Opinion

In this Opinion article, Byndloss and Bäumler propose that host control over the microbial ecosystem in the large bowel is critical for the composition and function of its resident microbial organ, while disruption of host control triggers microbial organ dysfunction. This concept provides a theoretical framework for linking the gut microbiota to non-communicable diseases.

Traditional strategies to treat lung infections are based on the premise that the lung is sterile; however, it is now thought that the lung contains a resident microbiota. Here, Cooksonet al. propose that concepts flowing from the Human Microbiome Project can transform the treatment of lung infections.

Risk assessment for the development of antibiotic resistance against a new drug candidate is of paramount importance in preclinical development. In this Opinion article, Sommeret al. propose a new preclinical paradigm for the prediction of antibiotic resistance.

The evolutionary function of natural competence remains controversial and several hypotheses for a function have been proposed. In this Opinion article, Veening and Blokesch propose that kin-discriminated predation that is linked to natural competence serves as a DNA acquisition strategy and therefore contributes to bacterial evolution.

The resilience of the microbiota can protect us from disease, but a resilient dysbiotic microbiota may also cause disease. This Opinion article discusses the concepts and mechanisms of microbial resilience against dietary, antibiotic or bacteriotherapy-induced perturbations and the implications these have for human health.

Zoonotic diseases present a substantial global health burden. In this Opinion article, Plowrightet al. present an integrative conceptual and quantitative model that reveals that all zoonotic pathogens must overcome a hierarchical series of barriers to cause spillover infections in humans.

Macromolecular crowding affects the physicochemistry of the cytoplasm and, in turn, microbial physiology. We propose that cells maintain the overall concentration of macromolecules within a narrow range (a process that we refer to as 'homeocrowding') and discuss possible mechanisms for achieving this.

Sequencing viral DNA and RNA is an important part of clinical practice, although, so far, mostly subgenomic fragments have been sequenced. In this Opinion article, Houldcroft, Beale and Breuer highlight the potential that sequencing whole viral genomes has for clinical applications.

The microbiota is central for host homeostasis and affects not only the gut but also other organs, including the lungs. In this Opinion article, Hansbro and colleagues explore the role of the microbiota in the gut–lung axis and lung disease.

The division of labour is an important strategy in microbial species. In this Perspective, Cooper and West propose a set of conditions that define division of labour, describe recent examples according to these conditions and discuss how clarifying what constitutes division of labour highlights key evolutionary questions.

Similarly to competing endogenous RNAs (ceRNAs) in mammalian cells, competition for regulatory RNAs and proteins can lead to crosstalk between bacterial mRNAs. In this Opinion article, Bossi and Figueroa-Bossi argue that such competition for regulatory targets may have a substantial influence on bacterial gene networks.

The placenta forms the foremost barrier that protects the developing fetus during pregnancy in eutherian organisms. However, diverse pathogens such asToxoplasma gondii, rubella virus and cytomegalovirus can breach this barrier. In this Opinion article, Coyne and Lazear review mechanisms of vertical transmission, with a focus on the current Zika virus epidemic.

The evolution of monoderm and diderm cell envelopes, and thus of Gram-positive and Gram-negative bacteria, is a long-standing question. In this Opinion article, Tocheva, Ortega and Jensen propose, based on recent electron cryotomography data, a new model that places sporulation at the heart of bacterial evolution.

In this Opinion article, Kreft and colleagues discuss how the combination of individual-based observations with individual-based models (IBMs) can lead to the new approach of microbial individual-based ecology (μIBE). They illustrate this point by describing how IBMs help to explore competitive and cooperative microbial interactions, which include the emergence of spatial patterns in biofilms and bacteria–phage dynamics.

The failure of antibiotics can arise by different bacterial survival strategies, each with implications for treatment. In this Opinion article, Balaban and colleagues propose a new experimental framework for distinguishing between several forms of resistance, tolerance and persistence to antibiotic treatment.

Transposon insertion sequencing (TIS) enables genome-wide definition of loci that are required for growth in diverse conditions. In this article, Waldor and colleagues discuss the benefits and limitations of different experimental approaches to TIS analyses.

Although there is currently no licensed vaccine against dengue virus (DENV), the chimeric yellow fever–DENV tetravalent dengue vaccine (CYD-TDV) has shown efficacy against DENV in two recent Phase III clinical trials. In this Opinion article, Guy and Jackson review the efficacy and safety data from these recent trials and discuss how interactions between the virus, pre-existing host immunity and vaccine-induced immune responses explain CYD-TDV-mediated protection.

In this Opinion article, Herskovits and colleagues introduce an emerging class of bacteria–phage symbiotic interaction — which they term 'active lysogeny' — in which phages regulate the expression of bacterial genes by precise insertion and excision events.

Following host cell invasion, many bacterial and parasitic pathogens hide from the immune system in an intracellular vacuolar niche. In this Opinion article, Mota and colleagues discuss how these 'professional' vacuolar pathogens can remain susceptible to recognition and clearance by the host.

In this Opinion article, López-Garcíaet al. describe recent archaeal phylogenomic data relating to the massive acquisition of bacterial genes by horizontal gene transfer. They argue that the findings presented suggest that the import of these bacterial genes was crucial for the adaptation of archaea to mesophilic lifestyles.