Frédéric Bigey
- Sciences Pour l'Oenologie (SPO)
- Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Présentation
I am a research scientist specializing in yeast genomics and bioinformatics, with a focus on the comparative genomics of yeasts associated with food processes. My expertise lies in bioinformatics and computational biology, particularly in sequence analysis of industrial yeast genomes and in comparative genomics of yeasts from both technological and natural habitats. In 2025, I was the first author of a comparative genomics study of the yeast Monosporozyma unispora (FEMS Yeast Research, DOI: 10.1093/femsyr/foaf016). This research highlighting their genetic diversity, adaptive traits, and relevance for both evolutionary studies and emerging biotechnological applications. In 2024, I was the first author of a study on the genomic, genetic and phenotypic landscape of Candida anglica yeast population isolated from french PDO cheeses (Food Microbiology, DOI: 10.1016/j.fm.2024.104584). This work investigated how domestication and adaptation to this specific environment have shaped their genomic signatures, thereby informing our understanding of evolutionary processes. In 2023, I was the first author of a comparative study of the oleagenous yeast Yarrowia lipolytica (Journal of Fungi, 9:76; DOI: 10.3390/jof9010076). With my colleagues I investigated 56 natural isolates and demonstrated that this species exhibits low genetic diversity, with a pan-genome closely resembling the core genome, suggesting a relatively recent evolutionary trajectory. Despite this, we observed substantial phenotypic diversity among strains, particularly regarding lipid metabolism. In 2021, I was the first author of a study on the domestication of bakery yeast (Current Biology, 31:1–12; DOI: 10.1016/j.cub.2020.11.016). This work focused on Saccharomyces cerevisiae strains used in bread-making and revealed that domestication has been accompanied by dispersion, hybridization, and divergent selection processes, shaped differently by industrial and artisanal practices. Earlier, in 2009, I co-authored the genome sequence analysis of the first wine yeast strain Saccharomyces cerevisiae EC1118 (PNAS, 106:16333–16338; DOI: 10.1073/pnas.0904673106), which uncovered unprecedented eukaryote-to-eukaryote horizontal gene transfer events. This study shed light on the genomic innovations that have contributed to the adaptation of S. cerevisiae wine strains to fermentation environments. Collectively, my research integrates genomic sequencing, bioinformatics, and comparative evolutionary analyses to better understand yeast diversity, adaptation, and domestication, with direct implications for biotechnology and food fermentation processes.
Compétences
Publications
Publications
Dici: a new Tc1/mariner transposon reshaping the genome of Diutina catenulataISSY 38 "Yeast - the omni-tool", Adrianna Skoneczna; Zbigniew Lazar, Sep 2025, Warsaw, Poland |
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Impacts de la domestication sur le génome des levures S. cerevisiae de vin et de pain14. Journées Jean Chevaugeon - Rencontres de Phytopathologie - Mycologie, Jan 2024, Aussois, France |
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Drivers of microbial communities dynamic in sourdoughSéminaire sur le bilan des recherches sur le palmier à huile au Bénin, Société Française de Microbiologie, Oct 2022, Montpellier, France |
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Mycotoxins throughout the life cycle of a wheat grain. A case study of organic farming with on-farm storage and processing43. Mycotoxin Workshop, May 2022, Toulouse, France |
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How different anthropogenic environments have shaped the genome of S. cerevisiae ?7. Conference on Physiology of Yeast and Filamentous Fungi, Jun 2019, Milan, Italy |
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Horizontal gene transfer: one of the key mechanisms involved into the adaptation of yeast to their environmentESF-EMBO Symposium, Comparative genomics of eukaryotic microbes: Genomes in flux, and flux between genomes, Oct 2019, Sant Feliu de Guíxols, Spain |
Horizontal Gene Transfer and Introgression: key mechanisms of adaptation of yeast to its ecological niches2. Joint Congress on Evolutionary Biology, Aug 2018, Montpellier, France |
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Domesticated lineages of S. cerevisiae from fermented food environments present customized genome with selective footprints2. Joint Congress on Evolutionary Biology, 2018, Montpellier, France |
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Adaptation of Yeast to Anthropogenic Environments Using Comparative Genomics27. International Conference on Yeast Genetics and Molecular Biology (ICYGMB), Aug 2017, Prague, Czech Republic |
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Horizontal Gene Transfer is a key mechanism permitting adaptation of S. cerevisiae to its ecological niches21. Evolutionary Biology Meeting at Marseilles, 2017, Marseille, France |
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Horizontal Gene Transfer is a key mechanism permitting adaptation of S. cerevisiae to its ecological nichesReunión anual conjunta genética y evolución, 2017, Puerto Varas, Chile |
Adaptive Advantage of Horizontally Transferred Oligopeptide Transporters in Wine Yeasts27. International Conference on Yeast Genetics and Molecular Biology (ICYGMB), 2015, Trento, Italy |
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The genetic basis of adaptation of flor strains : a comparative genome and genetic analysis32. International Specialised Symposium on Yeasts-Yeast biodiversity and biotechnology in the twenty-first century, 2015, Perugia, Italy |
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New insights into the adaptation of yeast to anthropic environment using comparative genomics27. International Conference on Yeast Genetics and Molecular Biology (ICYGMB), Sep 2015, Trentino, Italy. pp.1 |
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New insights into adaptation of yeast to anthropic environment using comparative genomics32. International Specialized Symposium on Yeasts-Yeast Biodiversity and biotechnology in the twenty-first century, 2015, Perugia, Italy |
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Improvement of wine yeast strains using adaptive evolutionISSY 32, Sep 2015, Perugia, Italy |
