PMID:11435407

Citation	Bochner, BR, Gadzinski, P and Panomitros, E (2001) Phenotype microarrays for high-throughput phenotypic testing and assay of gene function.Genome Res. 11:1246-55
Abstract	The bacterium Escherichia coli is used as a model cellular system to test and validate a new technology called Phenotype MicroArrays (PMs). PM technology is a high-throughput technology for simultaneous testing of a large number of cellular phenotypes. It consists of preconfigured well arrays in which each well tests a different cellular phenotype and an automated instrument that continuously monitors and records the response of the cells in all wells of the arrays. For example, nearly 700 phenotypes of E. coli can be assayed by merely pipetting a cell suspension into seven microplate arrays. PMs can be used to directly assay the effects of genetic changes on cells, especially gene knock-outs. Here, we provide data on phenotypic analysis of six strains and show that we can detect expected phenotypes as well as, in some cases, unexpected phenotypes.
Links	PubMed Online version:10.1101/gr.186501
Keywords	Escherichia coli; Gene Deletion; Cellular Respiration; Phenomics; Mutation; Oligonucleotide Array Sequence Analysis; Phenotype; Phenotype Microarray
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Main Points of the Paper

• Phenotype Microarrays are used to assay cellular respiration under a wide variety of conditions

Materials and Methods Used

• Phenotype Microarrays
  • ES- measuring carbon catabolism
  • EN- measuring nitrogen catabolism
  • EPS- measuring phosphate and sulfur catabolism
  • EA- measuring auxotrophy (growth stimulation by nutrients)
  • ES1, 2, and 3- measuring alterations in sensitivity or resistance to toxic chemicals
• OmniLog instrument
  • read and record the color change
• Color CCD camera
  • provide quantitative and kinetic information about the response of the cells

Phenotype Annotations

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Species	Taxon ID	Strain	Gene (if known)	OMP	Phenotype	Details	Evidence	Notes
Escherichia coli		fb753	xylA	abolished utilization of xylose as a C source no growth on xylose	Metabolic Activity	Biolog phenotype microarray	Biochemical Assay	Figure 2
Escherichia coli		fb753	xylA	abolished utilization of maltose as a C source no growth on maltose	Metabolic Activity	Biolog phenotype microarray	Biochemical Assay	Figure 2
Escherichia coli		fb753	xylA	abolished utilization of maltotriose as a C source no growth on maltotriose	Metabolic Activity	Biolog phenotype microarray	Biochemical Assay	Figure 2
Escherichia coli	NCBI:83333	EP014	ynjB::Tn10	abolished utilization of L-arginine as a N source no growth on L-arginine	Metabolic Activity	Biolog phenotype microarray	Biochemical Assay	Figure 2
Escherichia coli	NCBI:83333	EP014	ynjB::Tn10	abolished utilization of ornithine as a N source no growth on ornithine	Metabolic Activity	Biolog phenotype microarray	Biochemical Assay	Figure 2
Escherichia coli	NCBI:83333	EP0005	malF3089::Tn10	abolished utilization of maltose as a C source no growth on maltose	Metabolic Activity	Biolog phenotype microarray	Biochemical Assay	Figure 3
Escherichia coli	NCBI:83333	EP0005	malF3089::Tn10	abolished utilization of maltotriose as a C source no growth on maltotriose	Metabolic Activity	Biolog phenotype microarray	Biochemical Assay	Figure 3
Escherichia coli	NCBI:83333	EP0007	del-cya1400::kan	abolished utilization of secondary carbon sources no growth on secondary C sources	Metabolic Activity	Biolog phenotype microarray	Biochemical Assay	Figure 4- see for a list
Escherichia coli	NCBI:83333	EP0012	fruR::Tn5	increased utilization of some C sources decreased utilization of some C sources	Metabolic Activity	Biolog phenotype microarray	Biochemical Assay	Figure 5- see for a list
Escherichia coli	NCBI:83333	EP0007	del-cya1400::kan	increased sensitivity to toxic chemicals	Metabolic Activity	Biolog phenotype microarray	Biochemical Assay	Figure 4- see for a list
Escherichia coli	NCBI:83333	EP0007	del-cya1400::kan	abolished utilization of pyruvate no growth on pyruvate	Metabolic Activity	Biolog phenotype microarray	Biochemical Assay	Figure 4- as a result, this strain gave negative results on the EN, EPS, and EA arrays
Escherichia coli	NCBI:83333	fb757	phoP amber	aberrant utilization of several amino acid phosphates decreased growth on several amino acid phosphates	Metabolic Activity	Biolog phenotype microarray	Biochemical Assay	Figure 6- see for a list
Escherichia coli	NCBI:83333	fb757	phoP amber	aberrant utilization of glucosamine-6P as a phosphate source decreased growth on glucosamine-6P	Metabolic Activity	Biolog phenotype microarray	Biochemical Assay	Figure 6- see for a list
Escherichia coli	NCBI:83333	fb757	phoP amber	aberrant utilization of some sulfur sources decreased growth on some sulfur sources	Metabolic Activity	Biolog phenotype microarray	Biochemical Assay	Figure 6- see for a list
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References

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