Strain improvement and fermentation optimization are two fundamental tasks in industrial fermentation. Multi-scale study on the optimization of industrial fermentation has been proved to be an efficacious method. However, correlations of data used on inter-scale observation and operation are indirect, empirical and there is still much to be improved. Advances in our understanding of complex biological systems are addressed by comprehensive studies that include high-throughput measurements of mRNA, proteins, and low molecular weight metabolites over time and varied conditions during fermentation. Systems biology can be used to relate these omics datasets to the microbial genome and culture conditions in a bioreactor, then identify some new targets for metabolic engineering and elucidate the molecular mechanism of environmental effects. This approach provides a potentially powerful tool for integrating strain improvement and process optimization for industrial biotechnology. (c) 2006 Society of Chemical Industry.