Research programmes for constructing a ‘cell factory’ have been funded in several countries. In Japan, the ‘Minimum genome factory’ (MGF) project was launched in 2001. In this project, several model microbes have been genetically reconstructed to obtain a cell with fewer genes on a chromosome of reduced size. A microbe with a ‘minimum genome’ is expected to exhibit less regulation and therefore to be an ideal platform for a cell-factory system. The goal of this project is to construct such a minimum genome microbe for a cell factory. In this project, the 4.6 Mbp genome ofEscherichia coliK-12 has been successfully reduced to 3.6 Mbp. The constructed reduced-genome strain, MGF-01, shows better growth and higher threonine production compared with the wild-type strain. Furthermore functional analyses of allE. coligenes have also been performed. CGH (comparative genomic hybridization) analysis revealed that about 2600 genes were commonly conserved in the 23E. colistrains tested. This set of conserved genes was hypothesized as a core set forE. colispecies. Phenotype array analysis of a nearly complete collection of single-gene knockout mutants ofE. coliprovided insights intoE. colimetabolic networks. The data sets from the functional genomics will be used to improve design of anE. coliMGF. The present minireview summarizes the progress of theE. coliMGF project and overviews related research.