Microbiology articles within Nature Communications

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  • Article |

    Many viruses take advantage of microtubule-dependent motor proteins to move through the cell. Malikov et al. show that HIV-1 recruits the kinesin-1 adaptor FEZ1, and that the opposing activities of kinesin-1 and dynein motors are both required for the transport of HIV-1 capsids towards the nucleus.

    • Viacheslav Malikov
    • , Eveline Santos da Silva
    •  & Mojgan H. Naghavi

  • Article |

    The 2009 H1N1 influenza pandemic exposed major gaps in our knowledge of the spatial ecology and evolution of swine influenza A viruses. Here Nelson et al. perform an extensive phylogenetic analysis of these viruses and show that the global trade of live swine strongly predicts their spatial dissemination.

    • Martha I. Nelson
    • , Cécile Viboud
    •  & Philippe Lemey

  • Article
    | Open Access

    Populations of bacterial pathogens can be diverse within colonized individuals. Here, the authors sequence the genomes of methicillin-resistant Staphylococcus aureusisolated from staff and animal patients at a veterinary hospital and show considerable within-host diversity that can rise and fall over time.

    • Gavin K. Paterson
    • , Ewan M. Harrison
    •  & Mark A. Holmes

  • Article
    | Open Access

    The gut microbiomes of urban-industrialized societies differ from those of traditional rural societies and hunter-gatherers. Here the authors perform a comparative analysis of available and new gut microbiome data to provide fresh insight into these differences.

    • Alexandra J. Obregon-Tito
    • , Raul Y. Tito
    •  & Cecil M. Lewis

  • Article |

    Dimethylsulphide (DMS) is a volatile compound produced by marine microbes through degradation of dimethylsulphoniopropionate (DMSP). Here, Carrión et al.describe an alternative pathway for DMS production from methanethiol that is widespread among bacteria, especially from soil environments.

    • O. Carrión
    • , A. R. J. Curson
    •  & J. D. Todd

  • Article
    | Open Access

    Diversity-generating retroelements (DGRs) are genetic elements that introduce sequence variation within target genes in bacteria and their viruses. Here, Paul et al. report the discovery of DGRs in an archaeal virus and in two archaea from marine and terrestrial subsurface environments, respectively.

    • Blair G. Paul
    • , Sarah C. Bagby
    •  & David L. Valentine

  • Article
    | Open Access

    Primary plastids descend from an endosymbiosis involving cyanobacteria, an ancient eukaryotic host and, possibly, a chlamydial pathogen. Here, Domman and colleagues use sophisticated phylogenetic methods to show that Chlamydiaedid not play a role in establishing the primary plastid endosymbiosis.

    • Daryl Domman
    • , Matthias Horn
    •  & Tom A. Williams

  • Article |

    The gut microbiota is involved in the development of colorectal cancer. Here, the authors analyse the faecal microbiomes of healthy subjects and of patients with colorectal cancer or benign adenoma, revealing microbial genes, strains and functions enriched in each group.

    • Qiang Feng
    • , Suisha Liang
    •  & Jun Wang

  • Article
    | Open Access

    Serial femtosecond crystallography and the use of X-ray free-electron lasers (XFEL) promise to revolutionize structural biology. Here, the authors describe refinements that reduce the redundancy required to obtain quality XFEL data and report a 1.75-Å structure—not obtainable by synchrotron radiation—using less than 6,000 crystals.

    • Helen M. Ginn
    • , Marc Messerschmidt
    •  & David I. Stuart

  • Article
    | Open Access

    Ferrets are the main animal model used for research on influenza transmission. Here, the authors investigate the dynamics of infection and transmission in ferrets using a replication-competent influenza reporter virus and real-time bioluminescence imaging.

    • Erik A. Karlsson
    • , Victoria A. Meliopoulos
    •  & Stacey Schultz-Cherry

  • Article |

    Bacterial secretion systems deliver proteins to the extracellular milieu or directly into the cytoplasm of other cells. Here Souza et al. show that a type IV secretion system (T4SS) allows Xanthomonas citrito kill other Gram-negative bacterial species in a contact-dependent manner.

