title: High-throughput phenomics.
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.
authors.affiliation: Dipartimento di Scienze delle Produzioni Agroalimentari e dell'Ambiente (DISPAA), University of Florence, P.le delle Cascine, 24, Florence, 50144, Italy, carlo.viti@unifi.it.
authors.forename: Carlo
authors.initials: C
authors.lastname: Viti
authors.forename: Francesca
authors.initials: F
authors.lastname: Decorosi
authors.forename: Emmanuela
authors.initials: E
authors.lastname: Marchi
authors.forename: Marco
authors.initials: M
authors.lastname: Galardini
authors.forename: Luciana
authors.initials: L
authors.lastname: Giovannetti
mesh_terms: D001419:Bacteria / Q000378:metabolism*; D002244:Carbon / Q000378:metabolism; D003470:Culture Media / Q000737:chemistry; D005456:Fluorescent Dyes / Q000737:chemistry; D005658:Fungi / Q000378:metabolism*; D057166:High-Throughput Screening Assays / Q000295:instrumentation*; D006863:Hydrogen-Ion Concentration; D053858:Metabolic Networks and Pathways; D046228:Microarray Analysis; D008826:Microbial Sensitivity Tests / Q000295:instrumentation; D009391:Nephelometry and Turbidimetry; D009584:Nitrogen / Q000378:metabolism; D010641:Phenotype; D010758:Phosphorus / Q000378:metabolism; D012984:Software; D013455:Sulfur / Q000378:metabolism
chemical_list: D003470:Culture Media; D005456:Fluorescent Dyes; D010758:Phosphorus; D013455:Sulfur; D002244:Carbon; D009584:Nitrogen