title: Colony-live--a high-throughput method for measuring microbial colony growth kinetics--reveals diverse growth effects of gene knockouts in Escherichia coli.
abstract: BACKGROUND
  Precise quantitative growth measurements and detection of small growth changes in high-throughput manner is essential for fundamental studies of bacterial cell. However, an inherent tradeoff for measurement quality in high-throughput methods sacrifices some measurement quality. A key challenge has been how to enhance measurement quality without sacrificing throughput.
  
  
  RESULTS
  We developed a new high-throughput measurement system, termed Colony-live. Here we show that Colony-live provides accurate measurement of three growth values (lag time of growth (LTG), maximum growth rate (MGR), and saturation point growth (SPG)) by visualizing colony growth over time. By using a new normalization method for colony growth, Colony-live gives more precise and accurate growth values than the conventional method. We demonstrated the utility of Colony-live by measuring growth values for the entire Keio collection of Escherichia coli single-gene knockout mutants. By using Colony-live, we were able to identify subtle growth defects of single-gene knockout mutants that were undetectable by the conventional method quantified by fixed time-point camera imaging. Further, Colony-live can reveal genes that influence the length of the lag-phase and the saturation point of growth.
  
  
  CONCLUSIONS
  Measurement quality is critical to achieving the resolution required to identify unique phenotypes among a diverse range of phenotypes. Sharing high-quality genome-wide datasets should benefit many researchers who are interested in specific gene functions or the architecture of cellular systems. Our Colony-live system provides a new powerful tool to accelerate accumulation of knowledge of microbial growth phenotypes.
authors: Rikiya
authors: R
authors: Takeuchi
authors: Takeyuki
authors: T
authors: Tamura
authors: Toru
authors: T
authors: Nakayashiki
authors: Yuichirou
authors: Y
authors: Tanaka
authors: Ai
authors: A
authors: Muto
authors: Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, Japan. blwanner@purdue.edu.
authors: Barry L
authors: BL
authors: Wanner
authors: Hirotada
authors: H
authors: Mori
mesh_terms: D001431:Bacteriological Techniques / Q000379:methods*; D004926:Escherichia coli / Q000235:genetics* / Q000254:growth & development*; D055786:Gene Knockout Techniques; D005827:Genetics, Microbial / Q000379:methods*; D057166:High-Throughput Screening Assays / Q000379:methods*; D061848:Optical Imaging / Q000379:methods