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High-Throughput Phenomics

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Bacterial Pangenomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1231))

Abstract

Standard protocols are available in order to apply Phenotype MicroArray (PM) technology to characterize different groups of microorganisms. Nevertheless, there is the need to pay attention to several crucial steps in order to obtain high-quality and reproducible data from PM, such as the choice of the Dye mix, the type and concentration of the carbon source in metabolic experiments, the use of a buffered medium. A systematic research of auxotrophies in strains to be tested should be carefully evaluated before starting with PM experiments. Detailed protocols to obtain defined and reproducible phenotypic profiles for bacteria and yeasts are shown. Moreover, the innovative software opm R packages and DuctApe suite for the analysis of kinetic data produced by PM and panphenome description are reported.

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Author information

Authors and Affiliations

  1. Dipartimento di Scienze delle Produzioni Agroalimentari e dell’Ambiente (DISPAA), University of Florence, P.le delle Cascine, 24, Florence, 50144, Italy

    Carlo Viti, Francesca Decorosi, Emmanuela Marchi & Luciana Giovannetti

  2. EMBL-EBI, Wellcome Trust Genome Campus, Cambridge, UK

    Marco Galardini

Authors
  1. Carlo Viti
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  2. Francesca Decorosi
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  3. Emmanuela Marchi
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  4. Marco Galardini
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  5. Luciana Giovannetti
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Corresponding author

Correspondence to Carlo Viti .

Editor information

Editors and Affiliations

  1. Department of Biology, University of Florence, Florence, Italy

    Alessio Mengoni

  2. EMBL-EBI, Cambridge, United Kingdom

    Marco Galardini

  3. Department of Biology, University of Florence, Florence, Italy

    Marco Fondi

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© 2015 Springer Science+Business Media New York

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Viti, C., Decorosi, F., Marchi, E., Galardini, M., Giovannetti, L. (2015). High-Throughput Phenomics. In: Mengoni, A., Galardini, M., Fondi, M. (eds) Bacterial Pangenomics. Methods in Molecular Biology, vol 1231. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-1720-4_7

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  • DOI: https://doi.org/10.1007/978-1-4939-1720-4_7

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-1719-8

  • Online ISBN: 978-1-4939-1720-4

  • eBook Packages: Springer Protocols

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