title: Comparative phenomics and targeted use of genomics reveals variation in carbon and nitrogen assimilation among different Brettanomyces bruxellensis strains.
abstract: Recent studies have suggested a correlation between genotype groups of Brettanomyces bruxellensis and their source of isolation. To further explore this relationship, the objective of this study was to assess metabolic differences in carbon and nitrogen assimilation between different B. bruxellensis strains from three beverages, including beer, wine, and soft drink, using Biolog Phenotype Microarrays. While some similarities of physiology were noted, many traits were variable among strains. Interestingly, some phenotypes were found that could be linked to strain origin, especially for the assimilation of particular α- and β-glycosides as well as α- and β-substituted monosaccharides. Based upon gene presence or absence, an α-glucosidase and β-glucosidase were found explaining the observed phenotypes. Further, using a PCR screen on a large number of isolates, we have been able to specifically link a genomic deletion to the beer strains, suggesting that this region may have a fitness cost for B. bruxellensis in certain fermentation systems such as brewing. More specifically, none of the beer strains were found to contain a β-glucosidase, which may have direct impacts on the ability for these strains to compete with other microbes or on flavor production.
authors.affiliation: Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), KU Leuven, M2S, Campus De Nayer, Fortsesteenweg 30A, B-2860, Sint-Katelijne Waver, Belgium.
authors.forename: S
authors.initials: S
authors.lastname: Crauwels
authors.affiliation: Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), KU Leuven, M2S, Campus De Nayer, Fortsesteenweg 30A, B-2860, Sint-Katelijne Waver, Belgium.
authors.forename: A
authors.initials: A
authors.lastname: Van Assche
authors.affiliation: Department of Plant Systems Biology, VIB and Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Ghent, Belgium.
authors.forename: R
authors.initials: R
authors.lastname: de Jonge
authors.affiliation: The Australian Wine Research Institute, PO Box 197, Glen Osmond, Adelaide, SA, 5064, Australia.
authors.forename: A R
authors.initials: AR
authors.lastname: Borneman
authors.affiliation: Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), KU Leuven, M2S, Campus De Nayer, Fortsesteenweg 30A, B-2860, Sint-Katelijne Waver, Belgium.
authors.forename: C
authors.initials: C
authors.lastname: Verreth
authors.affiliation: White Labs, 9495 Candida Street, San Diego, CA, 92126, USA.
authors.forename: P
authors.initials: P
authors.lastname: Troels
authors.affiliation: Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), KU Leuven, M2S, Campus De Nayer, Fortsesteenweg 30A, B-2860, Sint-Katelijne Waver, Belgium.
authors.forename: G
authors.initials: G
authors.lastname: De Samblanx
authors.affiliation: Department of Plant Biotechnology and Bioinformatics and Department of Information Technology, IMinds, Ghent University, Technologiepark 927, B-9052, Ghent, Belgium.
authors.forename: K
authors.initials: K
authors.lastname: Marchal
authors.affiliation: Department of Plant Systems Biology, VIB and Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Ghent, Belgium.
authors.forename: Y
authors.initials: Y
authors.lastname: Van de Peer
authors.affiliation: Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), KU Leuven, M2S, Campus De Nayer, Fortsesteenweg 30A, B-2860, Sint-Katelijne Waver, Belgium.
authors.forename: K 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, KU Leuven, M2S, Gaston Geenslaan 1, B-3001, Leuven, Belgium.
authors.forename: K J
authors.initials: KJ
authors.lastname: Verstrepen
authors.affiliation: The Australian Wine Research Institute, PO Box 197, Glen Osmond, Adelaide, SA, 5064, Australia.
authors.forename: C D
authors.initials: CD
authors.lastname: Curtin
authors.affiliation: Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), KU Leuven, M2S, Campus De Nayer, Fortsesteenweg 30A, B-2860, Sint-Katelijne Waver, Belgium. bart.lievens@kuleuven.be.
authors.forename: B
authors.initials: B
authors.lastname: Lievens
mesh_terms: D001515:Beer / Q000382:microbiology; D055168:Brettanomyces / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification / Q000502:physiology*; D002244:Carbon / Q000378:metabolism*; D002253:Carbonated Beverages / Q000382:microbiology; D004271:DNA, Fungal / Q000235:genetics; D014644:Genetic Variation; D023281:Genomics; D005838:Genotype; D053858:Metabolic Networks and Pathways / Q000235:genetics*; D009584:Nitrogen / Q000378:metabolism*; D010641:Phenotype; D016133:Polymerase Chain Reaction; D017384:Sequence Deletion; D014920:Wine / Q000382:microbiology; D000520:alpha-Glucosidases / Q000235:genetics / Q000378:metabolism; D001617:beta-Glucosidase / Q000235:genetics / Q000378:metabolism
chemical_list: D004271:DNA, Fungal; D002244:Carbon; D000520:alpha-Glucosidases; D001617:beta-Glucosidase; D009584:Nitrogen
keywords: Biolog; Dekkera bruxellensis; Niche adaptation; Phenotypic and genetic diversity; α-Glucosidase; β-Glucosidase