title: Assessing genetic diversity among Brettanomyces yeasts by DNA fingerprinting and whole-genome sequencing.
abstract: Brettanomyces yeasts, with the species Brettanomyces (Dekkera) bruxellensis being the most important one, are generally reported to be spoilage yeasts in the beer and wine industry due to the production of phenolic off flavors. However, B. bruxellensis is also known to be a beneficial contributor in certain fermentation processes, such as the production of certain specialty beers. Nevertheless, despite its economic importance, Brettanomyces yeasts remain poorly understood at the genetic and genomic levels. In this study, the genetic relationship between more than 50 Brettanomyces strains from all presently known species and from several sources was studied using a combination of DNA fingerprinting techniques. This revealed an intriguing correlation between the B. bruxellensis fingerprints and the respective isolation source. To further explore this relationship, we sequenced a (beneficial) beer isolate of B. bruxellensis (VIB X9085; ST05.12/22) and compared its genome sequence with the genome sequences of two wine spoilage strains (AWRI 1499 and CBS 2499). ST05.12/22 was found to be substantially different from both wine strains, especially at the level of single nucleotide polymorphisms (SNPs). In addition, there were major differences in the genome structures between the strains investigated, including the presence of large duplications and deletions. Gene content analysis revealed the presence of 20 genes which were present in both wine strains but absent in the beer strain, including many genes involved in carbon and nitrogen metabolism, and vice versa, no genes that were missing in both AWRI 1499 and CBS 2499 were found in ST05.12/22. Together, this study provides tools to discriminate Brettanomyces strains and provides a first glimpse at the genetic diversity and genome plasticity of B. bruxellensis.
authors.affiliation: Laboratory for Process Microbial Ecology and Bioinspirational Management, Cluster for Bioengineering Technology (CBeT), Department of Microbial and Molecular Systems (M2S), Leuven Food Science and Nutrition Research Centre (LFoRCe), Leuven Institute for Beer Research (LIBR), KU Leuven, Campus De Nayer, Sint-Katelijne-Waver, Belgium.
authors.forename: Sam
authors.initials: S
authors.lastname: Crauwels
authors.affiliation: VIB Lab for Systems Biology and Centre of Microbial and Plant Genetics (CMPG) Lab for Genetics and Genomics, Department of Microbial and Molecular Systems (M2S), Leuven Food Science and Nutrition Research Centre (LFoRCe), Leuven Institute for Beer Research (LIBR), KU Leuven, Leuven, Belgium.
authors.forename: Bo
authors.initials: B
authors.lastname: Zhu
authors.affiliation: VIB Lab for Systems Biology and Centre of Microbial and Plant Genetics (CMPG) Lab for Genetics and Genomics, Department of Microbial and Molecular Systems (M2S), Leuven Food Science and Nutrition Research Centre (LFoRCe), Leuven Institute for Beer Research (LIBR), KU Leuven, Leuven, Belgium.
authors.forename: Jan
authors.initials: J
authors.lastname: Steensels
authors.affiliation: Laboratory for Process Microbial Ecology and Bioinspirational Management, Cluster for Bioengineering Technology (CBeT), Department of Microbial and Molecular Systems (M2S), Leuven Food Science and Nutrition Research Centre (LFoRCe), Leuven Institute for Beer Research (LIBR), KU Leuven, Campus De Nayer, Sint-Katelijne-Waver, Belgium.
authors.forename: Pieter
authors.initials: P
authors.lastname: Busschaert
authors.affiliation: Laboratory for Process Microbial Ecology and Bioinspirational Management, Cluster for Bioengineering Technology (CBeT), Department of Microbial and Molecular Systems (M2S), Leuven Food Science and Nutrition Research Centre (LFoRCe), Leuven Institute for Beer Research (LIBR), KU Leuven, Campus De Nayer, Sint-Katelijne-Waver, Belgium Electrical Engineering (ESAT) Technology Cluster, KU Leuven, Campus De Nayer, Sint-Katelijne-Waver, Belgium.
authors.forename: Gorik
authors.initials: G
authors.lastname: De Samblanx
authors.affiliation: Department of Plant Biotechnology and Bioinformatics and Department of Information Technology, IMinds, Ghent University, Ghent, Belgium Centre of Microbial and Plant Genetics (CMPG), Department of Microbial and Molecular Systems (M2S), KU Leuven, Leuven, Belgium.
authors.forename: Kathleen
authors.initials: K
authors.lastname: Marchal
authors.affiliation: Laboratory for Process Microbial Ecology and Bioinspirational Management, Cluster for Bioengineering Technology (CBeT), Department of Microbial and Molecular Systems (M2S), Leuven Food Science and Nutrition Research Centre (LFoRCe), Leuven Institute for Beer Research (LIBR), KU Leuven, Campus De Nayer, Sint-Katelijne-Waver, Belgium.
authors.forename: Kris A
authors.initials: KA
authors.lastname: Willems
authors.affiliation: VIB Lab for Systems Biology and Centre of Microbial and Plant Genetics (CMPG) Lab for Genetics and Genomics, Department of Microbial and Molecular Systems (M2S), Leuven Food Science and Nutrition Research Centre (LFoRCe), Leuven Institute for Beer Research (LIBR), KU Leuven, Leuven, Belgium kevin.verstrepen@biw.vib-kuleuven.be bart.lievens@kuleuven.be.
authors.forename: Kevin J
authors.initials: KJ
authors.lastname: Verstrepen
authors.affiliation: Laboratory for Process Microbial Ecology and Bioinspirational Management, Cluster for Bioengineering Technology (CBeT), Department of Microbial and Molecular Systems (M2S), Leuven Food Science and Nutrition Research Centre (LFoRCe), Leuven Institute for Beer Research (LIBR), KU Leuven, Campus De Nayer, Sint-Katelijne-Waver, Belgium kevin.verstrepen@biw.vib-kuleuven.be bart.lievens@kuleuven.be.
authors.forename: Bart
authors.initials: B
authors.lastname: Lievens
mesh_terms: D000483:Alleles; D001515:Beer; D055168:Brettanomyces / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification; D016172:DNA Fingerprinting; D004271:DNA, Fungal / Q000235:genetics; D005285:Fermentation; D005506:Food Contamination / Q000032:analysis; D005516:Food Microbiology; D017353:Gene Deletion; D016681:Genome, Fungal; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D004271:DNA, Fungal