Intracellular microbe whole-genome expression profiling: methodological considerations and biological inferences

Understanding the mechanisms by which microbes survive in their host intracellular environments is an essential precursor to developing novel intervention strategies that might exploit the interplay between host and microbe. Transcriptional profiling allows us a glimpse of these molecular interactions and promises to reveal much of this dialogue in both pathogenic and symbiotic settings. Such studies will underpin the development of antivirulence strategies for new therapeutics. This chapter aims to describe the challenges of studying microbial RNA expression from intracellular and in vivo scenarios, and to detail a fraction of the insights acquired from this rapidly expanding field, driven by the recent availability of microbe whole-genome sequence information.