Antibiotic research in the age of omics: from expression profiles to interspecies communication

The 'age of omics' has revolutionized our way of studying microbial physiology by introducing global analysis tools such as comparative genomics and global expression techniques including DNA microarrays (transcriptomics) and two-dimensional protein gel electrophoresis (proteomics). From the very beginning, such approaches have also been incorporated into the portfolio of antibiotic research. Genome mining has been used to explore the hidden biosynthetic potential in sequenced bacterial chromosomes, but also to search for novel antibiotic targets. Moreover, numerous studies investigating changes in expression patterns in response to antibiotic presence at the level of both the transcriptome and proteome have been performed over the years, which have helped us gain a deeper understanding of antimicrobial action. This review will focus on the impact that applying global expression studies has had on antibiotic research in the last decade. Signatures of differential gene expression in response to antibiotics have led to a deeper understanding of bacterial resistance mechanisms as well as stress response networks. They have also helped to predict the mechanism of action of novel antimicrobial compounds or to identify potential antibiotic-specific biosensors. Moreover, such studies have revealed novel inhibitory mechanisms of seemingly well-known drugs that might be useful for the development of co-drugs for antibiotic therapy and have identified the potential role of antibiotics as mediators of intercellular communication.