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

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Bioinformatics: from nucleotids to networks (N2N)
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 alpha- and beta-glycosides as well as alpha- and beta-substituted monosaccharides. Based upon gene presence or absence, an alpha-glucosidase and beta-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 beta-glucosidase, which may have direct impacts on the ability for these strains to compete with other microbes or on flavor production.
Keywords
IDENTIFICATION, SACCHAROMYCES, FERMENTATION, GENETIC DIVERSITY, WINE, CIDER, ECOLOGY, YEAST DEKKERA-BRUXELLENSIS, Phenotypic and genetic diversity, Niche adaptation, Dekkera bruxellensis, Biolog, beta-Glucosidase, alpha-Glucosidase, LEVEL, BEER

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Citation

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Chicago
Crauwels, S, A Van Assche, Ronnie de Jonge, AR Borneman, C Verreth, P Troels, G De Samblanx, et al. 2015. “Comparative Phenomics and Targeted Use of Genomics Reveals Variation in Carbon and Nitrogen Assimilation Among Different Brettanomyces Bruxellensis Strains.” Applied Microbiology and Biotechnology 99 (21): 9123–9134.
APA
Crauwels, S, Van Assche, A., de Jonge, R., Borneman, A., Verreth, C., Troels, P., De Samblanx, G., et al. (2015). Comparative phenomics and targeted use of genomics reveals variation in carbon and nitrogen assimilation among different Brettanomyces bruxellensis strains. APPLIED MICROBIOLOGY AND BIOTECHNOLOGY, 99(21), 9123–9134.
Vancouver
1.
Crauwels S, Van Assche A, de Jonge R, Borneman A, Verreth C, Troels P, et al. Comparative phenomics and targeted use of genomics reveals variation in carbon and nitrogen assimilation among different Brettanomyces bruxellensis strains. APPLIED MICROBIOLOGY AND BIOTECHNOLOGY. 2015;99(21):9123–34.
MLA
Crauwels, S, A Van Assche, Ronnie de Jonge, et al. “Comparative Phenomics and Targeted Use of Genomics Reveals Variation in Carbon and Nitrogen Assimilation Among Different Brettanomyces Bruxellensis Strains.” APPLIED MICROBIOLOGY AND BIOTECHNOLOGY 99.21 (2015): 9123–9134. Print.
@article{6982545,
  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 alpha- and beta-glycosides as well as alpha- and beta-substituted monosaccharides. Based upon gene presence or absence, an alpha-glucosidase and beta-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 beta-glucosidase, which may have direct impacts on the ability for these strains to compete with other microbes or on flavor production.},
  author       = {Crauwels, S and Van Assche, A and de Jonge, Ronnie and Borneman, AR and Verreth, C and Troels, P and De Samblanx, G and Marchal, Kathleen and Van de Peer, Yves and Willems, KA and Verstrepen, KJ and Curtin, CD and Lievens, B},
  issn         = {0175-7598},
  journal      = {APPLIED MICROBIOLOGY AND BIOTECHNOLOGY},
  keyword      = {IDENTIFICATION,SACCHAROMYCES,FERMENTATION,GENETIC DIVERSITY,WINE,CIDER,ECOLOGY,YEAST DEKKERA-BRUXELLENSIS,Phenotypic and genetic diversity,Niche adaptation,Dekkera bruxellensis,Biolog,beta-Glucosidase,alpha-Glucosidase,LEVEL,BEER},
  language     = {eng},
  number       = {21},
  pages        = {9123--9134},
  title        = {Comparative phenomics and targeted use of genomics reveals variation in carbon and nitrogen assimilation among different Brettanomyces bruxellensis strains},
  url          = {http://dx.doi.org/10.1007/s00253-015-6769-9},
  volume       = {99},
  year         = {2015},
}

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