Microbiology articles within Nature Communications

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  • Article |

    With paleovirology it is possible to identify ancient endogenous viral elements within eukaryotic genomes. Here Suh and colleagues report a genomic record of hepatitis endogenizations through bird’s evolution; they find a complete hepatitis genome sequence, the first discovery of a Mesozoic paleovirus genome.

    • Alexander Suh
    • , Jürgen Brosius
    •  & Jan Ole Kriegs

  • Article |

    The identification of hosts of blood-sucking insects is important for studying ecological factors that affect pathogen distribution. Önder et al. report a proteomics-based methodology for the analysis of blood remnants in ticks that identifies the host species from which the tick has fed up to 6 months earlier.

    • Özlem Önder
    • , Wenguang Shao
    •  & Dustin Brisson

  • Article
    | Open Access

    The coffee ring effect is commonly observed in drying droplets containing suspended matter leading to a deposition at the droplet edge. Sempels et al. show that self-generated biosurfactants in living bacterial systems reverse the coffee ring effect and result in a homogeneous deposition.

    • Wouter Sempels
    • , Raf De Dier
    •  & Jan Vermant

  • Article
    | Open Access

    Cyanobacterial symbionts of marine diatoms can localize intracellularly or externally to their host partners. Here Hilton et al. describe the genomes of two diazotroph cyanobacterial symbionts of diatoms and show that the location of the symbiont affects expression of nitrogen assimilation genes.

    • Jason A. Hilton
    • , Rachel A. Foster
    •  & Tracy A. Villareal

  • Article |

    Detecting and phenotyping Mycobacterium tuberculosis, especially in resource-limited settings, is important for global tuberculosis control. Here Liong et al. report a point-of-care diagnostic platform based on magnetic barcoding and nuclear magnetic resonance for the detection of mycobacterial nucleic acids.

    • Monty Liong
    • , Anh N. Hoang
    •  & Ralph Weissleder

  • Article |

    Light-driven proton-pumping rhodopsins are widely distributed in microorganisms and convert sunlight energy into proton gradients. Inoue et al. report the discovery of a light-driven sodium ion pump from marine bacteria.

    • Keiichi Inoue
    • , Hikaru Ono
    •  & Hideki Kandori

  • Article |

    The number of human infections caused by the primate malaria parasite P. knowlesi is increasing. Lim et al. demonstrate that host specificity is due to the preference of the parasite for young blood cells, and that the parasite can adapt to proliferate in human blood containing a range of differently aged cells.

    • Caeul Lim
    • , Elsa Hansen
    •  & Manoj T. Duraisingh

  • Article |

    The hepatitis C virus RNA genome is translated via an internal ribosome entry site. Pérard et al. present an atomic model of this site, and using molecular dynamics simulations, identify conformational flexibility that may underlie its function during translation initiation.

    • Julien Pérard
    • , Cédric Leyrat
    •  & Marc Jamin

  • Article |

    Bacterial type III secretion systems (T3SS) improve the delivery of vaccine antigens and antigen-specific immune responses but require the use of live vaccines. Carleton et al. report the assembly of a functional T3SS in replication-incompetent bacterial minicells that can deliver vaccine antigens in vitro and in vivo.

    • Heather A. Carleton
    • , María Lara-Tejero
    •  & Jorge E. Galán

  • Article |

    Shigella triggers an increase in intracellular calcium during invasion of host cells. Here the authors show that increased actin polymerization at the invasion site slows the diffusion of signalling mediators, thus sustaining localized calcium influx at invasion sites.

    • Guy Tran Van Nhieu
    • , Bing Kai Liu
    •  & Laurent Combettes

  • Article
    | Open Access

    The factors that modulate growth rate of the human malaria parasite Plasmodium falciparum remain poorly understood. Here Scherf and collaborators demonstrate that the Plasmodiumsirtuin PfSir2a regulates the transcription of ribosomal DNA, thereby modulating parasite proliferation rate and virulence.

    • Liliana Mancio-Silva
    • , Jose Juan Lopez-Rubio
    •  & Artur Scherf

  • Article |

    The recognition of viruses by synthetic materials is historically difficult. Here, a templating procedure using silica nanoparticles coated with organosilanes is used to form virus-imprinted particles, possessing both shape and chemical imprints, capable of virus recognition at picomolar concentrations.

    • Alessandro Cumbo
    • , Bernard Lorber
    •  & Patrick Shahgaldian

  • Article
    | Open Access

    Bacterial cell wall peptidoglycan is essential for viability and shape determination. Using high-resolution microscopy, Foster and colleagues elucidate the peptidoglycan architecture and insertion pattern in Escherichia coliand other Gram-negative bacteria, and propose a new model for cell wall elongation.

