":"2269","DOI":"10.1128\/aem.64.6.2269-2272.1998","article-title":"Antagonistic activity of Lactobacillus plantarum C11: two new two-peptide bacteriocins, plantaricins EF and JK, and the induction factor plantaricin A","volume":"64","author":"Anderssen","year":"1998","journal-title":"Appl. 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