{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,1]],"date-time":"2026-08-01T04:22:30Z","timestamp":1785558150493,"version":"3.56.0"},"reference-count":85,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2025,9,24]],"date-time":"2025-09-24T00:00:00Z","timestamp":1758672000000},"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:p><jats:italic>Oenococcus oeni<\/jats:italic> is the predominant species of lactic acid bacteria in wine, where it carries out malolactic fermentation (MLF), which helps to ensure and preserve the quality of the wine. Today, existing combinations of grape varieties, soil composition, fluctuating climatic parameters, and specific technical processes implemented by wineries lead to incredibly varied wine compositions that pose challenges for spontaneous MLF. Commercial starter cultures have been developed for use as inoculants. However, their effectiveness in ensuring consistent and reliable MLF is also limited in modern wines. The selection process must therefore adapt to these new challenges, which means expanding current portfolios by selecting more robust bacteria from wines that are more varied in terms of grape varieties and chemical constraints. We have assembled a set of 21 wines produced in Europe from different grape varieties, with varying and, in some cases, extreme ethanol contents, total polyphenolic indices, and pH levels. The isolation and MLVA typing of 385 dominant colonies were combined with whole-genome sequencing of 48 representative strains, and we observed several strains with unique accessory genomic content. Different selective pressures led to the formation of groups of genetically related individuals, particularly in white and ros\u00e9 wines with moderate ethanol content. However, cohabiting strains with contrasting genetic profiles were also observed in some red wines. Our data highlight the complexity of the factors involved in population heterogeneity and raise the possibility that this phenomenon may increase fitness through diversification of strategies or division of labor in specific production environments.<\/jats:p>","DOI":"10.3389\/fmicb.2025.1657712","type":"journal-article","created":{"date-parts":[[2025,9,24]],"date-time":"2025-09-24T05:42:45Z","timestamp":1758692565000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":1,"title":["A reassessment of the infra-species diversity patterns in the wine-associated Oenococcus oeni"],"prefix":"10.3389","volume":"16","author":[{"given":"Florencia","family":"Oviedo-Hernandez","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Magali","family":"Bou-Deleris","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sibylle","family":"Krieger-Weber","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Florian","family":"Claisse","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jovnna","family":"Dereme","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Claire","family":"Le Marrec","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Olivier","family":"Claisse","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2025,9,24]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"1259","DOI":"10.1007\/s10482-014-0296-z","article-title":"Oenococcus alcoholitolerans sp. nov., a lactic acid bacteria isolated from cacha\u00e7a and ethanol fermentation processes","volume":"106","author":"Badotti","year":"2004","journal-title":"Antonie Van Leeuwenhoek"},{"key":"ref2","doi-asserted-by":"publisher","first-page":"110276","DOI":"10.1016\/j.ijfoodmicro.2023.110276","article-title":"Alcoholic fermentation drives the selection of Oenococcus oeni strains in wine but not in cider","volume":"400","author":"Balmaseda","year":"2023","journal-title":"Int. J. Food Microbiol."},{"key":"ref3","doi-asserted-by":"publisher","first-page":"e14302","DOI":"10.1111\/1751-7915.14302","article-title":"The use of Torulaspora delbrueckii to improve malolactic fermentation","volume":"17","author":"Balmaseda","year":"2024","journal-title":"Microb. Biotechnol."