Nanopore based sequencing enables easy and accurate identification of yeasts in breweries

In breweries, rapid and accurate identification of unknown microbial contaminants and the associated risk assessment of beer spoilage are of critical importance to ensure proper corrective measures are taken. In this context, the nanopore based sequencer, MinION, developed by Oxford Nanopore Technologies, is of particular interest. MinION is a low cost, portable, real time device for DNA and RNA sequencing. Recently, our group developed and evaluated a MinION sequencer based microbial identification platform for beer spoilage bacteria. In this study, it is used to identify yeast strains. The nuclear ribosomal RNA genes and their internal transcribed spacer regions from a wide variety of beer spoilage yeasts, commonly found in the brewery environment, were sequenced using two different sequencing kits - Ligation Sequencing Kit and Rapid Barcoding Kit - and analysed using consensus sequence-based approach. Comparative evaluation of Sanger sequencing and MinION sequencing was performed to evaluate the performance of the MinION platform in the identification of yeasts. Our methods successfully identified yeasts at the species level rapidly (approximately 3.5 hours from DNA extraction to data analysis), and with high accuracy that is comparable to Sanger sequencing (average percentage identity >98.9%). The MinION sequencer based microbial identification platform, equipped for both bacterial and yeast identification, is a powerful tool for on-field rapid and accurate identification of beer spoilage and brewery related microorganisms. This new identification approach will potentially revolutionise the way microbial identification is performed in brewery quality control and assurance laboratories. (c) 2021 The Institute of Brewing & Distilling

Automated summary

The MinION sequencer, developed by Oxford Nanopore Technologies, is a low-cost, portable, real-time device for DNA and RNA sequencing. Our study successfully identified yeast strains rapidly (approximately 3.5 hours from DNA extraction to data analysis) and with high accuracy, comparable to Sanger sequencing. This new microbial identification platform is a powerful tool for on-field rapid and accurate identification of beer spoilage and brewery related microorganisms.