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High Throughput Sequencing as a novel quality control method for industrial yeast starter cultures
M. Michel, L. A. Hardulak, T. Meier-Drnberg, J. Morinire, A. Hausmann, W. Back, G. Haszprunar, F. Jacob and M. Hutzler

The use of pure starter cultures is largely responsible for the great success of todays fermentation products market. With their implementation, fermentations (e.g., beer fermentation) have become predictable, efficient, controllable and reproducible. The pureness of the applied starter culture is therefore of great interest for obtaining these advantages. Many protocols have been applied for quality control of the pureness of these cultures, and they have improved over the last century. The current state of the art of detecting interfering microorganisms consists of the use of selective media or targeted approaches via Real-Time PCR. These methods are time consuming and require suspicion of the identity of potential interfering microbe(s). The use of High Throughput Sequencing, however, offers the ability to apply a non-targeted approach for the detection of interfering spoilers in the applied case of spoilage yeasts. Here we used the 26S rDNA D1/D2 region of chromosome XII to verify the pureness of yeast cultures applied in brewing, wine and special beer fermentations. The results show that it is possible to detect differing species in supposedly pure yeast cultures by application of the new method. Some strains showed potential traits of intraspecific hybridization, horizontal gene transfer or syntrophic cultures, which interfered with the results. The 26S rDNA D1/D2 region showed to be discriminative for only some species, indicating the need to additionally apply more discriminative regions like ITS1. Furthermore, we propose a more comprehensive and powerful database, consisting of highly validated and identified cultures, that has to be built up to improve sequencing results.

Descriptors: HTS, quality control, yeast, fermentation, pure cultures

BrewingScience, 72 (March/April 2019), pp. 63-68