P. Almeida, R. Barbosa, P. Zalar, Y. Imanishi, K. Shimizu et al., A population genomics insight into the Mediterranean origins of wine yeast domestication, Molecular Ecology, vol.18, issue.Suppl 1, pp.5412-5427, 2015.
DOI : 10.1101/gr.074492.107

G. Antalick, Bilan biochimique et sensoriel des modifications de la note fruitée des vins rouges lors de la fermentation malolactique : rôle particulier des esters (Doctoral Dissertation), 2010.

G. Antalick and M. Perello, Development, validation and application of a specific method for the quantitative determination of wine esters by headspace-solid-phase microextraction-gas chromatography???mass spectrometry, Food Chemistry, vol.121, issue.4, pp.1236-1245, 2010.
DOI : 10.1016/j.foodchem.2010.01.011

G. Antalick, M. Perello, and G. De-revel, Characterization of Fruity Aroma Modifications in Red Wines during Malolactic Fermentation, Journal of Agricultural and Food Chemistry, vol.60, issue.50, pp.12371-12383, 2012.
DOI : 10.1021/jf303238n

A. Athané, E. Bilhère, E. Bon, G. Morel, P. Lucas et al., Characterization of an acquired dps -containing gene island in the lactic acid bacterium Oenococcus oeni, Journal of Applied Microbiology, vol.105, 2008.

R. K. Aziz, D. Bartels, A. A. Best, M. Dejongh, T. Disz et al., The RAST Server: Rapid Annotations using Subsystems Technology, BMC Genomics, vol.9, issue.1, pp.75-85, 2008.
DOI : 10.1186/1471-2164-9-75

URL : https://bmcgenomics.biomedcentral.com/track/pdf/10.1186/1471-2164-9-75?site=bmcgenomics.biomedcentral.com

E. J. Bartowsky, Oenococcus oeni and malolactic fermentation ??? moving into the molecular arena, Australian Journal of Grape and Wine Research, vol.135, issue.2, pp.174-187, 2005.
DOI : 10.1007/s00203-003-0599-3

E. Bilhère, P. M. Lucas, O. Claisse, and A. Lonvaud-funel, Multilocus Sequence Typing of Oenococcus oeni: Detection of Two Subpopulations Shaped by Intergenic Recombination, Applied and Environmental Microbiology, vol.75, issue.5, pp.1291-1300, 2009.
DOI : 10.1128/AEM.02563-08

N. A. Bokulich, J. H. Thorngate, P. M. Richardson, and D. A. Mills, PNAS Plus: From the Cover: Microbial biogeography of wine grapes is conditioned by cultivar, vintage, and climate, Proceedings of the National Academy of Sciences, vol.8, issue.6, pp.139-148, 2014.
DOI : 10.1371/journal.pone.0069885

E. Bon, A. Delaherche, E. Bilhere, A. De-daruvar, A. Lonvaud-funel et al., Oenococcus oeni Genome Plasticity Is Associated with Fitness, Applied and Environmental Microbiology, vol.75, issue.7, pp.2079-2090, 2009.
DOI : 10.1128/AEM.02194-08

URL : https://hal.archives-ouvertes.fr/inria-00392015

A. R. Borneman, E. J. Bartowsky, J. Mccarthy, and P. J. Chambers, Genotypic diversity in Oenococcus oeni by high-density microarray comparative genome hybridization and whole genome sequencing, Applied Microbiology and Biotechnology, vol.18, issue.2, pp.681-691, 2010.
DOI : 10.1099/00221287-146-12-3195

A. R. Borneman, J. M. Mccarthy, P. J. Chambers, and E. J. Bartowsky, Comparative analysis of the Oenococcus oeni pan genome reveals genetic diversity in industrially-relevant pathways, BMC Genomics, vol.13, issue.1, pp.373-383, 2012.
DOI : 10.1093/nar/gkm321

J. Bridier, O. Claisse, M. Coton, E. Coton, and A. Lonvaud-funel, Evidence of Distinct Populations and Specific Subpopulations within the Species Oenococcus oeni, Applied and Environmental Microbiology, vol.76, issue.23, pp.7754-7764, 2010.
DOI : 10.1128/AEM.01544-10

H. Campbell-sills, M. Khoury, M. Favier, A. Romano, F. Biasioli et al., Phylogenomic Analysis of Oenococcus oeni Reveals Specific Domestication of Strains to Cider and Wines, Genome Biology and Evolution, vol.7, issue.6, pp.1506-1518, 2015.
DOI : 10.1093/gbe/evv084

