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Phylogenomic Analysis of Oenococcus oeni Reveals Specific Domestication of Strains to Cider and Wines

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1007/978-94-017-2027-4_16openalex-snapshot

Lactic acid bacteria in the quality improvement and depreciation of wine

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Genotypic diversity in Oenococcus oeni by high-density microarray comparative genome hybridization and whole genome sequencing

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Oenococcus alcoholitolerans sp. nov., a lactic acid bacteria isolated from cachaça and ethanol fermentation processes

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Selection criteria and tools for malolactic starters development: an update

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Bread, beer and wine: Yeast domestication in the Saccharomyces sensu stricto complex

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Genomic analysis of PSU-1 and its relevance to winemaking

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The microbial pan-genome

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Leuconostoc, characteristics, use in dairy technology and prospects in functional foods

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The microbial ecology of wine grape berries

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Comparative genomics: the bacterial pan-genome

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Chemical Characterization of Asturian Cider

inferredcites →https://doi.org/10.1038/ncomms5044openalex-snapshot

A Gondwanan imprint on global diversity and domestication of wine and cider yeast Saccharomyces uvarum

inferredcites →https://doi.org/10.1073/pnas.0607117103openalex-snapshot

Comparative genomics of the lactic acid bacteria

inferredcites →https://doi.org/10.1073/pnas.0906412106openalex-snapshot

Shifting the genomic gold standard for the prokaryotic species definition

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APE: Analyses of Phylogenetics and Evolution in R language

inferredcites →https://doi.org/10.1093/bioinformatics/btm091openalex-snapshot

Enhancements and modifications of primer design program Primer3

inferredcites →https://doi.org/10.1093/bioinformatics/btn614openalex-snapshot

MFEprimer: multiple factor evaluation of the specificity of PCR primers

inferredcites →https://doi.org/10.1093/bioinformatics/btp324openalex-snapshot

Fast and accurate short read alignment with Burrows–Wheeler transform

inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot

The Sequence Alignment/Map format and SAMtools

inferredcites →https://doi.org/10.1093/bioinformatics/btp698openalex-snapshot

Fast and accurate long-read alignment with Burrows–Wheeler transform

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Inference of Population Structure Using Multilocus Genotype Data

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MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

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Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

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KAAS: an automatic genome annotation and pathway reconstruction server

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Primer3—new capabilities and interfaces

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A partial proteome reference map of the wine lactic acid bacterium Oenococcus oeni ATCC BAA-1163

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Genotype to phenotype: identification of diagnostic vibrio phenotypes using whole genome sequences

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Oenococcus kitaharae sp. nov., a non-acidophilic and non-malolactic-fermenting oenococcus isolated from a composting distilled shochu residue

inferredcites →https://doi.org/10.1101/gr.121285.111openalex-snapshot

Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution

inferredcites →https://doi.org/10.1101/gr.1224503openalex-snapshot

OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes

inferredcites →https://doi.org/10.1101/gr.335003openalex-snapshot

Evolutionary Implications of Microbial Genome Tetranucleotide Frequency Biases

inferredcites →https://doi.org/10.1111/j.1365-2672.2006.02890.xopenalex-snapshot

Lactic acid bacteria associated with wine grapes from several Australian vineyards

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Bread, beer and wine: Saccharomyces cerevisiae diversity reflects human history

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Evidence for autotetraploidy associated with reproductive isolation in Saccharomyces cerevisiae: towards a new domesticated species

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Application of tetranucleotide frequencies for the assignment of genomic fragments

inferredcites →https://doi.org/10.1111/j.1755-0238.2005.tb00286.xopenalex-snapshot

Oenococcus oeni and malolactic fermentation – moving into the molecular arena

inferredcites →https://doi.org/10.1111/j.1755-0998.2009.02591.xopenalex-snapshot

Inferring weak population structure with the assistance of sample group information

inferredcites →https://doi.org/10.1128/aem.01544-10openalex-snapshot

Evidence of Distinct Populations and Specific Subpopulations within the SpeciesOenococcus oeni

inferredcites →https://doi.org/10.1128/aem.02563-08openalex-snapshot

Multilocus Sequence Typing of Oenococcus oeni : Detection of Two Subpopulations Shaped by Intergenic Recombination

inferredcites →https://doi.org/10.1128/aem.48.5.1034-1038.1984openalex-snapshot

Evolution of Yeasts and Lactic Acid Bacteria During Fermentation and Storage of Bordeaux Wines

