Reviews & Analysis

In this Review, Malim and colleagues discuss the evidence that type I interferons (IFNs) can control HIV-1 replicationin vivoand debate the controversial role of IFNs in promoting the pathological sequelae of chronic HIV-1 infection.

Mignot and colleagues present an evolutionary scenario to explain the emergence of the two distinct machines — the Agl–Glt and Agl–Nfs complexes — that are involved in motility and assembly of the spore coat inMyxococcus xanthus. They argue that elucidation of the composition and mechanism of action of these complexes will improve our understanding of the evolution of macromolecular complexes.

Bacteria form biofilms as a strategy for survival and persistence. In this Review, Yildiz and colleagues discussVibrio cholerae surface attachment and the biofilm matrix components. They also review the regulatory network that governs V. choleraebiofilm formation, including the transcriptional regulators of key genes involved in this process, as well as the roles of small nucleotides and small RNAs.

In bacteria, ribosome stalling is a frequent event that threatens viability. In this Review, Kenneth Keiler discusses the triggers of ribosome stalling, the physiological consequences of stalling and the mechanisms used by bacteria to rescue stalled ribosomes, includingtrans-translation and the alternative pathways mediated by alternative ribosome-rescue factor A (ArfA) and ArfB.

Urinary tract infections (UTIs) pose a severe public health problem and are caused by a range of pathogens. In this Review, Hultgren and colleagues discuss how basic science studies are elucidating the molecular mechanisms of UTI pathogenesis and how this knowledge is being used for the development of novel clinical treatments for UTIs.

In this Review, Gerdes and colleagues discuss the multifaceted alarmones guanosine tetraphosphate and guanosine pentaphosphate (collectively referred to as (p)ppGpp) and their functions in the regulation of bacterial physiology, including their synthesis and degradation, as well as their role in transcriptional regulation, in GTP biosynthesis and in the formation of bacterial persisters.

Antibiotic resistance constitutes a threat to human and animal health worldwide. Here, Manaia and colleagues report the main findings of the European COST (Cooperation in Science and Technology) Action DARE (Detecting Evolutionary Hotspots of Antibiotic Resistance in Europe) and discuss the need for improved sampling of the environment and more comprehensive databases, as well as the policy and management options that should be considered as priorities to tackle antibiotic resistance in the environment.

Salmonella entericaserovars are human pathogens that are commonly used to study host–bacterium interaction mechanisms. In this Review, Bäumler and colleagues discuss how the innate immune system recognizes non-typhoidal and typhoidal serovars, and how specific virulence factors and changes in virulence gene regulation alter innate immune responses.

In this Review, Miller and colleagues discuss the arsenal of effector proteins that salmonellae use to manipulate their animal hosts, in addition to the host response to these infections. The authors also discuss the challenges ahead for unravelling the mechanistic details of effector function.

Predicting the future global distribution of vector-borne diseases is a complex task that depends on the generation of accurate mathematical models. Here, Messina and colleagues compare and contrast the main approaches that have been used to predict the future distribution of dengue and propose a set of minimum criteria for future projections that, by analogy, are applicable to other vector-borne diseases.

The detection and subsequent analysis of low-abundance microbial populations — the 'rare biosphere' — have demonstrated the persistence, population dynamics, dispersion and predation of these microbial species. Lynch and Neufeld discuss the ecology of rare microbial populations and highlight molecular and computational methods for targeting taxonomic 'blind spots' in the rare biosphere of complex microbial communities.

B cells are essential components of the immune response against infection. However, several bacteria, viruses and parasites are able to infect B cells and manipulate B cell functions and survival. Here, the authors review how pathogens use B cells as reservoirs, manipulate B cell differentiation and interfere with B cell survival, and they discuss the implications for ongoing immune responses.

In this Review, Fuhrman and colleagues summarize our current understanding of marine microbial community dynamics at various scales — from hours to decades — and consider how long-term time series illustrate important ecological concepts such as community resilience and seasonality, as well as interactions among microorganisms in the global oceans.

Plasmodium falciparum, the malaria parasite, relies on post-translational modifications of proteins to regulate several fundamental aspects of its life cycle and pathogenesis. Here, Doerig and colleagues focus on the roles of protein phosphorylation, acetylation, methylation and lipidation inP. falciparumbiology, and they discuss how the enzymes that mediate these modifications can be targeted by novel antimalarial drugs.

Marine viruses have important roles in modulating the dynamics of microbial life in the global oceans. Brum and Sullivan discuss the recent technological advances that are facilitating an accelerated pace of discovery in marine virology, including metagenomics and several cultivation-dependent and cultivation-independent tools.

In this Opinion article, Errington reviews the studies that describe the role of MreB in the determination and maintenance of rod cell shape in bacteria, and he presents a model to reconcile the conflicting data.

The base excision repair (BER) pathway is the most important mechanism for the repair of oxidative DNA damage, which is frequently encountered by host-adapted bacterial pathogens. Here, van der Veen and Tang review DNA repair in the human pathogensMycobacterium tuberculosis, Helicobacter pylori and Neisseria meningitidis, highlighting common and distinct mechanisms.