DNA metabarcoding as a novel quality control method for industrial yeast starter cultures

In a recent study, a new tool was developed and tested with the help of our DNA metabarcoding service, promising fast and reliable non-targeted quality control of yeast starter cultures.

In large part, the great success of today’s fermentation products market is due to the use of pure starter cultures. Thanks to them, modern fermentation procedures (e.g., beer fermentation) have got the advantage of being predictable, efficient, controllable, and reproducible. Testing the applied starter culture for pureness 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 approaches using Real-Time PCR. However, these methods are time consuming and targeted, meaning that they require foresight concerning the identity of potentially interfering microbe(s). The use of High Throughput Sequencing (DNA metabarcoding), on the other hand, offers us the ability to apply a non-targeted approach for the detection of interfering spoilers in the applied case of spoilage yeasts.

Here, in a first of its kind, proof of principle test, the 26S rDNA D1/D2 region of chromosome XII was used to verify the pureness of yeast cultures applied in brewing, wine and special beer fermentations. The results show that it is indeed possible to quickly and efficiently detect differing species in supposedly pure yeast cultures by the application of DNA metabarcoding. This first study also revealed the challenges confronting the new method for starter yeast cultures. Some strains showed potential traits of intraspecific hybridization, horizontal gene transfer, or syntrophic cultures, which interfered with the results. In some cases the 26S rDNA D1/D2 region was not able to discriminate between all species, indicating the need to apply cross-checks using other regions, such as ITS1, in such cases. Furthermore, a more comprehensive and powerful database, consisting of highly validated and identified cultures, will need to be built up to improve results.

We are currently developing new projects which will aim to improve and refine the metabarcoding approach for yeast cultures further by testing additional genetically diverse regions, such as internal transcribed spacers (e.g. ITS1).

In spite of these challenges, DNA metabarcoding has proven to be a major step forward in the quick and effective detection of multiple species of yeast in one sample with unknown composition, and thus represents a promising tool for non-targeted quality control of yeast starter cultures.

M. Michel, L. A. Hardulak, T. Meier-Dörnberg, J. Morinière, A. Hausmann, W. Back, G. Haszprunar, F. Jacob, M. Hutzler (2019): High Throughput Sequencing as a novel quality control method for industrial yeast starter cultures, Brewing Science, 72, 63-68, https://doi.org/10.23763/BrSc19-05michel

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