inferredcites →https://doi.org/10.1128/aem.50.4.872-876.1985openalex-snapshot

Occurrence and properties of bacteriophages of Leuconostoc oenos in Australian wines

inferredcites →https://doi.org/10.1128/genomea.01077-14openalex-snapshot

Genome Sequences of Five Oenococcus oeni Strains Isolated from Nero Di Troia Wine from the Same Terroir in Apulia, Southern Italy

inferredcites →https://doi.org/10.1128/jb.01351-06openalex-snapshot

Evolutionary Genomics of Lactic Acid Bacteria

inferredcites →https://doi.org/10.1128/jb.01457-07openalex-snapshot

Role of Hypermutability in the Evolution of the GenusOenococcus

inferredcites →https://doi.org/10.1128/jb.179.12.3899-3913.1997openalex-snapshot

Compositional biases of bacterial genomes and evolutionary implications

inferredcites →https://doi.org/10.1146/annurev.food.102308.124134openalex-snapshot

Genomic Evolution of Domesticated Microorganisms

inferredcites →https://doi.org/10.1155/2012/205274openalex-snapshot

Genome Signature Difference between Deinococcus radiodurans and Thermus thermophilus

inferredcites →https://doi.org/10.1155/2012/789125openalex-snapshot

Erratum to “Evolution of the FGF Gene Family”

inferredcites →https://doi.org/10.1186/1471-2148-6-84openalex-snapshot

The reach of the genome signature in prokaryotes.

inferredcites →https://doi.org/10.1186/1471-2164-11-464openalex-snapshot

Analysis of intra-genomic GC content homogeneity within prokaryotes

inferredcites →https://doi.org/10.1186/1471-2164-13-373openalex-snapshot

Comparative analysis of the Oenococcus oeni pan genome reveals genetic diversity in industrially-relevant pathways

inferredcites →https://doi.org/10.1186/1471-2164-14-913openalex-snapshot

Microbial genomic taxonomy

inferredcites →https://doi.org/10.1186/1471-2164-9-75openalex-snapshot

The RAST Server: Rapid Annotations using Subsystems Technology

inferredcites →https://doi.org/10.1186/gb-2004-5-2-r12openalex-snapshot

Versatile and open software for comparing large genomes

inferredcites →https://doi.org/10.1371/journal.pgen.0010005openalex-snapshot

Evidence for Domesticated and Wild Populations of Saccharomyces cerevisiae

inferredcites →https://doi.org/10.1371/journal.pone.0008113openalex-snapshot

Examination of Genome Homogeneity in Prokaryotes Using Genomic Signatures

inferredcites →https://doi.org/10.1371/journal.pone.0029626openalex-snapshot

Functional Divergence in the Genus Oenococcus as Predicted by Genome Sequencing of the Newly-Described Species, Oenococcus kitaharae

inferredcites →https://doi.org/10.1371/journal.pone.0030087openalex-snapshot

Direct Comparisons of Illumina vs. Roche 454 Sequencing Technologies on the Same Microbial Community DNA Sample

inferredcites →https://doi.org/10.1371/journal.pone.0049082openalex-snapshot

Identification of pOENI-1 and Related Plasmids in Oenococcus oeni Strains Performing the Malolactic Fermentation in Wine

inferredcites →https://doi.org/10.1371/journal.pone.0098898openalex-snapshot

Exopolysaccharide (EPS) Synthesis by Oenococcus oeni: From Genes to Phenotypes

inferredcites →https://doi.org/10.2436/20.1501.01.186openalex-snapshot

Isolation, selection, and characterization of highly ethanol-tolerant strains of Oenococcus oeni from south Catalonia.

inferredcites →https://doi.org/10.32614/r.manualsopenalex-snapshot

R: A Language and Environment for Statistical Computing

inferredcites →https://doi.org/10.4161/fly.19695openalex-snapshot

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.2139/ssrn.4679995openalex-extracted