    • Diorge P. Souza
    • , Gabriel U. Oka
    •  & Chuck S. Farah

  • Article
    | Open Access

    Retroviruses such as HIV integrate into the host genome as an essential step prior to their replication. Here Lelek et al. identify nuclear pore complex proteins that are essential for HIV nuclear import and productive integration, and show that the intranuclear protein Tpr influences integration into transcriptionally active chromatin.

    • Mickaël Lelek
    • , Nicoletta Casartelli
    •  & Francesca Di Nunzio

  • Article
    | Open Access

    The molecular basis for the high toxicity of cadmium is unclear. Here, Begg et al. use the bacterium Streptococcus pneumoniaeas a model system, and show that cadmium uptake increases sensitivity to oxidative stress by reducing intracellular concentrations of manganese and zinc through different mechanisms.

    • Stephanie L. Begg
    • , Bart A. Eijkelkamp
    •  & Christopher A. McDevitt

  • Article |

    Little is known about certain bacterial phyla because of our current inability to grow them in the lab. Here, Luef et al.combine metagenomics and ultrastuctural analyses to show that some of these bacteria have a very small cell size, tightly packed DNA, few ribosomes and diverse pili-like structures.

    • Birgit Luef
    • , Kyle R. Frischkorn
    •  & Jillian F. Banfield

  • Article |

    Recombination-based tools for generating targeted mutations in Mycobacterium tuberculosislack efficiency. Here the authors present a CRISPR interference approach that is able to efficiently repress the expression of target genes in mycobacteria, in a rapid and cost-effective manner.

    • Eira Choudhary
    • , Preeti Thakur
    •  & Nisheeth Agarwal

  • Article |

    Some bacteria can form nanotubes to transfer proteins and plasmids between neighbouring cells. Here, the authors show that nanotubes can also mediate the exchange of cytoplasmic amino acids between cells of the same or different bacterial species.

    • Samay Pande
    • , Shraddha Shitut
    •  & Christian Kost

  • Article
    | Open Access

    Soil-dwelling ectomycorrhizal fungi trigger remodelling of root architecture as part of a mutualistic symbiotic relationship with host plants. Here, Ditengou et al. identify fungal-derived sesquiterpenes as volatile signals capable of stimulating lateral root production in Arabidopsis and Populus.

    • Franck A. Ditengou
    • , Anna Müller
    •  & Andrea Polle

  • Article |

    Malaria parasites generate metabolic energy through anaerobic glycolysis, yielding lactate and protons that are then secreted out of the parasite cell by an unknown transporter. Here, the authors identify and characterize a lactate/proton transporter that may be carrying out such function in Plasmodium.

    • Binghua Wu
    • , Janis Rambow
    •  & Eric Beitz

  • Article
    | Open Access

    Neuraminidase inhibitors offer a line of defence against flu infections, but resistance can occur even in the absence of prior exposure. Here Wan et al. describe the mode of action of CD6, a monoclonal antibody that protects against a common influenza strain, as a new therapeutic intervention model.

    • Hongquan Wan
    • , Hua Yang
    •  & Maryna C. Eichelberger

  • Article |

    In yeast, the transcription factor Upc2 regulates genes involved in ergosterol biosynthesis, but how its activity is regulated is unknown. Here Yang et al. present the structure of the Upc2 C-terminal domain and discover that it functions as a sensor of the ergosterol level, regulating the transcriptional activity and cellular localization of Upc2.

    • Huiseon Yang
    • , Junsen Tong
    •  & Young Jun Im

  • Article
    | Open Access

    Pore-forming toxins are expressed as monomers and assemble into multimeric pores. Here, Benke et al. follow the kinetics of pore formation for the bacterial toxin ClyA with single-molecule methods and show that pore formation progresses through the assembly of oligomeric intermediates, rather than by the addition of monomers to a nascent pore.