},{"key":"ref4","doi-asserted-by":"publisher","first-page":"e0107222","DOI":"10.1128\/mra.01072-22","article-title":"Draft genome sequence of Oenococcus kitaharae CRBO2176, isolated from homemade water kefir","volume":"12","author":"Barchi","year":"2023","journal-title":"Microbiol. Resour. Announc."},{"key":"ref5","doi-asserted-by":"publisher","DOI":"10.3390\/v15010015","article-title":"Phage encounters recorded in CRISPR arrays in the genus Oenococcus","volume":"15","author":"Barchi","year":"2022","journal-title":"Viruses"},{"key":"ref6","doi-asserted-by":"publisher","first-page":"i651","DOI":"10.1093\/bioinformatics\/btaa792","article-title":"PanRGP: a pangenome-based method to predict genomic islands and explore their diversity","volume":"36","author":"Bazin","year":"2020","journal-title":"Bioinformatics"},{"key":"ref7","doi-asserted-by":"publisher","first-page":"188","DOI":"10.1111\/ajgw.12436","article-title":"Oenococcus oeni, a species born and moulded in wine: a critical review of the stress impacts of wine and the physiological responses","volume":"26","author":"Bech-Terkilsen","year":"2020","journal-title":"Aust. J. Grape Wine Res."},{"key":"ref8","doi-asserted-by":"publisher","first-page":"001171","DOI":"10.1099\/mgen.0.001171","article-title":"SOCfinder: a genomic tool for identifying social genes in bacteria","volume":"9","author":"Belcher","year":"2023","journal-title":"Microb. Genom."},{"key":"ref9","doi-asserted-by":"publisher","first-page":"921","DOI":"10.1007\/s00253-017-8593-x","article-title":"Application of directed evolution to develop ethanol tolerant Oenococcus oeni for more efficient malolactic fermentation","volume":"102","author":"Betteridge","year":"2018","journal-title":"Appl. Microbiol. Biotechnol."},{"key":"ref10","doi-asserted-by":"publisher","first-page":"2079","DOI":"10.1128\/AEM.02194-08","article-title":"Oenococcus oeni genome plasticity is associated with fitness","volume":"75","author":"Bon","year":"2009","journal-title":"Appl. Environ. Microbiol."},{"key":"ref11","doi-asserted-by":"publisher","first-page":"1303","DOI":"10.1038\/s41587-023-01953-y","article-title":"Identification of mobile genetic elements with geNomad","volume":"42","author":"Camargo","year":"2023","journal-title":"Nat. Biotechnol."},{"key":"ref12","doi-asserted-by":"publisher","first-page":"1506","DOI":"10.1093\/gbe\/evv084","article-title":"Phylogenomic analysis of Oenococcus oeni reveals specific domestication of strains to cider and wines","volume":"7","author":"Campbell-Sills","year":"2015","journal-title":"Genome Biol. Evol."},{"key":"ref13","doi-asserted-by":"publisher","first-page":"309","DOI":"10.20870\/oeno-one.2017.51.4.1861","article-title":"Two different Oenococcus oeni lineages are associated to either red or white wines in Burgundy: genomics and metabolomics insights","volume":"51","author":"Campbell-Sills","year":"2017","journal-title":"PLoS One"},{"key":"ref14","doi-asserted-by":"publisher","DOI":"10.3390\/fermentation7010024","article-title":"Biodiversity of oenological lactic acid bacteria: species- and strain-dependent plus\/minus effects on wine quality and safety","volume":"7","author":"Capozzi","year":"2021","journal-title":"Fermentation"},{"key":"ref15","doi-asserted-by":"publisher","first-page":"957","DOI":"10.1016\/j.tim.2024.02.014","article-title":"Critically evaluating the relative importance of phage in shaping microbial community composition","volume":"32","author":"Castledine","year":"2024","journal-title":"Trends Microbiol."},{"key":"ref16","doi-asserted-by":"publisher","first-page":"103947","DOI":"10.1016\/j.fm.2021.103947","article-title":"Assessment of the lysogenic status in the lactic acid bacterium O. oeni during the spontaneous malolactic fermentation of red wines","volume":"103","author":"Cha\u00efb","year":"","journal-title":"Food Microbiol."},{"key":"ref17","doi-asserted-by":"publisher","first-page":"109936","DOI":"10.1016\/j.ijfoodmicro.2022.109936","article-title":"Phage-host interactions as a driver of population dynamics during wine fermentation: betting on underdogs","volume":"383","author":"Cha\u00efb","year":"","journal-title":"Int. J. Food Microbiol."