Oenococcus Pseudoeni Sp. Nov., a Lactic Acid Bacterium Isolated from French Cider

inferred← citeshttps://doi.org/10.1002/9781119588320.ch4openalex-snapshot

Lactic Acid Bacteria

inferred← citeshttps://doi.org/10.1007/978-3-031-72000-0_5openalex-snapshot

Technological and Evolutionary Principles for the Domestication of Fermenting Microorganisms

inferred← citeshttps://doi.org/10.1007/978-3-319-60021-5_17openalex-snapshot

Physical and Chemical Stress Factors in Lactic Acid Bacteria

inferred← citeshttps://doi.org/10.1007/978-3-319-60021-5_19openalex-snapshot

Genomic Evolution and Adaptation to Wine of Oenococcus oeni

inferred← citeshttps://doi.org/10.1007/s00253-019-09689-zopenalex-snapshot

Distribution of Oenococcus oeni populations in natural habitats

inferred← citeshttps://doi.org/10.1007/s11274-021-03205-0openalex-snapshot

Molecular tools for the analysis of the microbiota involved in malolactic fermentation: from microbial diversity to selection of lactic acid bacteria of enological interest

inferred← citeshttps://doi.org/10.1007/s12033-017-0021-zopenalex-snapshot

Molecular Cloning, Expression and Characterization of Oenococcus oeni Priming Glycosyltransferases

inferred← citeshttps://doi.org/10.1016/b978-0-443-33914-1.00037-4openalex-snapshot

Malolactic fermentation

inferred← citeshttps://doi.org/10.1016/j.carbpol.2017.09.056openalex-snapshot

A dextran with unique rheological properties produced by the dextransucrase from Oenococcus kitaharae DSM 17330

inferred← citeshttps://doi.org/10.1016/j.copbio.2018.11.014openalex-snapshot

Multi-omics and potential applications in wine production

inferred← citeshttps://doi.org/10.1016/j.cub.2019.04.025openalex-snapshot

Domestication of Industrial Microbes

inferred← citeshttps://doi.org/10.1016/j.fm.2025.104886openalex-snapshot

Comparative genomics and phenotypes of Oenococcus alcoholitolerans and Oenococcus oeni, two sister species adapted to ethanol-rich environments

inferred← citeshttps://doi.org/10.1016/j.foodres.2017.09.039openalex-snapshot

Identification of variable genomic regions related to stress response in Oenococcus oeni

inferred← citeshttps://doi.org/10.1016/j.foodres.2024.114027openalex-snapshot

Influence of pH on Oenococcus oeni metabolism: Can the slowdown of citrate consumption improve its acid tolerance?

inferred← citeshttps://doi.org/10.1016/j.ijfoodmicro.2016.11.025openalex-snapshot

Linking wine lactic acid bacteria diversity with wine aroma and flavour

inferred← citeshttps://doi.org/10.1016/j.ijfoodmicro.2017.06.024openalex-snapshot

Whole transcriptome RNAseq analysis of Oenococcus oeni reveals distinct intra-specific expression patterns during malolactic fermentation, including genes involved in diacetyl metabolism

inferred← citeshttps://doi.org/10.1016/j.ijfoodmicro.2022.109617openalex-snapshot

The production of preconditioned freeze-dried Oenococcus oeni primes its metabolism to withstand environmental stresses encountered upon inoculation into wine

inferred← citeshttps://doi.org/10.1016/j.ijfoodmicro.2023.110276openalex-snapshot

Alcoholic fermentation drives the selection of Oenococcus oeni strains in wine but not in cider

inferred← citeshttps://doi.org/10.1016/j.ijfoodmicro.2025.111539openalex-snapshot

Cognac distillation wines host specific Oenococcus oeni strains representing a novel genetic lineage

inferred← citeshttps://doi.org/10.1016/j.ijfoodmicro.2026.111992openalex-snapshot

Wild Australian niches as a source of novel lactic acid bacteria and malolactic fermentation candidates

inferred← citeshttps://doi.org/10.1016/j.ijms.2016.02.001openalex-snapshot

Advances in wine analysis by PTR-ToF-MS: Optimization of the method and discrimination of wines from different geographical origins and fermented with different malolactic starters

inferred← citeshttps://doi.org/10.1016/j.lwt.2017.03.054openalex-snapshot

Presence of Oenococcus oeni and other lactic acid bacteria in grapes and wines from Priorat (Catalonia, Spain)

inferred← citeshttps://doi.org/10.1016/j.resmic.2023.104048openalex-snapshot

Experimental evolution forcing Oenococcus oeni acid tolerance highlights critical role of the citrate locus

inferred← citeshttps://doi.org/10.1016/j.syapm.2016.11.003openalex-snapshot

Exploring the biodiversity of two groups of Oenococcus oeni isolated from grape musts and wines: Are they equally diverse?