URL : https://hal.archives-ouvertes.fr/hal-01202801

V. Capozzi and G. Spano, Food Microbial Biodiversity and ?Microbes of Protected Origin?, Frontiers in Microbiology, vol.2, 2011.
DOI : 10.3389/fmicb.2011.00237

URL : http://journal.frontiersin.org/article/10.3389/fmicb.2011.00237/pdf

V. Capozzi, C. Garofalo, M. A. Chiriatti, F. Grieco, and G. Spano, Microbial terroir and food -319 - OENO One) innovation: The case of yeast biodiversity in wine, Microbiological Research, vol.51, issue.181, pp.309-322, 2015.

R. Chikhi and G. Rizk, Space-efficient and exact de Bruijn graph representation based on a Bloom filter, Algorithms for Molecular Biology, vol.8, pp.1748-7188, 2013.
DOI : 10.1007/978-3-642-33122-0_19

URL : https://hal.archives-ouvertes.fr/hal-00868805

A. Cibrario, C. Peanne, M. Lailheugue, H. Campbell-sills, and M. Dols-lafargue, Carbohydrate metabolism in Oenococcus oeni: a genomic insight, BMC Genomics, vol.56, issue.Suppl 1, pp.10-1186, 2016.
DOI : 10.1099/ijs.0.64288-0

URL : https://hal.archives-ouvertes.fr/hal-01607032

C. R. Davis, D. J. Wibowo, T. H. Lee, and G. H. Fleet, Growth and metabolism of lactic acid bacteria during and after malolactic fermentation of wines at different pH, Applied and Environmental Microbiology, vol.51, pp.539-545, 1986.

G. De-revel, Le diacétyle, les composés dicarbonyles et leurs produits de réduction dans le vin, 1999.

M. Dimopoulou, M. Vuillemin, H. Campbell-sills, P. M. Lucas, P. Ballestra et al., Exopolysaccharide (EPS) Synthesis by Oenococcus oeni: From Genes to Phenotypes, PLoS ONE, vol.Chem, issue.285(14), 2014.
DOI : 10.1371/journal.pone.0098898.s001

URL : https://doi.org/10.1371/journal.pone.0098898

M. Dols-lafargue, H. Y. Lee, L. Marrec, C. Heyraud, A. Chambat et al., Characterization of gtf, a Glucosyltransferase Gene in the Genomes of Pediococcus parvulus and Oenococcus oeni, Two Bacterial Species Commonly Found in Wine, Applied and Environmental Microbiology, vol.74, issue.13, pp.4079-40901000673, 1128.
DOI : 10.1128/AEM.00673-08

G. L. Douglas and T. R. Klaenhammer, Genomic Evolution of Domesticated Microorganisms, Annual Review of Food Science and Technology, vol.1, issue.1, 2010.
DOI : 10.1146/annurev.food.102308.124134

E. Khoury, M. Campbell-sills, H. Salin, F. Guichoux, E. Claisse et al., ABSTRACT, Applied and Environmental Microbiology, vol.83, issue.3, pp.2322-1602322, 2017.
DOI : 10.1128/AEM.02322-16

J. A. Gilbert, D. Van-der-lelie, and I. Zarraonaindia, Microbial terroir for wine grapes, Proceedings of the National Academy of Sciences, vol.157, issue.4, 2014.
DOI : 10.1078/0944-5013-00163

URL : http://www.pnas.org/content/111/1/5.full.pdf

P. Hernandez-orte, M. Cersosimo, N. Loscos, J. Cacho, E. Garcia-moruno et al., Aroma development from non-floral grape precursors by wine lactic acid bacteria, Food Research International, vol.42, issue.7, pp.773-781, 2009.
DOI : 10.1016/j.foodres.2009.02.023

I. S. Hornsey, The Chemistry and Biology of Winemaking, 2007.

I. Cañas, P. M. García-romero, E. , G. Alonso, S. et al., Changes in the aromatic composition of Tempranillo wines during spontaneous malolactic fermentation, Journal of Food Composition and Analysis, vol.21, issue.8, pp.724-730, 2008.
DOI : 10.1016/j.jfca.2007.12.005