    • Stephan Benke
    • , Daniel Roderer
    •  & Benjamin Schuler

  • Article |

    Broadly neutralizing antibodies targeting the Env protein of HIV-1 are being used to guide vaccine design. Here, Guttman et al.show that highly potent antibodies bind to the ‘closed’, prefusion form of Env, whereas less potent antibodies bind only to the ‘open’ form (typical of receptor-bound virus).

    • Miklos Guttman
    • , Albert Cupo
    •  & Kelly K. Lee

  • Article |

    Phagocytic activity of macrophages is reduced in HIV-1-infected patients, but the reason for this is unknown. Here, the authors report that secreted Tat protein inhibits phagocytosis by binding to the phospholipid PI(4,5)P2and impairing the recruitment of small GTPase Cdc42 to the phagocytic cup.

    • Solène Debaisieux
    • , Simon Lachambre
    •  & Bruno Beaumelle

  • Article
    | Open Access

    Toxocara canis is a zoonotic parasite of major worldwide socioeconomic importance. Here, the authors sequence the genome and transcriptome of T. canis, and highlight potential mechanisms involved in development and host–parasite interactions that could support the pursuit of new drug interventions.

    • Xing-Quan Zhu
    • , Pasi K. Korhonen
    •  & Robin B. Gasser

  • Article |

    Herpes simplex viruses cause a variety of diseases, from cold sores to encephalitis. Here, Martinez-Martin et al. show that the viral protein gG binds to cell surface glycosaminoglycans and induces chemokine receptor clustering, enhancing chemokine function and thus modulating the immune response.

    • Nadia Martinez-Martin
    • , Abel Viejo-Borbolla
    •  & Antonio Alcamí

  • Article
    | Open Access

    Herpes simplex virus type-1 (HSV-1) is a widespread human pathogen, the structure of which is not yet fully characterized. Here, the authors apply dSTORM super-resolution microscopy in combination with advanced data analysis tools to locate the position of four key protein layers in HSV-1 with unprecedented precision.

    • Romain F. Laine
    • , Anna Albecka
    •  & Clemens F. Kaminski

  • Article |

    In fission yeast, the telomerase RNA (TER) is produced through inhibition of the second step in splicing, resulting in spliceosomal cleavage. Here, the authors show that the inhibition of splicing is a conserved principle in fungal TER maturation that uses distinct molecular mechanisms across species.

    • Xiaodong Qi
    • , Dustin P. Rand
    •  & Julian J. -L. Chen

  • Article
    | Open Access

    Understanding the epidemiology of malaria transmission between humans and mosquitoes is crucial for successful disease control. Analysing data from an 18-year malaria control programme, Churcher et al. show that decreased parasite prevalence in humans can be found concurrently with an increase in transmission efficiency.

    • Thomas S. Churcher
    • , Jean-François Trape
    •  & Anna Cohuet

  • Article
    | Open Access

    The continual evolution of pathogens makes infectious disease control very challenging. Here the authors examine how host population structure influences disease evolution, and show that heterogeneous contact networks lower the fixation probability of newly arising pathogen strains.

    • Gabriel E. Leventhal
    • , Alison L. Hill
    •  & Sebastian Bonhoeffer

  • Article
    | Open Access

    Bacteria secrete signalling molecules (AHLs) to coordinate actions such as biofilm formation and the release of public goods, in a process called quorum sensing. Here, the authors show that AHLs are stochastically produced and control asocial (self-directed) traits in young biofilms of P. putida.

    • Gerardo Cárcamo-Oyarce
    • , Putthapoom Lumjiaktase
    •  & Leo Eberl

  • Article |

    Avian strains of the influenza virus sometimes infect human hosts with severe consequences. Here, Wang et al.report that the H10N8 avian influenza virus, for which two lethal human infections have been reported, possesses restricted affinity towards the human receptor and suggest a structural basis for H10N8’s limited virulence.

    • Min Wang
    • , Wei Zhang
    •  & George F. Gao

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