High-throughput sequencing and clinical microbiology: progress, opportunities and challenges
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Updated: Jun 8, 2026

Guided Protocol for Fecal Microbial Characterization by 16S rRNA-Amplicon Sequencing
Published on: March 19, 2018
Mark J Pallen1, Nicholas J Loman, Charles W Penn
1School of Biosciences, University of Birmingham, Birmingham, B15 2TT, United Kingdom. m.pallen@bham.ac.uk
Abstract:
High-throughput sequencing is sweeping through clinical microbiology, transforming our discipline in its wake. It is already providing an enhanced view of pathogen biology through rapid and inexpensive whole-genome sequencing and more sophisticated applications such as RNA-seq. It also promises to deliver high-resolution genomic epidemiology as the ultimate typing method for bacteria. However, the most revolutionary effect of this 'disruptive technology' is likely to be creation of a novel sequence-based, culture-independent diagnostic microbiology that incorporates microbial community profiling, metagenomics and single-cell genomics. We should prepare for the coming 'technological singularity' in sequencing, when this technology becomes so fast and so cheap that it threatens to out-compete existing diagnostic and typing methods in microbiology.
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