The goals of our researches can be organized  in 4 axes: 


• Genetic basis of phenotypic traits in S. cerevisiae and effect of the environment on population dynamics and fermentation dynamics.


Our research is focused on the detection of QTLs, X-QTLs, eQTLs, fQTLs which explain phenotypic variations such as fermentation rate, duration of the latency phase, responses to nutritional limitations (namely lipid and nitrogen deficiencies), aromas and sulphites production, life history traits (viability, growth rate, .etc..) and fitness. We also develop experimental evolution approaches that allow us to identify candidate genes involved in these phenotypes. Genome editing approaches are used to validate the candidate genes. Finally, we study genotype x environment interactions, for example the impact of phytosterols or dipeptide composition on the expression of genes of interest. These studies concern mainly the species Saccharomyces cerevisiae.

Projects: CASDAR NITROGENES, ANR ENZINVIVO, ITN AROMAGENESIS, ITN YEASTDOC, AIC IPSO

PhD students and post-docs: Carmen Becerra, Irene de Guidi, Alexandre Chamas, Marta Avramova, Amandine Deroite

• Evolutionary history of domesticated yeasts


We seek to trace the evolutionary history of oenology and bakery yeasts through population genomics approaches. Particular interest is also given to the characterization of adaptation mechanisms (horizontal gene transfer, functional analysis of loci under selection, etc ...) by comparative genomic, genetic and functional genomic approaches. These studies concern both the model species Saccharomyces cerevisiae and other yeast species present in grape must (Hanseniaspora uvarum and Hanseniaspora opuntia) or in bread sourdoughs (Kazachstania bulderi and Kazachstania humilis). We also work on ancient wines and breads in collaboration with archaeologists.

Projects: ANR BAKERY, ANR VINICULTURE

• Dynamic and evolution of microbial communities


Our projects aim to characterize the taxonomic and functional diversity of microbial species in grape must and bread sourdoughs, to explore the factors (terroir, grape variety / wheat variety, practices) that influence them and to analyze the microbial flux from the field to the fermented product. We are also interested in the evolutionary dynamics of microbial communities and the evolution of genetic diversity of particular species in a context of microbial community.
Project: ANR BAKERY, ANR PEAKYEAST, FdF "Gluten: myth or reality II", MEM METABAR-FOOD
PhD student (s): Elisa Michel, Lucas Von Gastrow, Jean-Nicolas Jasmin, Sonia Boudaoud

• Emerging properties of microbial interactions


Through the construction of simplified microbial communities, we aim to understand what is the nature of Yeast / Yeast  and Yeast / Bacteria interactions (competition, mutualism, commensalism, amensalism, etc.) in fermented food ecosystem. We would like to understand what are the emerging properties associated with the assembly of species and their complexity. This axis applies to wine and bread ecosystems.


Projects: INRA ModOeno, MEM ENovFood

In terms of finalized objectives, our activities aim to:


• Optimize the control of fermentation processes

• Improve Saccharomyces cerevisiae strains for wine-making

• Construct mixed microbial starter
• Conserve microbial biodiversity involved in fermented products and the associated know-how

Several approaches are used:



• QTLs, xQTLs, eQTLs, fQTLs
• Experimental evolution

• Genome editing

• Comparative genomics, Population genomics, and Metagenomics
• Functional genomics

• Metabolic modeling and ecological interaction

• Participatory research

Contacts:

Virginie Galeote Chargée de Recherches INRA Tél : 04 99 61 21 10 Courriel : virginie.galeote@inra.fr

Delphine Sicard Directrice de Recherches INRA Tél : 04 99 61 24 60 Courriel : delphine.sicard@inra.fr

Staffs:

Researchers, Lecturers and Engineers:

• Frédéric Bigey
• Bruno Blondin
• Sylvie Dequin
• Virginie Galeote (Team leader)
• Jean-Luc Legras
• Thibault Nidelet
• Jessica Noble (Détachée Lallemand)
• Diego Segond
• Delphine Sicard (Team leader)
• Catherine Tesnière

Technicians:

• Cécile Cadoux
• Stéphane Guézenec
• Sandrine Mallet
• Thérèse Marlin
• Martine Pradal
• Olivier Teuf (Détaché Lallemand)

PhD / Postdoc-students:

• Marta Avramova (Post-doc)
• Carmen Becerra (PhD)
• Sonia Boudaoud (PhD)
• Irene de Guidi (PhD)
• Lauriane Mietton (PhD)
• Lucas Von-Gastrow (PhD)

Former students:

• Alexandre Chamas (2017-2019)
• Amandine Deroite (2015-2018)
• Elisa Michel (2015-2018)
• Camille Duc (2014-2017)
• David Ferreira (2014-2017)
• Matthias Eder (2014-2017)
• Jean-Nicolas Jasmin (2017-2019)

Publications

2018:

Legras, J. L., Galeote, V., Bigey, F., Camarasa, C., Marsit, S., Nidelet, T., Sanchez, I., Couloux, A., Guy, Franco-Duarte, R., Marcet-Houben, M., Gabaldon, T., Schuller, D., Sampaio, J. P., Dequin, S. (2018). Adaptation of S. cerevisiae to Fermented Food Environments Reveals Remarkable Genome Plasticity and the Footprints of Domestication. Molecular Biology and Evolution, 35 (7), 1712-1727., DOI : 10.1093/molbev/msy066
Deroite, A., Legras, JL., Rigou, P., Ortiz-Julien, A., Dequin, S. (2018). Lipids modulate acetic acid and thiol final concentrations in wine during fermentation by Saccharomyces cerevisiae × Saccharomyces kudriavzevii hybrids, AMB Expr 8: 130. DOI : org/10.1186/s13568-018-0657-5
Fievet, J., Nidelet, T., Dillmann, C., de Vienne, D. (2018). Heterosis Is a Systemic Property Emerging From Non-linear Genotype-Phenotype Relationships: Evidence From in Vitro Genetics and Computer Simulations. Frontiers in Genetics, 9, 26 p., DOI : 10.3389/fgene.2018.00159
Carbonetto, B., Ramsayer, J., Nidelet, T., Legrand, J., and Sicard, D. (2018). Bakery yeasts, a new model for studies in ecology and evolution. Yeast 0.,1-13, DOI:10.1002/yea.3350.
Tesniere, C., Pradal, M., Bessiere, C., Sanchez, I., Blondin, B., Bigey, F. (2018). Relief from nitrogen starvation triggers transient destabilization of glycolytic mRNAs in Saccharomyces cerevisiae cells. Molecular Biology of the Cell, 29 (4), 490-498., DOI : 10.1091/mbc.E17-01-0061
Collot, D., Nidelet, T., Ramsayer, J., Martin, O. C., Meleard, S., Dillmann, C., Sicard, D., Legrand, J. (2018). Feedback between environment and traits under selection in a seasonal environment: consequences for experimental evolution. Proceedings of the Royal Society. B, Biological Sciences, 285 (1876), 9., DOI : 10.1098/rspb.2018.0284
Galeote, V., Bigey, F., Devillers, H., Dequin, S., Wolfe, K., Neuveglise-Degouy, C. (2018). Genome sequence of Torulaspora microellipsoides CLIB 830T. Genome Announcements, 6 (26), DOI : 10.1128/genomeA.00615-18
Eder, M., Sanchez, I., Brice, C., Camarasa, C., Legras, J. L., Dequin, S. (2018). QTL mapping of volatile compound production in Saccharomyces cerevisiae during alcoholic fermentation. BMC Genomics, 19 (1), 19 p., DOI : 10.1186/s12864-018-4562-8
Lucas, P., Masneuf, I., Legras, J. L., Bely, M., Miot-Sertier, C., Claisse, O., El Khoury, M., Campbell-Sills, H., Börlin, M., Maupeu, J., Vallet-Courbin, A., Pladeau , V., Becquet , S., Chovelon, M., Bauduin, R., Cottereau, P., Coarer, M., Vinsonneau , E., Colosio , M.-C. (2018). Des outils pour fiabiliser les fermentations des vins et cidres biologiques en utilisant les levures et bactéries indigènes. Innovations Agronomiques, 63, 279-291., DOI : 10.15454/1.5191176806543086E12
Englezos, V., Cocolin, Rantsiou, Ortiz-Julien, A., Bloem, A., Dequin, S., Camarasa, C. (2018). Specific phenotypic traits of Starmerella bacillaris related to nitrogen source consumption and central carbon metabolite production during wine fermentation. Applied and Environmental Microbiology, 84 (16)., DOI : 10.1128/AEM.00797-18
Brice, C., Cubillos, F. A., Dequin, S., Camarasa, C., Martínez (2018). Adaptability of the Saccharomyces cerevisiae yeasts to wine fermentation conditions relies on their strong ability to consume nitrogen. Plos One, 13 (2), 20 p., DOI : 10.1371/journal.pone.0192383

