High-throughput — or next-generation — sequencing has changed the face of microbiology. The genomic era for bacteriologists began less than 20 years ago, when the Sanger method was used to sequence the first complete bacterial genome sequence. Over the past 8–10 years, the advent of next-generation techniques has dramatically increased the speed and reduced the costs of sequencing, such that it is now possible to sequence a bacterial genome in a few days.
This Focus brings together a specially commissioned series of articles that looks at some of the most innovative and interesting applications of next-generation sequencing in microbiology, along with a realistic assessment of the advantages and disadvantages of the different sequencing platforms available.
Comment
Categorization of the gut microbiota: enterotypes or gradients?
doi:10.1038/nrmicro2859
Nature Reviews Microbiology 10, 591 (2012)
Progress
High-throughput bacterial genome sequencing: an embarrassment of choice, a world of opportunity
Nicholas J. Loman, Chrystala Constantinidou, Jacqueline Chan, Mihail Halachev, Martin Sergeant, Charles W. Penn, Esther R. Robinson & Mark J. Pallen
doi:10.1038/nrmicro2850
Nature Reviews Microbiology 10, 599–606 (2012)
In this Progress article, Pallen, Loman and colleagues present a snapshot of the high-throughput sequencing platforms available to microbiologists today, together with the relevant analytical tools, and evaluate their strengths and weaknesses in obtaining bacterial genome sequences.
Reviews
Going viral: next-generation sequencing applied to human gut phage populations
Alejandro Reyes, Nicholas P. Semenkovich, Katrine Whiteson, Forest Rohwer & Jeffrey I. Gordon
doi:10.1038/nrmicro2853
Nature Reviews Microbiology 10, 607–617 (2012)
Viruses are the most diverse and uncharacterized components of all the major ecosystems on Earth, including that within the mammalian gut. Here, Gordon and colleagues review our current understanding of the diversity and ecology of the bacteriophages present in the human gut and discuss how an improved understanding of phage dynamics could revitalize phage therapy.
Dual RNA-seq of pathogen and host
Alexander J. Westermann, Stanislaw A. Gorski & Jörg Vogel
doi:10.1038/nrmicro2852
Nature Reviews Microbiology 10, 618–630 (2012)
The infection process is accompanied by widespread changes in gene expression in both host and pathogen. Here, Vogel and colleagues explore the feasibility of simultaneously analysing the transcriptomes of both host and pathogen using RNA deep-sequencing approaches.
Genomic sequencing of uncultured microorganisms from single cells
Roger S. Lasken
doi:10.1038/nrmicro2857
Nature Reviews Microbiology 10, 631–640 (2012)
In recent years, thanks to the development of whole-genome amplification methods, it has become possible to sequence the genome of a single bacterial cell. Here, Roger Lasken reviews the development of single-cell sequencing techniques and their most recent applications.
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