inferred← citeshttps://doi.org/10.1093/femsre/fux034openalex-snapshot

Oenococcus oeni and the genomic era

inferred← citeshttps://doi.org/10.1111/ajgw.12436openalex-snapshot

Oenococcus oeni, a species born and moulded in wine: a critical review of the stress impacts of wine and the physiological responses

inferred← citeshttps://doi.org/10.1111/jam.13946openalex-snapshot

Adaptation of two groups ofOenococcus oenistrains to red and white wines: the role of acidity and phenolic compounds

inferred← citeshttps://doi.org/10.1128/aem.00997-19openalex-snapshot

Lysogeny in the Lactic Acid Bacterium Oenococcus oeni Is Responsible for Modified Colony Morphology on Red Grape Juice Agar

inferred← citeshttps://doi.org/10.1128/aem.02322-16openalex-snapshot

Biogeography of Oenococcus oeni Reveals Distinctive but Nonspecific Populations in Wine-Producing Regions

inferred← citeshttps://doi.org/10.1128/mra.01072-22openalex-snapshot

Draft Genome Sequence of Oenococcus kitaharae CRBO2176, Isolated from Homemade Water Kefir

inferred← citeshttps://doi.org/10.1186/s12864-016-2604-7openalex-snapshot

Consensus pan-genome assembly of the specialised wine bacterium Oenococcus oeni

inferred← citeshttps://doi.org/10.1186/s12864-016-3338-2openalex-snapshot

Carbohydrate metabolism in Oenococcus oeni: a genomic insight

inferred← citeshttps://doi.org/10.1186/s12864-019-5692-3openalex-snapshot

Expanding the biodiversity of Oenococcus oeni through comparative genomics of apple cider and kombucha strains

inferred← citeshttps://doi.org/10.1371/journal.pone.0190094openalex-snapshot

Wine yeast phenomics: A standardized fermentation method for assessing quantitative traits of Saccharomyces cerevisiae strains in enological conditions

inferred← citeshttps://doi.org/10.20870/oeno-one.2017.51.4.1861openalex-snapshot

Two different Oenococcus oeni lineages are associated to either red or white wines in Burgundy: genomics and metabolomics insights

inferred← citeshttps://doi.org/10.20870/oeno-one.2018.52.1.1908openalex-snapshot

Selection and characterization of autochthonous strains of Oenococcus oeni for vinification in Priorat (Catalonia, Spain)

inferred← citeshttps://doi.org/10.2139/ssrn.5388133openalex-snapshot

Cognac Distillation Wines Host Specific Oenococcus Oeni Strains Representing a Novel Genetic Lineage

inferred← citeshttps://doi.org/10.21548/38-2-1333openalex-snapshot

Microbial Resources and Innovation in the Wine Production Sector

inferred← citeshttps://doi.org/10.33073/pjm-2022-026openalex-snapshot

Genomic Analysis of an Excellent Wine-Making Strain Oenococcus oeni SD-2a

inferred← citeshttps://doi.org/10.3389/fmicb.2017.00534openalex-snapshot

Genome-Scale Reconstruction of the Metabolic Network in Oenococcus oeni to Assess Wine Malolactic Fermentation

inferred← citeshttps://doi.org/10.3389/fmicb.2017.00995openalex-snapshot

Microbial Resources and Enological Significance: Opportunities and Benefits

inferred← citeshttps://doi.org/10.3389/fmicb.2018.00090openalex-snapshot

Oenococcus oeni in Chilean Red Wines: Technological and Genomic Characterization

inferred← citeshttps://doi.org/10.3389/fmicb.2018.00291openalex-snapshot

Mapping the Physiological Response of Oenococcus oeni to Ethanol Stress Using an Extended Genome-Scale Metabolic Model

inferred← citeshttps://doi.org/10.3389/fmicb.2018.02415openalex-snapshot

Conversion of Methionine to Cysteine in Lactobacillus paracasei Depends on the Highly Mobile cysK-ctl-cysE Gene Cluster

inferred← citeshttps://doi.org/10.3389/fmicb.2023.1100501openalex-snapshot

Metabolic behavior for a mutant Oenococcus oeni strain with high resistance to ethanol to survive under oenological multi-stress conditions

inferred← citeshttps://doi.org/10.3389/fmicb.2025.1452334openalex-snapshot

Effects of regional location on the genotype and phenotype of historical Irish brewing yeast

inferred← citeshttps://doi.org/10.3389/fmicb.2025.1657712openalex-snapshot

A reassessment of the infra-species diversity patterns in the wine-associated Oenococcus oeni

