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Biolog Phenotype Microarrays

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Microbial Systems Biology

Part of the book series: Methods in Molecular Biology ((MIMB,volume 881))

Abstract

Phenotype microarrays nicely complement traditional genomic, transcriptomic, and proteomic analysis by offering opportunities for researchers to ground microbial systems analysis and modeling in a broad yet quantitative assessment of the organism’s physiological response to different metabolites and environments. Biolog phenotype assays achieve this by coupling tetrazolium dyes with minimally defined nutrients to measure the impact of hundreds of carbon, nitrogen, phosphorous, and sulfur sources on redox reactions that result from compound-induced effects on the electron transport chain. Over the years, we have used Biolog’s reproducible and highly sensitive assays to distinguish closely related bacterial isolates, to understand their metabolic differences, and to model their metabolic behavior using flux balance analysis. This chapter describes Biolog phenotype microarray system components, reagents, and methods, particularly as they apply to bacterial identification, characterization, and metabolic analysis.

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Acknowledgments

This work was funded in part by a grant from the United States Defense Threat Reduction Agency (TMTI0049_09_RD_T) and Joint Program Executive Office-Chemical and Biological Defense, Medical Identification & Treatment Systems, Critical Reagents Program (JPEO-CBD, CBMS, MITS, and CRP). Opinions, interpretations, conclusions, and recommendations are those of the authors and are not necessarily endorsed by the United States Army.

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Authors and Affiliations

  1. Bacteriology Division, United States Army Medical Research Institute for Infectious Diseases, Fort Detrick, MD, USA

    April Shea & Mark Wolcott

  2. Mount Sinai School of Medicine, New York, NY, USA

    Simon Daefler

  3. Bacteriology Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD, USA

    David A. Rozak

Authors
  1. April Shea
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  2. Mark Wolcott
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  3. Simon Daefler
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  4. David A. Rozak
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Corresponding author

Correspondence to David A. Rozak .

Editor information

Editors and Affiliations

  1. Physics & Life Sciences Directorate, Biosciences & Biotechnology Div., Lawrence Livermore National Laboratory, East Avenue 7000, Livermore, 94551, California, USA

    Ali Navid

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Shea, A., Wolcott, M., Daefler, S., Rozak, D.A. (2012). Biolog Phenotype Microarrays. In: Navid, A. (eds) Microbial Systems Biology. Methods in Molecular Biology, vol 881. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-61779-827-6_12

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  • DOI: https://doi.org/10.1007/978-1-61779-827-6_12

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-61779-826-9

  • Online ISBN: 978-1-61779-827-6

  • eBook Packages: Springer Protocols

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