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

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.

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Acknowledgments

This work, through the involvement of the technical facilities of the GenoSol platform of the ANAEE-Services infrastructure, received a grant from the French state through the National Research Agency, as part of the “Investments for the Future” program (reference ANR-11-INBS-0001), and a grant from the Regional Council of Burgundy.

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Correspondence to Hervé Alexandre.

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David, V., Terrat, S., Herzine, K. et al. High-throughput sequencing of amplicons for monitoring yeast biodiversity in must and during alcoholic fermentation. J Ind Microbiol Biotechnol 41, 811–821 (2014). https://doi.org/10.1007/s10295-014-1427-2

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Keywords

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