Rapid identification of the genus Dekkera/Brettanomyces, the Dekkera subgroup and all individual species

• The genus Dekkera/Brettanomyces includes several important spoilage organisms
• Rapid identification is important for the wine, brewing and beverage industries
• Eight primer pairs for direct colony PCR can identify targets in under 3 h
• The genus as a whole, just Dekkera and each individual species can be identified
• The method is fast, cheap, accurate and requires only standard laboratory equipment

The genus Dekkera/Brettanomyces comprises five described species: Dekkera bruxellensis, D. anomala, Brettanomyces custersianus, B. naardenensis and B. nanus. Some of them, especially D. bruxellensis, are important spoilage organisms, particularly in the wine and beverage industries. Because of their economic importance many different methods have been developed to identify members of the genus in general and D. bruxellensis in particular. These methods vary in their rapidity, complexity and cost but, partly because of confidentiality issues, it is unclear which methods are used, or how widely, in the relevant industries. Building on previous work with the genera Saccharomyces and Zygosaccharomyces, a suite of eight PCR primer pairs has been designed either on the D1–D2 region of the 26S rRNA gene or translation elongation factor TEF1-α. These primers can specifically identify the genus as a whole, only Dekkera species, each one of the five recognised species as well as a significant subgroup of D. bruxellensis represented by NCYC 3426. Multiplexing has also been tried and it has been shown to be possible with some combinations of genus or Dekkera-level and species-specific primers. Using direct colony PCR amplification followed by gel electrophoresis, a clear positive result can be obtained in less than 3 h, thus providing a quick, reliable and inexpensive way to identify target species.