Transcriptome of Escherichia coli DH5α cultured under static liquid conditions in a gas-permeable film bag

We previously proposed an air-permeable film bag culture as a novel method in microbiological studies. In this bag, oxygen molecules are passively supplied through the film. Here, we report the transcriptome differences between aerobic static liquid cultured cells and conventional shaking liquid cultured cells. The comparison was performed using Escherichia coli DH5α in early exponential phase, a period when cell growth is accelerating and the effects of substrate depletion and secreted products are considered to be negligible. We found a significant difference in the transcriptome between the shaking-cultured cells and the static film-cultured cells. Notably, a greater number of prophage sequences and small proteins, mainly predicted as gene expression regulators and cold shock proteins, were detected in the static-cultured cells. Furthermore, the enhanced expression of flagella-related genes, genes involved in nitrate/nitrite metabolism, and several chaperones (with different predicted targets) were detected in the static liquid culture compared with the shaken culture. Our results suggest that the aerobic static liquid culture method offers a novel insight into the physiology of microorganisms.