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Deciphering the adaptation of yeast to anthropic environment using comparative genomicsESF-EMBO Symposium, Exploring the genomic complexity and diversity of eukaryotes, 2015, Sant Feliu de Guixols, Spain |
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Exploring the adaptation of yeast to wine making environment using comparative genomicsSMBE Satellite meeting SMBEBA 2015 "Investigating biological adaptation with NGS: data and models", May 2015, Montpellier, France |
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Adaptive Advantage Conferred by an Eukaryote-to-Eukaryote Gene Transfer Event in Wine YeastsESF-EMBO Symposium, Exploring the genomic complexity and diversity of eukaryotes, 2015, Sant Feliu de Guixols, Spain |
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New insights into the adaptation of yeast to anthropic niches using comparative genomics. Focus on flor yeast.EMBO Conference Series: Experimental Approaches to Evolution and Ecology, Oct 2014, Heidelberg, Germany. pp.1 |
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Adaptation des levures S. cerevisiae à des niches anthropiques à partir d’une approche de génomique des populations. Exemple de l’élevage en voileLevures, Modèles & Outils – 11ème Rencontre des Levuristes Francophones, 2014, Bordeaux, France |
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Avantage adaptatif des transporteurs d’oligopeptides Fot1/2 acquis par transfert horizontal de gènes durant la fermentation alcooliqueLevures, Modèles & Outils – 11ème Rencontre des Levuristes Francophones, 2014, Bordeaux, France |
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Evolutionnary and reverse engineering of commercially important metabolic traits in wine yeast31. International Specialised Symposium on Yeast, 2014, Nova Gorica/Vipava, Slovenia |
Characterization of genes involved in the adaptation of flor strains to biological ageing conditions of sherry wines31. International Specialised Symposium on Yeast, 2014, Nova-Gorica/Vipava, Slovenia |
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Adaptive role of horizontal gene transfers in wine yeasts: how to improve resource utilization to survive betterInternational Union of Microbiological Societies Congresses - IUMS2014, 2014, Montreal, Canada |
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Adaptive role of horizontally transferred oligopeptide transporters in wine yeasts31. International Specialised Symposium on Yeast, 2014, Nova-Gorica/Vipava, Slovenia |
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New insights into the adaptation of yeast to anthropic niches using comparative genomics. Focus on flor yeast genomeESF-EMBO Comparative Genomics of Eukaryotic Microorganisms: Complexity Patterns in Eukaryotic Genomes, 2013, Sant Feliu de Guixols, Spain |
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Role of horizontally transfered genes in the adaptation of wine yeasts to their environnment5. Conference on Physiology of Yeast and Filamentous Fungi- PYFF5, 2013, Montpellier, France |
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Adaptive role of horizontally transferred genes during wine fermentation.ESF-EMBO Comparative Genomics of Eukaryotic Microorganisms: Complexity Patterns in Eukaryotic Genomes, 2013, Sant Feliu de Guixols, Spain |
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First insight into the adaptation of yeast to anthropic niches from genome sequence5. Conference on Physiology of Yeast and Filamentous Fungi, Institut National de Recherche Agronomique (INRA). UMR Sciences Pour l'Oenologie (1083)., 2013, Montpellier, France |
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Characterization of genes involved in yeast adaptation to Sherry-like wines’ biological ageing identified by a genome based approachESFEMBO Comparative Genomics of Eukaryotic Microorganisms: Complexity Patterns in Eukaryotic Genomes, 2013, Sant Feliu de Guixols, Spain |
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Diversity and adaptation of flor yeast : new data for an old questionJournées des Microbiologistes de l’INRA 2012, Nov 2012, Avignon, France |
Diversity and adaptation of flor yeast : new data for an old question13. International Congress on Yeasts (ICY 2012), 2012, Madison, United States |
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Genetic and phenotypic diversity of wine yeasts: Role of horizontal gene transfer13. International Congress on Yeasts (ICY 2012), Aug 2012, Madison, United States |
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Transformation of whole cells of Brevibacterium SP. R312, a nitrile hydratase producing strain6. Forum for applied biotechnology, Sep 1992, Bruges, Belgium |
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Candida anglica, a yeast species newly found in cheeseWDS 2024, Oct 2024, Paris, France |
Yeast dispersion is the main driver of microbial community diversity in sourdough bread-makingPYYF8 - 8. Conference on Physiology of Yeasts and Filamentous Fungi, Jun 2023, Cork, Ireland |
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Genome and gene copy number variation in bakery yeast domesticationEMBL Conference: Molecular Mechanisms in Evolution and Ecology, Sep 2020, Online, Germany |
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Multiple genetic origins of Saccharomyces cerevisiae in bakeryComparative genomics of eukaryotic microbes: genomes in flux, and flux between genomes, Oct 2019, Sant Feliu de Guixols, Spain |
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New insights into the adaptation of yeast to wine making using comparative genomics10. Symposium International d’Œnologie de Bordeaux, Œno2015, Jun 2015, Bordeaux, France. 2015 |
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Adaptive advantage of oligopetide transporters acquired by horizontal transfer during wine fermentation10. Symposium International d’Œnologie de Bordeaux, Œno2015, Jun 2015, Bordeaux, France. 2015 |
Enhanced production of volatile esters by adaptively evolved Saccharomyces cerevisiae wine yeasts26. International Conference on Yeast Genetics and Molecular Biology, Aug 2013, Francfort-sur-le-Main, Germany. Wiley-Blackwell, Yeast, 30 (suppl.1), 2013, Yeast |
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Stochastic gene expression, phenotypic variability and adaptation of budding yeast to environmental stressesEMBO conference: Comparative Genomics Of Eukaryotic Microorganisms: Understanding The Complexity Of Diversity, Oct 2011, Sant Feliu de Guixols, Spain |
Lipase/acyltransferaseGermany, Patent n° : WO 03/006644 A2. 2003 |