Transposon insertion sequencing: a new tool for systems-level analysis of microorganisms

The combination of transposon mutagenesis with next-generation sequencing has emerged as a useful tool for identifying putative gene function in a high-throughput manner. Here, van Opijnen and Camilli describe the four main techniques that are used for this purpose, with a focus on their application for uncovering bacterial gene function. Our knowledge of gene function has increasingly lagged behind gene discovery, hindering our understanding of the genetic basis of microbial phenotypes. Recently, however, massively parallel sequencing has been combined with traditional transposon mutagenesis in techniques referred to as transposon sequencing (Tn-seq), high-throughput insertion tracking by deep sequencing (HITS), insertion sequencing (INSeq) and transposon-directed insertion site sequencing (TraDIS), making it possible to identify putative gene functions in a high-throughput manner. Here, we describe the similarities and differences of these related techniques and discuss their application to the probing of gene function and higher-order genome organization.