Systematic elucidation of independently modulated genes in Lactiplantibacillus plantarum reveals a trade‐off between secondary and primary metabolism

Lactiplantibacillus plantarum is a probiotic bacterium widely used in food and health industries, but its gene regulatory information is limited in existing databases, which impedes the research of its physiology and its applications. To obtain a better understanding of the transcriptional regulatory network of L. plantarum, independent component analysis of its transcriptomes was used to derive 45 sets of independently modulated genes (iModulons). Those iModulons were annotated for associated transcription factors and functional pathways, and active iModulons in response to different growth conditions were identified and characterized in detail. Eventually, the analysis of iModulon activities reveals a trade‐off between regulatory activities of secondary and primary metabolism in L. plantarum. The independent component analysis of Lactiplantibacillus plantarum's transcriptomes obtained 45 sets of independently modulated genes (iModulons), and 24 iModulons were annotated. The characterization of active iModulons illustrates how L. plantarum responds to stress, and the analysis of iModulon activities reveals how L. plantarum balances secondary and primary metabolism.