The identification of novel diagnostic marker genes for the detection of beer spoiling Pediococcus damnosus strains using the BlAst diagnostic gene findEr

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Abstract

As the number of bacterial genomes increases dramatically, the demand for easy to use tools with transparent functionality and comprehensible output for applied comparative genomics grows as well.We present BlAst Diagnostic Gene findEr (BADGE), a tool for the rapid prediction of diagnosticmarker genes (DMGs) for the differentiation of bacterial groups (e.g. pathogenic / nonpathogenic).DMGidentification settings can be modified eas- ily and installing and running BADGE does not require specific bioinformatics skills. During the BADGE run the user is informed step by step about theDMGfinding process, thus mak- ing it easy to evaluate the impact of chosen settings and options.On the basis of an exam- ple with relevance for beer brewing, being one of the oldest biotechnological processes known, we show a straightforward procedure, from phenotyping, genome sequencing, assembly and annotation, up to a discriminant marker gene PCR assay, making compara- tive genomics a means to an end. The value and the functionality of BADGE were thor- oughly examined, resulting in the successful identification and validation of an outstanding novelDMG(fabZ) for the discrimination of harmless and harmful contaminations of Pedio- coccus damnosus, which can be applied for spoilage risk determination in breweries. Con- comitantly, we present and compare five complete P. damnosus genomes sequenced in this study, finding that the ability to produce the unwanted, spoilage associated off-flavor diacetyl is a plasmid encoded trait in this important beer spoiling species.

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Behr, J., Geissler, A. J., Schmid, J., Zehe, A., & Vogel, R. F. (2016). The identification of novel diagnostic marker genes for the detection of beer spoiling Pediococcus damnosus strains using the BlAst diagnostic gene findEr. PLoS ONE, 11(3). https://doi.org/10.1371/journal.pone.0152747

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