Metabolic footprinting as a tool for discriminating between brewing yeasts

The characterization of industrial yeast strains by examining their metabolic footprints (exometabolomes) was investigated and compared to genome‐based discriminatory methods. A group of nine industrial brewing yeasts was studied by comparing their metabolic footprints, genetic fingerprints and comparative genomic hybridization profiles. Metabolic footprinting was carried out by both direct injection mass spectrometry (DIMS) and gas chromatography time‐of‐flight mass spectrometry (GC–TOF–MS), with data analysed by principal components analysis (PCA) and canonical variates analysis (CVA). The genomic profiles of the nine yeasts were compared by PCR–restriction fragment length polymorphism (PCR–RFLP) analysis, genetic fingerprinting using amplified fragment length polymorphism (AFLP) analysis and microarray comparative genome hybridizations (CGH). Metabolomic and genomic analysis comparison of the nine brewing yeasts identified metabolomics as a powerful tool in separating genotypically and phenotypically similar strains. For some strains discrimination not achieved genomically was observed metabolomically. Copyright © 2007 John Wiley & Sons, Ltd.

[1]  D. Kell,et al.  Metabolic footprinting and systems biology: the medium is the message , 2005, Nature Reviews Microbiology.

[2]  T. Ferenci,et al.  Metabolomic diversity in the species Escherichia coli and its relationship to genetic population structure , 2005, Metabolomics.

[3]  T. Deák.  Handbook of Food Spoilage Yeasts , 1996 .

[4]  J. Hansen,et al.  Saccharomyces carlsbergensis contains two functional MET2 alleles similar to homologues from S. cerevisiae and S. monacensis. , 1994, Gene.

[5]  S. Villas-Bôas,et al.  Extracellular metabolomics: a metabolic footprinting approach to assess fiber degradation in complex media. , 2006, Analytical biochemistry.

[6]  J. Selbig,et al.  Parallel analysis of transcript and metabolic profiles: a new approach in systems biology , 2003, EMBO reports.

[7]  F Baganz,et al.  Systematic functional analysis of the yeast genome. , 1998, Trends in biotechnology.

[8]  D. Kell.  Metabolomics and systems biology: making sense of the soup. , 2004, Current opinion in microbiology.

[9]  J. Nielsen,et al.  Global metabolite analysis of yeast: evaluation of sample preparation methods , 2005, Yeast.

[10]  J. Haber,et al.  Analysis of meiosis-defective mutations in yeast by physical monitoring of recombination. , 1986, Genetics.

[11]  N. Shirley,et al.  Evidence for multiple interspecific hybridization in Saccharomyces sensu stricto species. , 2002, FEMS yeast research.

[12]  József Baranyi,et al.  Comparison of different approaches for comparative genetic analysis using microarray hybridization , 2006, Applied Microbiology and Biotechnology.

[13]  C. Gaillardin,et al.  Molecular typing demonstrates homogeneity of Saccharomyces uvarum strains and reveals the existence of hybrids between S. uvarum and S. cerevisiae, including the S. bayanus type strain CBS 380. , 2000, Systematic and applied microbiology.

[14]  D. Kell,et al.  Metabolomics by numbers: acquiring and understanding global metabolite data. , 2004, Trends in biotechnology.

[15]  D. Kell,et al.  A functional genomics strategy that uses metabolome data to reveal the phenotype of silent mutations , 2001, Nature Biotechnology.

[16]  C. Vandenbroucke-Grauls,et al.  Comparison of Amplified Ribosomal DNA Restriction Analysis, Random Amplified Polymorphic DNA Analysis, and Amplified Fragment Length Polymorphism Fingerprinting for Identification ofAcinetobacter Genomic Species and Typing ofAcinetobacter baumannii , 1998, Journal of Clinical Microbiology.

[17]  Douglas B. Kell,et al.  Discrimination of Modes of Action of Antifungal Substances by Use of Metabolic Footprinting , 2004, Applied and Environmental Microbiology.

[18]  P. Fernandes.  How does yeast respond to pressure? , 2005, Brazilian journal of medical and biological research = Revista brasileira de pesquisas medicas e biologicas.

[19]  N. Goto-Yamamoto,et al.  AFLP analysis of type strains and laboratory and industrial strains of Saccharomyces sensu stricto and its application to phenetic clustering , 2001, Yeast.

[20]  W. Dunn,et al.  Measuring the metabolome: current analytical technologies. , 2005, The Analyst.

[21]  D. Kell.  Systems biology, metabolic modelling and metabolomics in drug discovery and development. , 2006, Drug discovery today.

[22]  D. Kell,et al.  High-throughput classification of yeast mutants for functional genomics using metabolic footprinting , 2003, Nature Biotechnology.

[23]  Douglas B. Kell,et al.  Functional Genomics Via Metabolic Footprinting: Monitoring Metabolite Secretion by Escherichia Coli Tryptophan Metabolism Mutants Using FT–IR and Direct Injection Electrospray Mass Spectrometry , 2003, Comparative and functional genomics.

[24]  A. Martini,et al.  A Taxonomic Key for the Genus Saccharomyces , 1993 .

[25]  R. M. Walsh,et al.  GROWTH OF SACCHAROMYCES CEREVISIAE AND SACCHAROMYCES UVARUM IN A TEMPERATURE GRADIENT INCUBATOR , 1977 .

[26]  B. Pearson,et al.  Comparative genome analysis of Campylobacter jejuni using whole genome DNA microarrays , 2003, FEBS letters.

[27]  Douglas B. Kell,et al.  Metabolic control theory: its role in microbiology and biotechnology , 1986 .

[28]  T. Ferenci,et al.  Global metabolite analysis: the influence of extraction methodology on metabolome profiles of Escherichia coli. , 2003, Analytical biochemistry.

[29]  A. Vanlaere.  Trehalose, reserve and/or stress metabolite? , 1989 .

[30]  O. Fiehn,et al.  Metabolite profiling for plant functional genomics , 2000, Nature Biotechnology.

[31]  T. Ogata,et al.  Differentiation between brewing and non‐brewing yeasts using a combination of PCR and RFLP , 1999, Journal of applied microbiology.

[32]  C. Kurtzman,et al.  Deoxyribonucleic acid relatedness among species of the genus Saccharomyces sensu stricto , 1985 .

[33]  Daniel Cozzolino,et al.  Metabolic profiling as a tool for revealing Saccharomyces interactions during wine fermentation. , 2006, FEMS yeast research.

[34]  R. Somorjai,et al.  Rapid Identification of Candida Species by Using Nuclear Magnetic Resonance Spectroscopy and a Statistical Classification Strategy , 2003, Applied and Environmental Microbiology.

[35]  D. Dlauchy,et al.  Delimination of brewing yeast strains using different molecular techniques. , 2000, International journal of food microbiology.

[36]  Tetsuya Hayashi,et al.  Escherichia coli , 1983, CABI Compendium.

[37]  Y. Kaneko,et al.  Pure and Mixed Genetic Lines of Saccharomyces bayanus and Saccharomyces pastorianus and Their Contribution to the Lager Brewing Strain Genome , 2006, Applied and Environmental Microbiology.

[38]  R. Somorjai,et al.  A rapid screening test to distinguish between Candida albicans and Candida dubliniensis using NMR spectroscopy. , 2005, FEMS microbiology letters.

[39]  J. Pierce,et al.  ABSORPTION OF AMINO ACIDS FROM WORT BY YEASTS , 1964 .

[40]  K. Ito,et al.  Tolerance mechanism of the ethanol-tolerant mutant of sake yeast. , 2000, Journal of bioscience and bioengineering.