Decoding bioprocesses with transcriptomics: current status and future potential

Transcriptomic analyses represent widely used state-of-the art methodologies in molecular biosciences going back to the early 1960s. Over the last years, transcriptomics has become increasingly important in the field of bioprocess engineering. Systematic transcriptomics platform technologies (especially RNA-seq) play an accelerating role to investigate the gene expression profiles of cells in diverse bioprocesses, covering prokaryotic and eukaryotic cell systems. This review summarizes how different transcriptomics methodologies from RT-qPCR to microarrays and RNA-seq have been applied in bioprocess engineering to date. The major scopes of the reviewed works can be categorized as the following: strain/cell line characterization, investigation of culture/media conditions, process operations as well as scale-up/down studies. Subsequently, a perspective is given how emerging sequencing-based transcriptomics could envision the understanding of population diversities in space and time aided by single cell analysis (scRNA-seq) as well as transcriptional histories (Record-Seq).