},{"key":"ref18","doi-asserted-by":"publisher","first-page":"e00997","DOI":"10.1128\/AEM.00997-19","article-title":"Lysogeny in the lactic acid bacterium Oenococcus oeni is responsible for modified colony morphology on red grape juice agar","volume":"85","author":"Cha\u00efb","year":"2019","journal-title":"Appl. Environ. Microbiol."},{"key":"ref19","doi-asserted-by":"publisher","first-page":"e03265-24","DOI":"10.1128\/spectrum.03265-24","article-title":"Comparative genomic analysis of 255 Oenococcus oeni isolates from China: unveiling strain diversity and genotype-phenotype associations of acid resistance","volume":"13","author":"Chi","year":"2025","journal-title":"Microbiol. Spectr."},{"key":"ref20","doi-asserted-by":"publisher","first-page":"112168","DOI":"10.1016\/j.celrep.2023.112168","article-title":"Phenotypic heterogeneity in the bacterial oxidative stress response is driven by cell-cell interactions","volume":"42","author":"Choudhary","year":"2023","journal-title":"Cell Rep."},{"key":"ref21","doi-asserted-by":"publisher","first-page":"984","DOI":"10.1186\/s12864-016-3338-2","article-title":"Carbohydrate metabolism in Oenococcus oeni: a genomic insight","volume":"17","author":"Cibrario","year":"2016","journal-title":"BMC Genomics"},{"key":"ref22","doi-asserted-by":"publisher","first-page":"856","DOI":"10.3390\/microorganisms9040856","article-title":"Distribution of prophages in the Oenococcus oeni species","volume":"9","author":"Claisse","year":"2021","journal-title":"Microorganism"},{"key":"ref23","doi-asserted-by":"publisher","first-page":"80","DOI":"10.1016\/j.fm.2013.08.012","article-title":"Multiplex variable number of tandem repeats for Oenococcus oeni and applications","volume":"38","author":"Claisse","year":"2014","journal-title":"Food Microbiol."},{"key":"ref24","doi-asserted-by":"publisher","first-page":"1100501","DOI":"10.3389\/fmicb.2023.1100501","article-title":"Metabolic behavior for a mutant Oenococcus oeni strain with high resistance to ethanol to survive under oenological multi-stress conditions","volume":"14","author":"Contreras","year":"2023","journal-title":"Front. Microbiol."},{"key":"ref25","doi-asserted-by":"publisher","first-page":"e00496-19","DOI":"10.1128\/JB.00496-19","article-title":"Elevated expression of a functional suf pathway in Escherichia coli BL21(DE3) enhances recombinant production of an iron-sulfur cluster-containing protein","volume":"202","author":"Corless","year":"2020","journal-title":"J. Bacteriol."},{"key":"ref26","doi-asserted-by":"publisher","first-page":"302","DOI":"10.1016\/j.syapm.2018.12.006","article-title":"Oenococcus sicerae sp. nov., isolated from French cider","volume":"42","author":"Cousin","year":"2019","journal-title":"Syst. Appl. Microbiol."},{"key":"ref27","doi-asserted-by":"publisher","first-page":"395","DOI":"10.1099\/00207713-45-2-395","article-title":"Proposal to reclassify Leuconostoc oenos as Oenococcus oeni [corrig.] gen. nov., comb. nov","volume":"45","author":"Dicks","year":"1995","journal-title":"Int. J. Syst. Bacteriol."},{"key":"ref28","doi-asserted-by":"publisher","first-page":"2204","DOI":"10.3390\/foods10092204","article-title":"Exopolysaccharides producing lactic acid bacteria in wine and other fermented beverages: for better or for worse?","volume":"10","author":"Dimopoulou","year":"2021","journal-title":"Foods"},{"key":"ref29","doi-asserted-by":"publisher","first-page":"e98898","DOI":"10.1371\/journal.pone.0098898","article-title":"Exopolysaccharide (EPS) synthesis by Oenococcus oeni: from genes to phenotypes","volume":"9","author":"Dimopoulou","year":"2014","journal-title":"PLoS One"},{"key":"ref30","doi-asserted-by":"publisher","first-page":"14","DOI":"10.1016\/j.ijfoodmicro.2012.06.009","article-title":"IS30 elements are mediators of genetic diversity in Oenococcus oeni","volume":"158","author":"El Gharniti","year":"2012","journal-title":"Int. J. Food Microbiol."