Volume 10 Issue 9, September 2012

Grouping the microbiota of individual subjects into compositional categories, or enterotypes, based on the dominance of certain genera may have oversimplified a complex situation.

The insect pathogenPseudomonas entomophila arrests host protein synthesis in the gut of its Drosophila melanogasterhost.

A promising new treatment regimen, consisting of three drugs administered in combination, offers renewed hope in the battle against tuberculosis.

Promoter inversion mediates the switch from a mutualistic to a pathogenic form ofP. luminescens.

A bacterial symbiont of mosquitoes, genetically engineered to secrete antiparasitic effector proteins, arrests the development ofPlasmodiumspp. in these vectors.

Two studies suggest that using inhibitors of histone deacetylases to reactivate latent HIV-1 is a realistic route to coaxing the latent virus out of its genomic hiding place.

Super-resolution microscopy combined with immunostaining of extracellular matrix proteins reveals the dynamics and spatial organization of an actively growingVibrio choleraebiofilm.

Identification of a new pathway connecting TLR4 and activation of the NLR3P inflammasome in response to Gram-negative bacteria.

This month's Genome Watch highlightsin natura cases showing the role of recombination in bacterial evolution, and in vitrostudies that focus on the mechanisms of recombination.

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.

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.

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.

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.

Marine sponges can contain dense and diverse microbial communities that can constitute up to 35% of the sponge biomass. In this Review, Hentschel and colleagues describe how genomic insights into both sponges and their associated microbiota are beginning to illuminate the functional and evolutionary roles of each partner in this association.

Even when receiving antiretroviral therapy, HIV-infected individuals have an increased risk of mortality owing to systemic immune activation. Sandler and Douek review evidence showing that the translocation of microbial products from the intestine into the circulation may contribute to this risk and discuss potential therapeutic strategies.

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.