S. Knight, S. Klaere, B. Fedrizzi, and M. R. Goddard, Regional microbial signatures positively correlate with differential wine phenotypes: evidence for a microbial aspect to terroir, Scientific Reports, vol.6, issue.1, 2015.
DOI : 10.1111/j.1471-8286.2005.01155.x

C. Knoll, M. Du-toit, S. Schnell, D. Rauhut, and S. Irmler, Cloning and characterisation of a cystathionine ??/??-lyase from two Oenococcus oeni oenological strains, Applied Microbiology and Biotechnology, vol.11, issue.12, pp.1051-1060, 2011.
DOI : 10.1016/S0958-6946(01)00049-8

P. Kotrba, M. Inui, and H. Yukawa, Bacterial phosphotransferase system (PTS) in carbohydrate uptake and control of carbon metabolism, Journal of Bioscience and Bioengineering, vol.92, issue.6, pp.502-517, 2001.
DOI : 10.1016/S1389-1723(01)80308-X

S. Lahtinen, A. C. Ouwehand, S. Salminen, V. Wright, and A. , Lactic Acid Bacteria: Microbiological and Functional Aspects, 2011.

J. Lee, G. Hwang, C. Lee, and Y. Hong, Metabolomics Reveals Alterations in Both Primary and Secondary Metabolites by Wine Bacteria, Journal of Agricultural and Food Chemistry, vol.57, issue.22, pp.10772-1078310, 1021.
DOI : 10.1021/jf9028442

J. Lee, Y. Hong, and C. Lee, H NMR- and GC-Based Metabolic Profiling, Journal of Agricultural and Food Chemistry, vol.57, issue.11, pp.4810-481710, 1021.
DOI : 10.1021/jf900502a

J. Legras, D. Merdinoglu, J. Cornuet, and F. Karst, Bread, beer and wine: Saccharomyces cerevisiae diversity reflects human history, Molecular Ecology, vol.163, issue.10, 2007.
DOI : 10.1016/j.tig.2006.07.008

M. Liu, A. Nauta, C. Francke, and R. J. Siezen, Comparative Genomics of Enzymes in Flavor-Forming Pathways from Amino Acids in Lactic Acid Bacteria, Applied and Environmental Microbiology, vol.74, issue.15, pp.4590-4600, 2008.
DOI : 10.1128/AEM.00150-08

A. Lonvaud-funel, Lactic acid bacteria in the quality improvement and depreciation of wine, pp.309-322, 1999.
DOI : 10.1007/978-94-017-2027-4_16

T. Magoc and S. L. Salzberg, FLASH: fast length adjustment of short reads to improve genome assemblies, Bioinformatics, vol.27, issue.21, pp.2957-2963, 2011.
DOI : 10.1093/bioinformatics/btr507

S. Malherbe, E. Menichelli, M. Du-toit, A. Tredoux, N. Muller et al., starter cultures, Journal of the Science of Food and Agriculture, vol.43, issue.11, pp.2829-28406115, 2013.
DOI : 10.1021/jf010283u

D. Mills, H. Rawsthorne, C. Parker, D. Tamir, and K. Makarova, Genomic analysis of Oenococcus oeni PSU-1 and its relevance to winemaking, FEMS Microbiology Reviews, vol.29, pp.465-475, 2005.

R. Overbeek, T. Begley, M. Butler, R. , V. Choudhuri et al., The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes, Nucleic Acids Research, vol.33, issue.17, pp.5691-5702, 2005.
DOI : 10.1093/nar/gki866

R. Overbeek, R. Olson, G. D. Pusch, G. J. Olsen, J. J. Davis et al., The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST), Nucleic Acids Research, vol.42, issue.D1, pp.206-214
DOI : 10.1093/nar/gkt1226

M. A. Pozo-bayón, E. G-alegría, M. C. Polo, C. Tenorio, P. J. Martín-Álvarez et al., Starter Cultures, Journal of Agricultural and Food Chemistry, vol.53, issue.22, pp.8729-873510, 1021.
DOI : 10.1021/jf050739y

F. Remize, A. Gaudin, Y. Kong, J. Guzzo, H. Alexandre et al., Oenococcus oeni preference for peptides: qualitative and quantitative analysis of nitrogen assimilation, Archives of Microbiology, vol.23, issue.4, pp.459-469, 2006.
DOI : 10.1016/S0378-1097(97)00109-2

