Next-generation sequencing or high-throughput sequencing (HTS) should be considered as an enabling technology that permits unprecedented sequencing coverage, unraveling the existence of a multitude of single nucleotide polymorphisms within a single bacterial colony (see Genome Research paper), while preserving a genome-wide perspective. More importantly, this knowledge can be expanded by multiplexing experiments during a single run, for providing time-series analyses or for comparing series of experimental conditions. Alternatively, this approach permits a systematic analysis of transcripts, including detection small non-coding RNA (ncRNA).