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  • Assessing the genetic variation of bacteria has become ever more complex as more sequencing data has become available. Here, Maiden and colleagues propose a gene-by-gene approach of analysing whole-genome data; this approach is based on their experience with multilocus sequence typing (MLST) and reflects the functional and evolutionary relationships among bacteria.

    • Martin C. J. Maiden
    • Melissa J. Jansen van Rensburg
    • Noel D. McCarthy
  • In budding yeast, growth at the neck region connecting the mother and daughter cell is prevented by a septin ring inside the cell membrane and a chitin ring in the cell wall. Cabib and Arroyo describe recent work supporting the hypothesis that the attachment of the chitin ring to β-1,3-glucan is crucial for the control of morphogenesis at the neck.

    • Enrico Cabib
    • Javier Arroyo
  • Although the gut microbiota has been linked to a wide range of diseases in humans, including type 2 diabetes and obesity, moving from correlation to causation is notoriously difficult. In this Opinion article, Liping Zhao discusses some of the correlations that have been made between the microbiota and obesity to date, and how to move towards causation using the conceptual framework of Koch's postulates.

    • Liping Zhao
  • Although great progress has been made in the field of dengue research, there are still many unanswered questions concerning the interactions between dengue virus and the human immune system. In this Opinion article, Gubler and colleagues discuss the gaps in our understanding of the molecular pathogenesis of dengue virus and call for a reassessment of the animal models used in the preclinical stages of dengue research.

    • Ashley L. St. John
    • Soman N. Abraham
    • Duane J. Gubler
  • The bacterial nucleoid was first described more than 50 years ago, but the recent application of new imaging technologies and physical analytical methods has brought fresh insights to the structure of the DNA within the nucleoid. Here, Charles Dorman discusses these insights and argues that, in addition to DNA topology and nucleoid-associated proteins, gene regulation is an important organizing principle of nucleoid architecture.

    • Charles J. Dorman
  • Perturbations in the gut microbiota can lead to a state of dysbiosis, which may involve 'blooming' of potentially harmful bacteria. Here, Hardt and colleagues propose that such bacteria blooms promote horizontal gene transfer between members of the gut ecosystem, thereby facilitating pathogen evolution.

    • Bärbel Stecher
    • Lisa Maier
    • Wolf-Dietrich Hardt
  • In this Opinon article, Cornforth and Foster argue that several of the major bacterial stress responses detect ecological competition directly through competition sensing, a physiological response that detects harm caused by other cells and that evolved, at least in part, for that purpose. In support of this argument, they show that bacteriocins and antibiotics are frequently upregulated by stress responses to nutrient limitation and cell damage but not by responses to abiotic stress.

    • Daniel M. Cornforth
    • Kevin R. Foster
  • Regulated cell death is a key process in plant and animal development, but does it occur in parasitic protozoa? Jeremy Mottram and colleagues assess the evidence of regulated cell death in these organisms and propose that protozoan cell death should be classified as either necrotic or incidental.

    • William R. Proto
    • Graham H. Coombs
    • Jeremy C. Mottram
  • It has recently emerged that environmental factors such as ambient temperature can strongly influence insect immunity and, thus, shape the outcome of host–parasite interactions. Here, Murdock, Thomas and colleagues argue that, to get more accurate insights into vector resistance, we need to incorporate temperature variation into studies.

    • Courtney C. Murdock
    • Krijn P. Paaijmans
    • Matthew B. Thomas
  • Predicting the virulence of a particular bacterial strain is a complex task that currently cannot be achieved from genome sequence data alone. In this Opinion article, Massey and colleagues present a framework for the construction of a systems biology-based tool that they think could be used to predict virulence phenotypes fromStaphylococcus aureusgenomic sequences using existing technologies.

    • Nicholas K. Priest
    • Justine K. Rudkin
    • Ruth C. Massey
  • In this Opinion article, Hajishengallis and colleagues propose that certain low-abundance microorganisms, termed 'keystone pathogens', can disrupt a normally benign commensal microbiota, leading to a microbial community structure that is associated with the development of disease.

    • George Hajishengallis
    • Richard P. Darveau
    • Michael A. Curtis
  • Recent high-throughput sequencing studies have provided a first glimpse of the microbiome associated with late-stage colorectal cancer. In this Opinion article, Tjalsma and colleagues present a driver–passenger model to account for the distinct temporal associations of particular bacteria with the diseased tissue during oncogenesis.

    • Harold Tjalsma
    • Annemarie Boleij
    • Bas E. Dutilh
  • Did the cenancestor have a phospholipid membrane? In this Opinion article, Lombard, López-García and Moreira discuss how recent top-down phylogenomic analyses have provided new information to address this question.

    • Jonathan Lombard
    • Purificación López-García
    • David Moreira
  • During their life cycle, trypanosomes must overcome conflicting demands to ensure their survival and transmission. In this Opinion article, Matthews and colleagues suggest that infection chronicity and transmissibility result from an interplay between programmes of antigenic variation and development.

    • Paula MacGregor
    • Balazs Szöőr
    • Keith R. Matthews
  • Understanding how microorganisms interact with other species in a community is a major goal for microbial ecologists. In this Opinion article, Zengler and Palsson describe how successes from systems biology efforts can be used as a road map for the emerging field of community systems (CoSy) biology.

    • Karsten Zengler
    • Bernhard O. Palsson
  • Some individuals who are infected with both HIV and an opportunistic pathogen develop immune reconstitution inflammatory syndrome (IRIS) when CD4+T cell numbers are restored. This reaction may arise from a hyper-responsiveness of innate immune cells to the newly reconstituted T cell help, and may apply to other cases of inflammatory pathology.

    • Daniel L. Barber
    • Bruno B. Andrade
    • Alan Sher
  • The CRISPR–Cas (clustered regularly interspaced short palindromic repeats–CRISPR-associated proteins) systems are immunity systems that are present in many bacteria and archaea. Here, Koonin and colleagues present a new classification of these systems and introduce a new nomenclature of the genes in the CRISPR–casloci that better reflects the relationships between the proteins.

    • Kira S. Makarova
    • Daniel H. Haft
    • Eugene V. Koonin
  • One promising application of synthetic biologies lies in the production of new drugs from secondary metabolites. In this Opinion article, Takano and colleagues describe potential strategies to spatially and temporally regulate the activity of metabolite biosynthetic modules for the design of efficient drug production systems.

    • Marnix H. Medema
    • Rainer Breitling
    • Eriko Takano
  • Many bacterial species shut down metabolism and enter a dormant state in order to survive in unfavourable conditions. Exit from dormancy in response to cell wall muropeptide signals from neighbouring cells has recently been observed forBacillus subtilisspores. In this Opinion article, Dworkin and Shah propose that this might be a more general phenomenon.

    • Jonathan Dworkin
    • Ishita M. Shah