},{"key":"ref31","doi-asserted-by":"publisher","first-page":"e02322","DOI":"10.1128\/AEM.02322-16","article-title":"Biogeography of Oenococcus oeni reveals distinctive but non-specific populations in wine-producing regions","volume":"83","author":"El Khoury","year":"2017","journal-title":"Appl. Environ. Microbiol."},{"key":"ref32","doi-asserted-by":"publisher","first-page":"2345","DOI":"10.1099\/ijs.0.64288-0","article-title":"Oenococcus kitaharae sp. nov., a non-acidophilic and non-malolactic-fermenting Oenococcus isolated from a composting distilled shochu residue","volume":"56","author":"Endo","year":"2006","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref33","doi-asserted-by":"publisher","first-page":"99","DOI":"10.1016\/j.tifs.2022.06.015","article-title":"Microbial interactions in winemaking: ecological aspects and effect on wine quality","volume":"127","author":"Englezos","year":"2022","journal-title":"Trends Food Sci. Technol."},{"key":"ref34","doi-asserted-by":"publisher","first-page":"e49082","DOI":"10.1371\/journal.pone.0049082","article-title":"Identification of pOENI-1 and related plasmids in Oenococcus oeni strains performing the malolactic fermentation in wine","volume":"7","author":"Favier","year":"2012","journal-title":"PLoS One"},{"key":"ref35","volume-title":"Ecosyst\u00e8mes. Structure, Fonctionnement, \u00c9volution","author":"Frontier","year":"2008"},{"key":"ref36","doi-asserted-by":"publisher","first-page":"1395","DOI":"10.1111\/jam.12789","article-title":"Autochthonous starter cultures and indigenous grape variety for regional wine production","volume":"118","author":"Garofalo","year":"2015","journal-title":"J. Appl. Microbiol."},{"key":"ref37","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1371\/journal.pcbi.1007732","article-title":"PPanGGOLiN: depicting microbial diversity via a partitioned pangenome graph","volume":"16","author":"Gautreau","year":"2020","journal-title":"PLoS Comput. Biol."},{"key":"ref38","article-title":"Oenococcus oeni clonal diversity in the carbonic maceration winemaking","author":"Gonz\u00e1lez-Arenzana","year":"2023"},{"key":"ref39","first-page":"81","article-title":"Historiographie et r\u00e9invention du vignoble de Cahors, XXe-XXIe si\u00e8cles","volume-title":"Revista Iberoamericana de Viticultura, Agroindustria y Ruralidad","author":"Griset","year":"2016"},{"key":"ref40","doi-asserted-by":"publisher","first-page":"e0037524","DOI":"10.1128\/msystems.00375-24","article-title":"Versatile roles of protein flavinylation in bacterial extracyotosolic electron transfer","volume":"9","author":"Huang","year":"2024","journal-title":"mSystems"},{"key":"ref41","doi-asserted-by":"publisher","first-page":"111856","DOI":"10.1016\/j.foodres.2022.111856","article-title":"Dynamic changes in the diversity and function of bacterial community during black tea processing","volume":"161","author":"Jia","year":"2022","journal-title":"Food Res. Int."},{"key":"ref42","doi-asserted-by":"publisher","first-page":"104048","DOI":"10.1016\/j.resmic.2023.104048","article-title":"Experimental evolution forcing Oenococcus oeni acid tolerance highlights critical role of the citrate locus","volume":"174","author":"Julliat","year":"2023","journal-title":"Res. Microbiol."},{"key":"ref43","doi-asserted-by":"publisher","first-page":"223","DOI":"10.1016\/j.tree.2021.11.006","article-title":"Bacterial cooperation through horizontal gene transfer","volume":"37","author":"Lee","year":"2022","journal-title":"Trends Ecol. Evol."},{"key":"ref44","doi-asserted-by":"publisher","first-page":"26892","DOI":"10.1073\/pnas.191567811","article-title":"Extracellular electron transfer powers flavinylated extracellular reductases in gram-positive bacteria","volume":"116","author":"Light","year":"2019","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref45","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1038\/s43705-023-00250-8","article-title":"Metabolic cooperation between conspecific genotypic groups contributes to bacterial fitness","volume":"3","author":"Lin","year":"2023","journal-title":"ISME Commun."