2017:

Viel, A., Legras, J. L., Nadai, C., Carlot, M., Lombardi, A., Crespan, M. (Collaborateur), Migliaro, D., Giacomini, A., Corich, V. (2017). The geographic distribution of Saccharomyces cerevisiae isolates within three Italian neighboring winemaking regions reveals strong differences in yeast abundance, genetic diversity and industrial strain dissemination. Frontiers in Microbiology, 8., DOI : 10.3389/fmicb.2017.01595
Casalta, E., Vernhet, A., Sablayrolles, J.-M., Tesniere, C., Salmon, J.-M. (2017). Caractéristiques et rôle des particules solides au cours de la fermentation alcoolique. Revue des Oenologues et des Techniques Vitivinicoles et Oenologiques, 44 (162), 32-34.
Ferreira, D., Galeote, V., Sanchez, I., Legras, J. L., Julien Ortiz, A., Dequin, S. (2017). Yeast multi-stress resistance and lag phase characterization during wine fermentation. FEMS Yeast Research, 11 p.
Mendes, I., Sanchez, I., Franco-Duarte, R., Camarasa, C., Schuller, D., Dequin, S., Sousa, M. J. (2017). Integrating transcriptomics and metabolomics for the analysis of the aroma profiles of Saccharomyces cerevisiae strains from diverse origins. BMC Genomics, 18, 13 p., DOI : 10.1186/s12864-017-3816-1
Di Gianvito, P., Tesniere, C., Suzzi, G., Blondin, B., Tofalo, R. (2017). FLO5 gene controls flocculation phenotype and adhesive properties in a Saccharomyces cerevisiae sparkling wine strain. Scientific Reports, 7, 12., DOI : 10.1038/s41598-017-09990-9
Coi, A. L., Bigey, F., Mallet, S., Marsit, S., Zara, G., Gladieux, P., Galeote, V., Budroni, M., Dequin, S., Legras, J. L. (2017). Genomic signatures of adaptation to wine biological aging conditions in biofilm-forming flor yeasts. Molecular Ecology, 26 (7), 2150-2166. , DOI : 10.1111/mec.14053
Stefanini, I., Albanese, Sordo, Legras, J. L., De Filippo, C., Cavalieri, Donati (2017). SaccharomycesIDentifier, SID: strain-level analysis of Saccharomyces cerevisiae populations by using microsatellite meta-patterns. Scientific Reports, 7 (1), 10 p., DOI : 10.1038/s41598-017-15729-3
Dequin, S., Escudier, J.-L., Bely, M., Noble, J., Albertin, W., Masneuf-Pomarède, I., Marullo, P., Salmon, J.-M., Sablayrolles, J.-M. (2017). How to adapt winemaking practices to modified grape composition under climate change conditions. OENO One, 51 (2), 205-214. , DOI : 10.20870/oeno-one.2016.0.0.1584
Duc, C., Pradal, M., Sanchez, I., Noble, J., Tesniere, C., Blondin, B. (2017). A set of nutrient limitations trigger yeast cell death in a nitrogen-dependent manner during wine alcoholic fermentation. Plos One, 12 (9), 22 p., DOI : 10.1371/journal.pone.0184838
Magalhães, F., Krogerus, Castillo, S., Ortiz-Julien, A., Dequin, S., Gibson (2017). Exploring the potential of Saccharomyces eubayanus as a parent for new interspecies hybrid strains in winemaking. FEMS Yeast Research., DOI : 10.1093/femsyr/fox049
Rollero, S., Mouret, J.-R., Bloem, A., Sanchez, I., Ortiz-Julien, A., Sablayrolles, J.-M., Dequin, S., Camarasa, C. (2017). Quantitative 13 C-isotope labelling-based analysis to elucidate the influence of environmental parameters on the production of fermentative aromas during wine fermentation. Microbial Biotechnology, 14 p., DOI : 10.1111/1751-7915.12749
Dupont, J., Dequin, S., Giraud, T., Le Tacon, F., Marsit, S., Ropars, J., Richard, F., Selosse, M.-A. (2017). Fungi as a source of food. Microbiology Spectrum, 5 (3), 22 p., DOI : 10.1128/microbiolspec.FUNK-0030-2016
Crepin, L., Truong, N. M., Bloem, A., Sanchez, I., Dequin, S., Camarasa, C. (2017). Management of multiple nitrogen sources during wine fermentation by Saccharomyces cerevisiae. Applied and Environmental Microbiology, 85 (4), 21, DOI : 10.1128/aem.02617-16
Sarilar, V., Sterck, L., Matsumoto, S., Jacques, N., Neuveglise, C., Tinsley, C. R., Sicard, D., Casaregola, S. (2017). Genome sequence of the type strain CLIB 1764 T (= CBS 14374 T ) of the yeast species Kazachstania saulgeensis isolated from French organic sourdough. Genomics Data, 13, 41-43, DOI : 10.1016/j.gdata.2017.07.003