P. Ribéreau-gayon, Y. Glories, A. Maujean, and D. Dubourdieu, Traité d'oenologie -Tome 2 - 6 e éd. -Chimie du vin, 2012.

M. Richter and R. Rosselló-móra, Shifting the genomic gold standard for the prokaryotic species definition, Proceedings of the National Academy of Sciences, vol.361, issue.12, 2009.
DOI : 10.1098/rstb.2006.1914

H. Richter, D. Graaf, A. A. Hamann, I. Unden, and G. , Significance of phosphoglucose isomerase for the shift between heterolactic and mannitol fermentation of fructose by Oenococcus oeni, Archives of Microbiology, vol.180, issue.6, pp.465-470, 2003.
DOI : 10.1007/s00203-003-0617-5

H. Richter, I. Hamann, and G. Unden, Use of the mannitol pathway in fructose fermentation of Oenococcus oeni due to limiting redox regeneration capacity of the ethanol pathway, Archives of Microbiology, vol.175, issue.4, pp.227-233, 2003.
DOI : 10.1128/jb.175.13.3941-3948.1993

R. J. Rowbury and D. D. Woods, O-Succinylhomoserine as an Intermediate in the Synthesis of Cystathionine by Escherichia coli, Journal of General Microbiology, vol.36, issue.3, pp.341-358, 1964.
DOI : 10.1099/00221287-36-3-341

R. J. Rowbury and D. D. Woods, Repression by Methionine of Cystathionase Formation in Escherichia coli, Journal of General Microbiology, vol.35, issue.1, pp.145-158, 1964.
DOI : 10.1099/00221287-35-1-145

I. Saint-girons, C. Parsot, M. M. Zakin, O. Barzu, and G. N. Cohen, Methionine Biosynthesis in Enterobacteriaceae: Biochemical, Regulatory, and Evolutionary Aspect, Critical Reviews in Biochemistry, vol.261, issue.sup1, 1988.
DOI : 10.1128/jb.169.9.3932-3937.1987

S. E. Stein, An integrated method for spectrum extraction and compound identification from gas chromatography/mass spectrometry data, Journal of the American Society for Mass Spectrometry, vol.10, issue.3, pp.770-781, 1999.
DOI : 10.1002/(SICI)1097-0231(19990228)13:4<279::AID-RCM478>3.0.CO;2-I

P. R. Sternes, A. R. Borneman, J. B. Stevens, N. G. De-luca, J. E. Beringer et al., Consensus pangenome assembly of the specialised wine bacterium Oenococcus oeni The purMN Genes of Rhizobium leguminosarum and a superficial link with siderophore production, BMC Genomics MPMI, vol.17, issue.13, pp.228-231, 2000.

K. M. Sumby, V. Jiranek, and P. R. Grbin, Ester synthesis and hydrolysis in an aqueous environment, and strain specific changes during malolactic fermentation in wine with Oenococcus oeni, Food Chemistry, vol.141, issue.3, 2013.
DOI : 10.1016/j.foodchem.2013.03.087

K. Tamura, G. Stecher, D. Peterson, A. Filipski, and S. Kumar, MEGA6: Molecular Evolutionary -321 - OENO One, pp.309-322, 2013.
DOI : 10.1093/molbev/mst197

URL : https://academic.oup.com/mbe/article-pdf/30/12/2725/19498310/mst197.pdf

A. Vallet, P. Lucas, A. Lonvaud-funel, and G. De-revel, Pathways that produce volatile sulphur compounds from methionine in Oenococcus oeni, Journal of Applied Microbiology, vol.181, issue.6, 2008.
DOI : 10.1128/AEM.66.2.571-577.2000

URL : http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2672.2007.03713.x/pdf

J. Vestner, G. De-revel, S. Krieger-weber, D. Rauhut, M. Du-toit et al., Toward automated chromatographic fingerprinting: A non-alignment approach to gas chromatography mass spectrometry data, Analytica Chimica Acta, vol.911, pp.42-58, 2016.
DOI : 10.1016/j.aca.2016.01.020

I. Zarraonaindia, S. M. Owens, P. Weisenhorn, K. West, J. Hampton-marcell et al., The Soil Microbiome Influences Grapevine-Associated Microbiota, mBio, vol.6, issue.2, pp.2527-2541, 2015.
DOI : 10.1128/mBio.02527-14

URL : http://mbio.asm.org/content/6/2/e02527-14.full.pdf