inferred← citeshttps://doi.org/10.3390/beverages6010008openalex-snapshot

Lactic Fermented Fruit or Vegetable Juices: Past, Present and Future

inferred← citeshttps://doi.org/10.3390/fermentation12100466openalex-snapshot

Comparative Genomic Characterization of Indigenous Oenococcus oeni Strains from Northwestern Argentina

inferred← citeshttps://doi.org/10.3390/fermentation5010001openalex-snapshot

Changes in the Composition of the Lactic Acid Bacteria Behavior and the Diversity of Oenococcus oeni Isolated from Red Wines Supplemented with Selected Grape Phenolic Compounds

inferred← citeshttps://doi.org/10.3390/fermentation6040115openalex-snapshot

Lactic Acid Bacterial Production of Exopolysaccharides from Fruit and Vegetables and Associated Benefits

inferred← citeshttps://doi.org/10.3390/fermentation7010024openalex-snapshot

Biodiversity of Oenological Lactic Acid Bacteria: Species- and Strain-Dependent Plus/Minus Effects on Wine Quality and Safety

inferred← citeshttps://doi.org/10.3390/fermentation8120726openalex-snapshot

Analysis of the Genome Architecture of Lacticaseibacillus paracasei UNQLpc 10, a Strain with Oenological Potential as a Malolactic Starter

inferred← citeshttps://doi.org/10.3390/microorganisms5030039openalex-snapshot

Microorganisms in Fermented Apple Beverages: Current Knowledge and Future Directions

inferred← citeshttps://doi.org/10.3390/microorganisms9040856openalex-snapshot

Distribution of Prophages in the Oenococcus oeni Species

inferred← citeshttps://doi.org/10.5281/zenodo.55140openalex-snapshot

Cosmopolitismo, Paz Y Democracia: Repensando El Lugar Kantiano De La Política En Un Mundo Global

inferred← citeshttps://doi.org/10.62517/jlsa.202507312openalex-snapshot

Optimization of Lactic Acid Bacteria Fermentation and Antioxidant Activity of Lycium Ruthenicum Murr. Juice

inferred← citeshttps://doi.org/10.70675/09c43d24z25f3z4d43z9c40zdcecbea7eb32openalex-snapshot

Bactériophages infectant la bactérie lactique Oenococcus oeni : diversité et rôles dans l'écosystème oenologique

inferred← citeshttps://doi.org/10.70675/2388969dz6b30z4402zb34cz2172eebe7be7openalex-snapshot

Diversity and genomic characteristics of Oenococcus oeni

inferred← citeshttps://doi.org/10.70675/902cde75za1a5z4c44zadc3zd89e019a4958openalex-snapshot

Étude de la tolérance à l’acidité et aux polyphénols chez Oenococcus oeni, de la caractérisation des effets à l’identification des mécanismes de réponse aux stress

inferred← citeshttps://doi.org/10.70675/a34fb787zb479z41deza686z0356d08abd2fopenalex-snapshot

La lysogénie dans l'espèce Oenococcus oeni : incidence et impacts sur la performance de levains malolactiques

inferred← citeshttps://doi.org/10.70675/b593be6ez7ef2z4455z9844z134d293ae5a6openalex-snapshot

Mécanismes moléculaires impliqués dans la régulation de la réponse au stress chez Oenococcus oeni et évolution expérimentale

inferred← citeshttps://doi.org/10.70675/c15bf6d8zf0a9z4303za8c4za834ecfd87f1openalex-snapshot

Study of the biodiversity of lactic acid bacteria in Cognac distillation wines

inferred← citeshttps://doi.org/10.70675/d473c943z420fz449cza66ezcd8c0b5257d0openalex-snapshot

Experimental evolution of the wine-associated bacterium Oenococcus oeni in extreme environments : application to the selection of improved malolactic starters

inferred← citeshttps://doi.org/10.70675/dd0af923z80d1z4b78zbc93z591d9d352cddopenalex-snapshot

Phylogenomic Structure of Oenococcus oeni and its Adaptation to Different Products Unveiled by Comparative Genomics and Metabolomics.

inferred← citeshttps://doi.org/10.70675/dd84a82bz12e9z4c30zbb7czbc5ddcb79cc0openalex-snapshot

Étude des causes génétiques de la plasticité phénotypique par une approche de cartographie de QTLs : cas de la levure oenologique Saccharomyces cerevisiae

inferred← citeshttps://doi.org/10.70675/ff94577azbd3dz406az95daz8dbc19f50d2aopenalex-snapshot

Bioversité des oenocoques dans les boissons fermentées et modalités d'intéractions avec leurs bactériophages

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