Reducing native complexity from living organisms has significance in several aspects such as academic application as model organism and industrial application as factory of useful material. In particular, reduced complexity is also interesting in the field investigating the minimal form of "life-as-we-knowit." However, subtracting or inactivating genes from the genome without growth defects is difficult due to the complexity of gene network and error proofing functions. In this study, using model bacteria Escherichia coli (E. coli), we designed a culture system using ultraviolet as a mutagen in order to select possible mutants growing rapidly with genomic inactivation. Here, we demonstrated that the culture system could accumulation of many mutations and preservation of growth ability. These results suggest that our method is effective to obtain functionally reduced genome of E. coli.