    • Robert D. Turner
    • , Alexander F. Hurd
    •  & Simon J. Foster

  • Article |

    The bacterial tetracycline resistance protein Tet(O) binds to the ribosome, preventing tetracycline from inhibiting translation. Using cryo-electron microscopic reconstruction, the authors present an atomic model of Tet(O) bound to the 70S ribosome, and reveal how Tet(O) promotes antibiotic resistance.

    • Wen Li
    • , Gemma C. Atkinson
    •  & Joachim Frank

  • Article |

    The bullet shape of Rhabdoviruses is thought to depend on their matrix protein, which stabilizes the nucleocapsid coil. Desfosses and colleagues show that the nucleoprotein of the vesicular stomatitis virus can fold the genome into a bullet-shaped skeleton in the absence of other viral components.

    • Ambroise Desfosses
    • , Euripedes A. Ribeiro Jr
    •  & Irina Gutsche

  • Article |

    Bacterial CRISPR–Cas systems provide adaptive immunity against phage by transcribing interfering RNA from phage DNA inserted into the bacterial genome. Using deep-sequencing, the authors detect a bias in the phage genome locations sampled, suggestive of selection.

    • David Paez-Espino
    • , Wesley Morovic
    •  & Jillian F. Banfield

  • Article |

    In microbial biogeography, little is known about processes involved in soil bacterial diversity turnover. By conducting a wide-scale investigation, this study shows that dispersal limitation and environmental selection of bacteria are not mutually exclusive, highlighting the importance of landscape diversity.

    • L. Ranjard
    • , S. Dequiedt
    •  & P. Lemanceau

  • Article |

    Microbes living in human skin are known to influence the immune system; however, the deeper layers in which immune cells reside were thought to be largely impervious to bacteria. Nakatsuji et al.show that the skin microbiome extends into the dermis, enabling contact with cells below the basement membrane.

    • Teruaki Nakatsuji
    • , Hsin-I. Chiang
    •  & Richard L. Gallo

  • Article
    | Open Access

    A variant in the IFITM3gene increases the risk of severe influenza, but homozygosity is rare in Caucasians. The authors show that the variant gene is homozygous in 25% of healthy Chinese people, and 69% of those with severe pandemic influenza, suggesting that this gene influences the epidemiology of influenza in South-East Asia.

    • Yong-Hong Zhang
    • , Yan Zhao
    •  & Tao Dong

  • Article
    | Open Access

    The rice sheath blight pathogen, Rhizoctonia solani, is an important fungal pathogen that can devastate rice and maize crops. Zheng and colleagues sequence and assemble the R. solani AG1 IA genome—the first to be sequenced from the Rhizoctoniagenus—using Illumina sequencing technology.

    • Aiping Zheng
    • , Runmao Lin
    •  & Ping Li

  • Article
    | Open Access

    During red blood cell infection, malaria parasites export hundreds of proteins that remodel the host cell surface. Cowman and colleagues identify a putative protein translocator complex spatially associated with exported proteins, revealing the cellular domains involved in protein export.

    • David T. Riglar
    • , Kelly L. Rogers
    •  & Alan F. Cowman

  • Article |

    Microbial fatty acid-derived fuels represent promising alternatives to the traditionally used fossil fuels. Koffas and colleagues report that E. colicentral metabolism can be modified to produce large quantities of fatty acids through a modular pathway engineering strategy.

    • Peng Xu
    • , Qin Gu
    •  & Mattheos A.G. Koffas

  • Article |

    Biological invasion varies under different environmental stressors. Here, using a fully controlled system of bacterial communities, De Roy et al. find that community evenness affects the level of invasion, and that the community’s response depends on specific environmental conditions as well as the community evenness.

    • Karen De Roy
    • , Massimo Marzorati
    •  & Nico Boon

  • Article
    | Open Access

    Plant pathogens encode effector proteins that trigger immunity in plants carrying appropriate resistance genes. Here Qutob et al. show non-Mendelian interactions between naturally occurring Phytophthora sojaealleles that result in transgenerational gene silencing and gain of virulence in soybean plants.

    • Dinah Qutob
    • , B. Patrick Chapman
    •  & Mark Gijzen

  • Article |

    Natural populations are complex systems where interactions can lead to chaotic dynamics. This study tests how cyclic and chaotic microbial predator–prey communities synchronize, showing different phase-locking responses for cyclic and chaotic systems.

