High-throughput sequencing of amplicons for monitoring yeast biodiversity in must and during alcoholic fermentation

  • Vanessa David
  • Sébastien Terrat
  • Khaled Herzine
  • Olivier Claisse
  • Sandrine Rousseaux
  • Raphaëlle Tourdot-Maréchal
  • Isabelle Masneuf-Pomarede
  • Lionel Ranjard
  • Hervé Alexandre
Environmental Microbiology

Abstract

We compared pyrosequencing technology with the PCR-ITS-RFLP analysis of yeast isolates and denaturing gradient gel electrophoresis (DGGE). These methods gave divergent findings for the yeast population. DGGE was unsuitable for the quantification of biodiversity and its use for species detection was limited by the initial abundance of each species. The isolates identified by PCR-ITS-RFLP were not fully representative of the true population. For population dynamics, high-throughput sequencing technology yielded results differing in some respects from those obtained with other approaches. This study demonstrates that 454 pyrosequencing of amplicons is more relevant than other methods for studying the yeast community on grapes and during alcoholic fermentation. Indeed, this high-throughput sequencing method detected larger numbers of species on grapes and identified species present during alcoholic fermentation that were undetectable with the other techniques.

Keywords

Yeast biodiversity 454 pyrosequencing Grape Wine DGGE PCR-ITS-RFLP DNA fingerprints 

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Copyright information

© Society for Industrial Microbiology and Biotechnology 2014

Authors and Affiliations

  • Vanessa David
    • 1
  • Sébastien Terrat
    • 4
  • Khaled Herzine
    • 1
  • Olivier Claisse
    • 2
  • Sandrine Rousseaux
    • 1
  • Raphaëlle Tourdot-Maréchal
    • 1
  • Isabelle Masneuf-Pomarede
    • 2
  • Lionel Ranjard
    • 3
    • 4
  • Hervé Alexandre
    • 1
  1. 1.UMR 02102 PAM Université de Bourgogne-AgroSup Dijon Laboratoire VALMIS Institut Universitaire de la Vigne et du Vin Jules GuyotUniversité de BourgogneDijon CedexFrance
  2. 2.INRA, USC 1366 ŒnologieUniversité de BordeauxVillenave d’OrnonFrance
  3. 3.INRA, UMR 1347 AgroécologieDijonFrance
  4. 4.INRA, UMR 1347 Agroécologie-Plateforme GenosolDijonFrance

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