},{"key":"ref46","doi-asserted-by":"publisher","first-page":"330","DOI":"10.1186\/s12864-019-5692-3","article-title":"Expanding the biodiversity of Oenococcus oeni through comparative genomics of apple cider and kombucha strains","volume":"20","author":"Lorentzen","year":"2019","journal-title":"BMC Genomics"},{"key":"ref47","doi-asserted-by":"publisher","first-page":"2937","DOI":"10.1007\/s00253-019-09689-z","article-title":"Distribution of Oenococcus oeni populations in natural habitats","volume":"103","author":"Lorentzen","year":"2019","journal-title":"Appl. Microbiol. Biotechnol."},{"key":"ref48","doi-asserted-by":"publisher","first-page":"381","DOI":"10.1146\/annurev-micro-032521-041956","article-title":"Microbiome assembly in fermented foods","volume":"77","author":"Louw","year":"2023","journal-title":"Ann. Rev. Microbiol."},{"key":"ref49","doi-asserted-by":"publisher","first-page":"14899","DOI":"10.1021\/acs.jafc.4c02461","article-title":"Unraveling the metabolic behavior and interspecific interaction pattern of lactic acid bacteria within chinese rice wine","volume":"72","author":"Luo","year":"2024","journal-title":"J. Agric. Food Chem."},{"key":"ref50","doi-asserted-by":"publisher","first-page":"109456","DOI":"10.1016\/j.carres.2025.109456","article-title":"Isolation and structure elucidation of cell surface polysaccharides from Oenococcus oeni","volume":"552","author":"Maes","year":"2025","journal-title":"Carbohydr. Res."},{"key":"ref51","doi-asserted-by":"publisher","first-page":"564","DOI":"10.1128\/JB.01457-07","article-title":"Role of hypermutability in the evolution of the genus Oenococcus","volume":"190","author":"Marcobal","year":"2008","journal-title":"J. Bacteriol."},{"key":"ref52","doi-asserted-by":"publisher","first-page":"625","DOI":"10.1016\/j.foodres.2017.09.039","article-title":"Identification of variable genomic regions related to stress response in Oenococcus oeni","volume":"102","author":"Margalef-Catal\u00e0","year":"2017","journal-title":"Food Res. Int."},{"key":"ref53","doi-asserted-by":"publisher","first-page":"3396","DOI":"10.1093\/bioinformatics\/btx440","article-title":"VICTOR: genome-based phylogeny and classification of prokaryotic viruses","volume":"33","author":"Meier-Kolthoff","year":"2017","journal-title":"Bioinformatics"},{"key":"ref54","doi-asserted-by":"publisher","first-page":"e01376-14","DOI":"10.1128\/genomeA.01376-14","article-title":"Draft genome sequence of Oenococcus oeni strain X2L (CRL1947), isolated from red wine of Northwest Argentina","volume":"3","author":"Mendoza","year":"2015","journal-title":"Genome Announc."},{"key":"ref55","doi-asserted-by":"publisher","first-page":"149","DOI":"10.1006\/plas.2001.1537","article-title":"Nucleotide sequence analysis of pRS2 and pRS3, two small cryptic plasmids from Oenococcus oeni","volume":"46","author":"Mesas","year":"2001","journal-title":"Plasmid"},{"key":"ref56","doi-asserted-by":"publisher","first-page":"465","DOI":"10.1016\/j.femsre.2005.04.011","article-title":"Genomic analysis of Oenococcus oeni PSU-1 and its relevance to winemaking","volume":"29","author":"Mills","year":"2005","journal-title":"FEMS Microbiol. Rev."},{"key":"ref57","doi-asserted-by":"publisher","first-page":"e00149","DOI":"10.1128\/mSystems.00149-20","article-title":"Strain-level diversity impacts cheese rind microbiome assembly and function","volume":"5","author":"Niccum","year":"2020","journal-title":"mSystems"},{"key":"ref58","doi-asserted-by":"publisher","first-page":"6032","DOI":"10.1128\/AEM.69.10.6032-6040.2003","article-title":"ISLpl1 is a functional IS30-related insertion element in Lactobacillus plantarum that IS also found in other lactic acid bacteria","volume":"69","author":"Nicoloff","year":"2003","journal-title":"Appl. Environ. Microbiol."},{"key":"ref59","doi-asserted-by":"publisher","first-page":"2800","DOI":"10.3390\/nu12092800","article-title":"Whole blueberry and isolated polyphenol-rich fractions modulate specific gut microbes in an in vitro colon model and in a pilot study in human consumers","volume":"12","author":"Ntemiri","year":"2020","journal-title":"Nutrients"},{"key":"ref60","doi-asserted-by":"publisher","first-page":"4751","DOI":"10.1038\/s41467-022-32504-9","article-title":"Adaptation to novel spatially-structured environments is driven by the capsule and alters virulence-associated traits","volume":"13","author":"Nucci","year":"2022","journal-title":"Nat. Commun."