2016:

Nidelet, T., Brial, P., Camarasa, C., Dequin, S. (2016). Diversity of flux distribution in central carbon metabolism of S. cerevisiae strains from diverse environments. Microbial Cell Factories, 15 (1), 13 p., DOI : 10.1186/s12934-016-0456-0
Tapsoba, F., Savadogo, A., Legras, J. L., Zongo, C., Traore, A. S. (2016). Microbial diversity and biochemical characteristics of Borassus akeassii wine. Letters in Applied Microbiology, 63 (4), 297-306., DOI : 10.1111/lam.12619
Casalta, E., Vernhet, A., Sablayrolles, J.-M., Tesniere, C., Salmon, J.-M. (2016). Review: Characterization and Role of Grape Solids during Alcoholic Fermentation under Enological Conditions. American Journal of Enology and Viticulture, 67 (1), 18 p., DOI : 10.5344/ajev.2015.15060
Börlin, M., Venet, P., Claisse, O., Salin, F., Legras, J. L., Masneuf-Pomarede, I. (2016). Cellar-associated Saccharomyces cerevisiae population structure revealed high diversity and perennial persistence in Sauternes wine estates. Applied and Environmental Microbiology, 82 (10), 2909-2918., DOI : 10.1128/AEM.03627-15
Legras, J. L., Moreno-Garcia, J., Zara, S., Zara, G., Garcia-Martinez, T., Mauricio, J. C., Mannazzu, I., Coi, A. L., Bou Zeidan, M., Dequin, S., Moreno, J., Budroni, M. (2016). Flor yeast: new perspectives beyond wine aging. Frontiers in Microbiology, 7, 11 p., DOI : 10.3389/fmicb.2016.00503
Masneuf-Pomarede, I., Salin, F., Börlin, M., Coton, E., Coton, M., Jeune, C. L., Legras, J. L. (2016). Microsatellite analysis of Saccharomyces uvarum diversity. FEMS Yeast Research, 16 (2), 12 p., DOI : 10.1093/femsyr/fow002
Jacques, N., Sarilar, V., Urien, C., Lopes, M. R., Morais, C. G., Uetanabaro, A. P. T., Tinsley, C., Rosa, C. A., Sicard, D., Casaregola, S. (2016). Three novel ascomycetous yeast species of the Kazachstania clade, Kazachstania saulgeensis sp. nov., Kazachstania serrabonitensis sp. nov. and Kazachstania australis sp. nov. Reassignment of Candida humilis to Kazachstania humilis f.a. comb. nov. and Candida pseudohumilis to Kazachstania pseudohumilis f.a. comb. nov. International Journal of Systematic and Evolutionary Microbiology, 66 (12), 5192-5200., DOI : 10.1099/ijsem.0.001495
Michel, E., Monfort, C., Deffrasnes, M., Guezenec, S., Lhomme, E., Barret, M., Sicard, D., Dousset, X., Onno, B. (2016). Characterization of relative abundance of lactic acid bacteria species in french organic sourdough by cultural, qPCR and MiSeq high-throughput sequencing methods. International Journal of Food Microbiology, 239, 35-43., DOI : 10.1016/j.ijfoodmicro.2016.07.034