    • Lutz Becks
    •  & Hartmut Arndt

  • Article |

    The antibiotic streptomycin increases errors in protein translation, but it is unclear how streptomycin exerts its effect on the ribosome. Demirci et al. present X-ray crystal structures that reveal conformational changes induced by streptomycin, which may inspire future efforts in antibiotics design.

    • Hasan Demirci
    • , Frank Murphy IV
    •  & Gerwald Jogl

  • Article |

    In vitro, retroviruses spread between cells via structures resembling synapses. Sewaldet al. now demonstrate that virological synapses can also be observed in living mice by intravital microscopy, validating this concept in vivo.

    • Xaver Sewald
    • , David G. Gonzalez
    •  & Walther Mothes

  • Article |

    The functioning of bacterial communities is affected by selection, but the role of predation by single or multiple predators is unclear. In a study of 465 bacterial microcosms, Saleem et al.find that multiple predation causes positive bacterial diversity effects due to increased evenness among bacterial species.

    • Muhammad Saleem
    • , Ingo Fetzer
    •  & Antonis Chatzinotas

  • Article
    | Open Access

    Selected reaction monitoring mass spectrometry (SRM-MS) can quantify dynamic changes in protein expression with high sensitivity. Karlsson et al. define optimal detection parameters for 10,412 distinct group A Streptococcus pyogenespeptides, which facilitates proteome-wide SRM-MS studies in this bacterium.

    • Christofer Karlsson
    • , Lars Malmström
    •  & Johan Malmström

  • Article
    | Open Access

    Host–pathogen relationships can be mediated by polyvalent glycan ligand–protein interactions. Here well-defined highly valent glycodendrimeric constructs are synthesized that can mimic pathogens, and can inhibit a model of infection by the Ebola virus.

    • Renato Ribeiro-Viana
    • , Macarena Sánchez-Navarro
    •  & Benjamin G. Davis

  • Article |

    The proteome of the malarial parasite Plasmodium falciparum has an overabundance of aggregation-prone asparagine repeat-containing proteins. Muralidharan et al. show that PlasmodiumHsp110 protein potently prevents aggregation of asparagine-rich proteins, thereby allowing the parasite to survive febrile episodes.

    • Vasant Muralidharan
    • , Anna Oksman
    •  & Daniel E. Goldberg

  • Article |

    RNA viruses are known to rapidly evolve new features through errors in replication and reshuffling of genomic segments. These authors report another strategy used by the measles virus to improve infectivity; the cooperation between wild-type and mutant fusion proteins in the same viral particle.

    • Yuta Shirogane
    • , Shumpei Watanabe
    •  & Yusuke Yanagi

  • Article |

    Species coexistence can be explained by the competition–colonization trade-off theory. Here, Livingston et al. illustrate this theory in a metacommunity experiment using two bacterial strains, finding a negative correlation between diversity and productivity when scaled to full metacommunities.

    • George Livingston
    • , Miguel Matias
    •  & Nicolas Mouquet

  • Article
    | Open Access

    The gut microbiota has emerged as an environmental factor that can influence the development of obesity and diabetes. Here, Karlsson et al. report compositional and functional alterations of the gut metagenome in patients with symptomatic atherosclerosis.

    • Fredrik H. Karlsson
    • , Frida Fåk
    •  & Jens Nielsen

  • Article
    | Open Access

    Malaria can persist at levels that escape detection by standard microscopy, but can be detected by PCR. Okell et al.now show that rates of submicroscopic infection can be predicted using more widely available microscopy data, and are most epidemiologically significant in areas with low malaria transmission.

    • Lucy C. Okell
    • , Teun Bousema
    •  & Chris J. Drakeley

  • Article |

    Microbes appear to play an important role in carbon sequestration. Here, the composition of microbial residues in a California grassland with elevated carbon dioxide, warming and nitrogen deposition reveals that warming and nitrogen deposition can both alter the fraction of carbon derived from microbes in soils.

    • Chao Liang
    •  & Teri C. Balser

  • Article |

    Humans tend to adopt one of a limited number of different bacterial community structures in the gut, known as enterotypes. Moeller et al.now show that these microbial fingerprints are conserved in chimpanzees, and that individuals can switch between enterotypes over periods of several years.

    • Andrew H. Moeller
    • , Patrick H. Degnan
    •  & Howard Ochman

  • Article |

    Large-scale sequencing techniques have helped to understand the genetic diversity of little-known microbial communities. These authors demonstrate a cheaper alternative to direct sequencing—the construction of virtual metagenomes using gel electrophoresis and related genome sequences.

    • Shujiro Okuda
    • , Yuki Tsuchiya
    •  & Hisao Morisaki

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