},{"key":"ref61","doi-asserted-by":"publisher","first-page":"e0115421","DOI":"10.1128\/Spectrum.01154-21","article-title":"Analysis of transcriptomic response to SO2 by Oenococcus oeni growing in continuous culture","volume":"9","author":"Onetto","year":"2021","journal-title":"Microbiol. Spectr."},{"key":"ref62","doi-asserted-by":"publisher","first-page":"112875","DOI":"10.1016\/j.celrep.2023.112875","article-title":"MtrA modulates Mycobacterium tuberculosis cell division in host microenvironments to mediate intrinsic resistance and drug tolerance","volume":"42","author":"Peterson","year":"2023","journal-title":"Cell Rep."},{"key":"ref63","doi-asserted-by":"publisher","first-page":"12","DOI":"10.1039\/C5AY02550H","article-title":"Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens","volume":"8","author":"Pritchard","year":"2016","journal-title":"Anal. Methods"},{"key":"ref9001","doi-asserted-by":"crossref","first-page":"277","DOI":"10.1016\/j.ijbiomac.2021.06.097","article-title":"Auxin transport mechanism of membrane transporter encoded by AEC gene of Bacillus licheniformis isolated from metagenome of Tapta Kund Hotspring of Uttrakhand, India","volume":"185","author":"Rai","year":"2021","journal-title":"Int. J. Biol. Macromol"},{"key":"ref64","doi-asserted-by":"publisher","first-page":"344","DOI":"10.1046\/j.1365-2672.2003.01985.x","article-title":"Typification of Oenococcus oeni strains by multiplex RAPD-PCR and study of population dynamics during malolactic fermentation","volume":"95","author":"Reguant","year":"2003","journal-title":"J. Appl. Microbiol."},{"key":"ref65","doi-asserted-by":"publisher","first-page":"veae028","DOI":"10.1093\/ve\/veae028","article-title":"Lytic\/lysogenic transition as a life-history switch","volume":"10","author":"Roughgarden","year":"2024","journal-title":"Virus Evol."},{"key":"ref66","doi-asserted-by":"crossref","first-page":"145","DOI":"10.51926\/ISTE.9167.ch8","article-title":"La domestication D\u2019oenococcus oeni: une bact\u00e9rie fa\u00e7onn\u00e9e pour la production du vin","volume-title":"G\u00e9n\u00e9tique des domestications","author":"Rudolf","year":"2024"},{"key":"ref67","doi-asserted-by":"publisher","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","article-title":"Prokka: rapid prokaryotic genome annotation","volume":"30","author":"Seemann","year":"2014","journal-title":"Bioinformatics"},{"key":"ref68","doi-asserted-by":"publisher","first-page":"W244","DOI":"10.1093\/nar\/gki408","article-title":"The HHpred interactive server for protein homology detection and structure prediction","volume":"33","author":"S\u00f6ding","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"ref69","doi-asserted-by":"publisher","first-page":"3022","DOI":"10.1093\/molbev\/msab120","article-title":"MEGA11: molecular evolutionary genetics analysis version 11","volume":"38","author":"Tamura","year":"2021","journal-title":"Mol. Biol. Evol."},{"key":"ref70","doi-asserted-by":"publisher","first-page":"5519","DOI":"10.1074\/jbc.RA119.010844","article-title":"Three distinct glycosylation pathways are involved in the decoration of Lactococcus lactis cell wall glycopolymers","volume":"295","author":"Theodorou","year":"2021","journal-title":"J. Biol. Chem."},{"key":"ref71","doi-asserted-by":"publisher","first-page":"e00028-23","DOI":"10.1128\/mbio.00028-23","article-title":"Three bacterial DedA subfamilies with distinct functions and phylogenetic distribution","volume":"14","author":"Todor","year":"2023","journal-title":"MBio"},{"key":"ref72","doi-asserted-by":"publisher","first-page":"e0093021","DOI":"10.1128\/msphere.00930-21","article-title":"Plasmid-mediated stabilization of prophages","author":"Tuttle","year":"2022","journal-title":"mSphere"},{"key":"ref73","doi-asserted-by":"publisher","first-page":"mgen000855","DOI":"10.1099\/mgen.0.000855","article-title":"Insertion sequences and other mobile elements associated with antibiotic resistance genes in Enterococcus isolates from an inpatient with prolonged bacteraemia","volume":"8","author":"Udaondo","year":"2022","journal-title":"Microb. Genom."