Volume 14 Issue 4, April 2016

Three new studies investigate the links between microbiome composition and growth in underweight infants and identify specific diet components and microbial taxa that can counteract the

effects of poor nutrition.

A role in targeting late-stage phage genes explains the presence of RNases in type III-A CRISPR–Cas systems.

This study shows that the SakA stress-sensing pathway is required for phytochrome-dependent light signalling inAspergillus nidulans.

Using data collected during theTaraOceans expedition, this study elucidates how trans-kingdom interactions in marine microbial communities influence the export of carbon from the atmosphere

to the deep ocean.

MIMIVIRE, an antivirophage defence system that includes Cas-like proteins, provides an intriguing new example of the unusual biology of giant viruses.

This study identifies the first β-lactam receptor in Gram-negative bacteria, VbrK, a histidine kinase that belongs to a two-component system inVibrio parahaemolyticus.

Genomics studies are prompting a re-evaluation of the diversity ofEscherichia colipathovars and how this diversity corresponds to virulence.

In this Progress article, Stephanie Karst describes how the gut microbiota promotes intestinal infection by enteric viruses. She discusses direct mechanisms by which bacteria stabilize viral

particles and facilitate viral attachment to host cells, and indirect mechanisms by which the microbiota suppresses antiviral immune responses.

In this Review, Oikonomou and Jensen discuss how electron cryotomography has provided structural and mechanistic insights into the physiology of bacteria and archaea, from morphogenesis to

subcellular compartmentalization and from metabolism to complex interspecies interactions.

The metabolism of pathogens and hosts are intertwined — they compete for resources, sense metabolites produced by each other and target metabolic processes to mediate virulence and immunity.

In this Review, Olive and Sassetti discuss the emerging roles of metabolism in host–pathogen interactions.

Shigellaspp. harbour an arsenal of virulence factors that enable host invasion. Here, Baker and colleagues review how these bacteria have evolved fromEscherichia colion several occasions

into highly specialized, human-restricted pathogens that have spread globally.

Biofilms dominate microbial life in streams and rivers. In this Review, Battin and colleagues describe the interactions between the microbiome of stream biofilms and ecosystem processes, and

they consider the effects of global ecosystem change and climate change on these biofilms.