Protocol

Microbial Systems Biology

Volume 881 of the series Methods in Molecular Biology pp 331-373

Date:

Biolog Phenotype Microarrays

  • April SheaAffiliated withBacteriology Division, United States Army Medical Research Institute for Infectious Diseases
  • , Mark WolcottAffiliated withBacteriology Division, United States Army Medical Research Institute for Infectious Diseases
  • , Simon DaeflerAffiliated withMount Sinai School of Medicine
  • , David A. RozakAffiliated withBacteriology Division, United States Army Medical Research Institute of Infectious Diseases Email author 

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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.

Key words

Phenotype microarrays Biolog Bacterial metabolism Tetrazolium redox dyes