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 of Escherichia coli K-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 all E. coli genes have also been performed. CGH (comparative genomic hybridization) analysis revealed that about 2600 genes were commonly conserved in the 23 E. coli strains tested. This set of conserved genes was hypothesized as a core set for E. coli species. Phenotype array analysis of a nearly complete collection of single-gene knockout mutants of E. coli provided insights into E. coli metabolic networks. The data sets from the functional genomics will be used to improve design of an E. coli MGF. The present minireview summarizes the progress of the E. coli MGF project and overviews related research.