Provided is a method of producing a novel microorganism having a minimal genome. In particular, provided are a method of producing a novel microorganism having a smaller genome size than a wild-type,the method including the step of culturing the microorganism in a medium containing LB broth with stepwise decreasing concentrations of the LB broth; and a novel microorganism having a smaller genomesize than a wild-type, produced by the above method. Despite the small genome size, the novel microorganism of the present disclosure may have a high growth rate, pyruvate production capacity, and protein translation efficiency thereby being usefully applied to industry such as production of recombinant proteins or pyruvate.