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Comparative phenomics and targeted use of genomics reveals variation in carbon and nitrogen assimilation among different Brettanomyces bruxellensis strains

Authors
  • Crauwels, S.1
  • Van Assche, A.1
  • de Jonge, R.2
  • Borneman, A. R.3
  • Verreth, C.1
  • Troels, P.4
  • De Samblanx, G.1
  • Marchal, K.5
  • Van de Peer, Y.2
  • Willems, K. A.1
  • Verstrepen, K. J.6
  • Curtin, C. D.3
  • Lievens, B.1
  • 1 KU Leuven, Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), M2S, Campus De Nayer, Fortsesteenweg 30A, Sint-Katelijne Waver, B-2860, Belgium , Sint-Katelijne Waver (Belgium)
  • 2 Ghent University, Department of Plant Systems Biology, VIB and Department of Plant Biotechnology and Bioinformatics, Technologiepark 927, Ghent, B-9052, Belgium , Ghent (Belgium)
  • 3 The Australian Wine Research Institute, Glen Osmond, Adelaide, SA, 5064, Australia , Adelaide (Australia)
  • 4 White Labs, 9495 Candida Street, San Diego, CA, 92126, USA , San Diego (United States)
  • 5 Ghent University, Department of Plant Biotechnology and Bioinformatics and Department of Information Technology, IMinds, Technologiepark 927, Ghent, B-9052, Belgium , Ghent (Belgium)
  • 6 KU Leuven, VIB Lab for Systems Biology and Centre of Microbial and Plant Genetics (CMPG) Lab for Genetics and Genomics, M2S, Gaston Geenslaan 1, Leuven, B-3001, Belgium , Leuven (Belgium)
Type
Published Article
Journal
Applied Microbiology and Biotechnology
Publisher
Springer-Verlag
Publication Date
Jul 02, 2015
Volume
99
Issue
21
Pages
9123–9134
Identifiers
DOI: 10.1007/s00253-015-6769-9
Source
Springer Nature
Keywords
License
Yellow

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.

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