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Colony-live a high-throughput method for measuring microbial colony growth kinetics reveals diverse growth effects of gene knockouts in Escherichia coli

Rikiya Takeuchi1, Takeyuki Tamura2, Toru Nakayashiki13, Yuichirou Tanaka1, Ai Muto1, Barry L Wanner4* and Hirotada Mori1*

Author Affiliations

1 Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, Japan

2 Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan

3 Graduate School of Agricultural Science, Kobe University, Nada, Kobe, Japan

4 Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA

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BMC Microbiology 2014, 14:171  doi:10.1186/1471-2180-14-171

Published: 26 June 2014



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.


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.


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.

Growth kinetics; Phenotype screening; High-throughput; Single-gene knockout; Keio collection; Lag time of growth (LTG); Maximum growth rate (MGR); Saturation point growth (SPG)