Amplicon-seq of Saccharomyces cerevisiae: LTR-transposon delta element PCR

Identifying beer spoilage microbes is readily accomplished using PCR analyses targeting specific types of microbes, but the general classification of wild yeast versus brewing yeast using cultivation independent molecular methods has remained challenging. The approach presented in this study utilized genetic fingerprint matching to determine if an unknown yeast isolate matches the fingerprint of catalogued brewing yeast strains. Interdelta Next Generation Sequencing (NGS) fingerprints were produced using PCR amplification of delta elements, also known as long terminal repeat sequences of transposons of yeast. Fingerprints identifying different yeast strains were generated by processing reads produced by NGS of the interdelta PCR amplicons using open source software. The interdelta NGS fingerprint comprises DNA sequences that can be recorded, compared, and utilized as a fixed reference for yeast strain identification. Interdelta NGS fingerprints were shown to be reproducible and capable of distinguishing between strains of brewing yeast and wild yeast. Experimental yeast contamination demonstrated the utility of the approach for identifying in-house brewing yeast cross contamination versus foreign wild yeast contamination.