},{"key":"ref74","doi-asserted-by":"publisher","first-page":"e00008-18","DOI":"10.1128\/MMBR.00008-18","article-title":"Experimental design, population dynamics, and diversity in microbial experimental evolution","volume":"82","author":"Van den Bergh","year":"2018","journal-title":"Microbiol. Mol. Biol. Rev."},{"key":"ref75","doi-asserted-by":"publisher","first-page":"R30","DOI":"10.1186\/gb-2011-12-3-r30","article-title":"ISsaga: an ensemble of web-based methods for high throughput identification and semi-automatic annotation of insertion sequences in prokaryotic genomes","volume":"12","author":"Varani","year":"2011","journal-title":"Genome Biol."},{"key":"ref76","doi-asserted-by":"publisher","first-page":"e12194","DOI":"10.7717\/peerj.12194","article-title":"Phage strategies facilitate bacterial coexistence under environmental variability","volume":"9","author":"Voigt","year":"2021","journal-title":"PeerJ"},{"key":"ref77","doi-asserted-by":"publisher","first-page":"143","DOI":"10.1146\/annurev-micro-102215-095325","article-title":"Kin recognition in Bacteria","volume":"70","author":"Wall","year":"2016","journal-title":"Ann. Rev. Microbiol."},{"key":"ref78","doi-asserted-by":"publisher","first-page":"1187","DOI":"10.3390\/foods14071187","article-title":"How does extended maceration affect tannin and color of red wines from cold-hardy grape cultivars?","volume":"14","author":"Watrelot","year":"2025","journal-title":"Foods"},{"key":"ref79","doi-asserted-by":"publisher","first-page":"e0315822","DOI":"10.1128\/mbio.03158-22","article-title":"Insertion sequences determine plasmid adaptation to new bacterial hosts","volume":"14","author":"Wedel","year":"2023","journal-title":"MBio"},{"key":"ref80","doi-asserted-by":"publisher","first-page":"648","DOI":"10.3390\/genes14030648","article-title":"Social diversification driven by Mobile genetic elements","volume":"14","author":"Weltzer","year":"2023","journal-title":"Genes"},{"key":"ref81","doi-asserted-by":"publisher","first-page":"2494","DOI":"10.3390\/app11062494","article-title":"Population dynamics and yeast diversity in early winemaking stages without sulfites revealed by three complementary approaches","volume":"11","author":"Windholtz","year":"2021","journal-title":"Appl. Sci."},{"key":"ref82","doi-asserted-by":"publisher","first-page":"e0207626","DOI":"10.1371\/journal.pone.0207626","article-title":"Predicting osmotic potential from measurements of refractive index in cherries, grapes and plums","volume":"13","author":"Winkler","year":"2018","journal-title":"PLoS One"},{"key":"ref83","doi-asserted-by":"publisher","first-page":"2405","DOI":"10.1016\/j.scib.2023.09.001","article-title":"Intraspecific microdiversity and ecological drivers of lactic acid bacteria in naturally fermented milk ecosystem","volume":"68","author":"You","year":"2023","journal-title":"Sci. Bull."},{"key":"ref84","doi-asserted-by":"publisher","first-page":"370","DOI":"10.1186\/s12866-024-03498-9","article-title":"Heterologous expression of the Oenococcus oeni two-component signal transduction response regulator in the Lactiplantibacillus plantarum WCFS1 strain enhances acid stress tolerance","volume":"24","author":"Zheng","year":"2024","journal-title":"BMC Microbiol."}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2025.1657712\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,9,24]],"date-time":"2025-09-24T05:42:48Z","timestamp":1758692568000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2025.1657712\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,9,24]]},"references-count":85,"alternative-id":["10.3389\/fmicb.2025.1657712"],"URL":"https:\/\/doi.org\/10.3389\/fmicb.2025.1657712","relation":{},"ISSN":["1664-302X"],"issn-type":[{"value":"1664-302X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,9,24]]},"article-number":"1657712"}}