Dulermo, R., Legras, J. L., Brunel, F., Devillers, H., Sarilar, V., Neuveglise-Degouy, C., Nguyen, H.-V., Daran-Lapujade, P. (2016). Truncation of Gal4p explains the inactivation of the GAL/MEL regulon in both Saccharomyces bayanus and some Saccharomyces cerevisiae wine strains. FEMS Yeast Research, 16 (6), 11 p., DOI : 10.1093/femsyr/fow070
Bloem, A. (Auteur de correspondance), SANCHEZ, I., Dequin, S., Camarasa, C. (2016). Metabolic impact of redox cofactor perturbations on the formation of aroma compounds in Saccharomyces cerevisiae. Applied and Environmental Microbiology, 82 (1), 174-183., DOI : 10.1128/AEM.02429-15
Lhomme, E., Urien, C., Legrand, J., Dousset, X., Onno, B., Sicard, D. (2016). Sourdough microbial community dynamics: an analysis during French organic bread-making processes. Food Microbiology, 53 (part A), 41-50., DOI : 10.1016/j.fm.2014.11.014
Calam, E., González-Roca, E., Fernández, M. R., Dequin, S., Parés, X., Virgili, A., Biosca, J. A. (2016). Enantioselective synthesis of vicinal (R,R)-diols by Saccharomyces cerevisiae butanediol dehydrogenase. Applied and Environmental Microbiology, 82 (6), 1706-1721., DOI : 10.1128/AEM.03717-15
Marsit, S., Sanchez, I., Galeote, V., Dequin, S. (2016). Horizontally acquired oligopeptide transporters favor adaptation of Saccharomyces cerevisiae wine yeast to enological environment. Environmental Microbiology, 18, 1148-1161., DOI : 10.1111/1462-2920.13117
Legrand, J., Bolotin-Fukuhara, M., Bourgais, A., Fairhead, C., Sicard, D. (2016). Life-history strategies and carbon metabolism gene dosage in the Nakaseomyces yeasts. FEMS Yeast Research, 16, 14 p., DOI : 10.1093/femsyr/fov112
Vallverdu Queralt, A., Biler, M., Meudec, E., Le Guerneve, C., Vernhet, A., Mazauric, J. P., Legras, J. L., Loonis, M., Trouillas, P., Cheynier, V., Dangles, O. (2016). p-Hydroxyphenyl-pyranoanthocyanins: An Experimental and Theoretical Investigation of Their Acid-Base Properties and Molecular Interactions. International Journal of Molecular Sciences, 17 (11)., DOI : 10.3390/ijms17111842
Coi, A. L. (Auteur de correspondance), Legras, J. L., Zara, G., Dequin, S., Budroni, M. (2016). A set of haploid strains available for genetic studies of Saccharomyces cerevisiae flor yeasts. FEMS Yeast Research, 16 (6), 9 p. , DOI : 10.1093/femsyr/fow066
Rollero, S., Mouret, J.-R., Sanchez, I., Camarasa, C., Ortiz-Julien, A., Sablayrolles, J.-M., Dequin, S. (2016). Key role of lipid management in nitrogen and aroma metabolism in an evolved wine yeast strain. Microbial Cell Factories, 15, 15 p. , DOI : 10.1186/s12934-016-0434-6