Microbiology articles within Nature Communications

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  • 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

  • Article |

    The sulfation of protein tyrosine residues is a common post-translational modification in eukaryotes. Here, Han et al.show that the protein RaxST, produced by a plant bacterium, has tyrosine sulfotransferase activity, demonstrating for the first time tyrosine sulfation in prokaryotes.

    • Sang-Wook Han
    • , Sang-Won Lee
    •  & Pamela C. Ronald

  • Article |

    Microsporidia are widespread human parasites, but limited genome annotation has hampered efforts to understand their biology. Peyretailladeet al. use sequence motifs upstream of start codons to annotate or re-annotate microsporidian genomes and find new genes potentially involved in interactions with the host.

    • Eric Peyretaillade
    • , Nicolas Parisot
    •  & Pierre Peyret

  • Article |

    It has been proposed that phylogenetic diversity can be used as a proxy to estimate functional diversity and to predict ecosystem functioning. Here, the rapid evolutionary response of marine bacteria is used to study the positive effects of evolutionary history and species diversity on ecosystem productivity.

    • Dominique Gravel
    • , Thomas Bell
    •  & Nicolas Mouquet

  • Article
    | Open Access

    The ability of oleaginous fungi to produce lipids for biofuels remains untapped, in part due to a lack of genetic information required to engineer industrial strains. Zhuet al. present the genome of R. toruloides, and identify transcriptomic and proteomic changes associated with lipid production.

    • Zhiwei Zhu
    • , Sufang Zhang
    •  & Zongbao K. Zhao

  • Article
    | Open Access

    Sodium-gated ion channels open and close in response to the flow of ions. Here, McCusker et al.report the open structure of a sodium-gated ion channel pore from a bacterial homologue, and show, by comparison with the closed structure, that the movement of a C-terminal helix is sufficient to open the channel.

    • Emily C. McCusker
    • , Claire Bagnéris
    •  & B.A. Wallace

  • Article |

    Methane is an important anthropogenic greenhouse gas and is thought to be produced by industrial processes and prokaryotic methanogenic Archaea. In this study, the saprotrophic fungi,Basidiomycetes, is shown to produce methane in the absence of methanogenic Archaea.

    • Katharina Lenhart
    • , Michael Bunge
    •  & Frank Keppler

  • Article |

    Mechanosensitive channels are required to sense cell swelling in response to osmotic shock. Nakayamaet al.report that Msy1 and Msy2 are the fission yeast homologues of the bacterial mechanosensitive channel MscS, and are required for regulating intracellular calcium in response to cell swelling.

    • Yoshitaka Nakayama
    • , Kenjiro Yoshimura
    •  & Hidetoshi Iida

  • Article |

    The bacterial channel protein MscL opens in response to mechanical forces and could be exploited for vesicular-based drug delivery. Doerneret al. show that functional MscL can be expressed in mammalian cells and facilitate the controlled cellular uptake of relatively large, membrane-impermeable bioactive molecules.

    • Julia F. Doerner
    • , Sebastien Febvay
    •  & David E. Clapham

  • Article
    | Open Access

    The clustered regularly interspaced short palindromic repeats (CRISPR) system protects prokaryotes from foreign DNA. Here, bacteriophage DNA containing mutations that can circumvent this response are shown to be incorporated into the CRISPR locus, allowing bacteria to remember previous infections in an adaptive manner.

    • Kirill A. Datsenko
    • , Ksenia Pougach
    •  & Ekaterina Semenova

  • Article
    | Open Access

    Ganoderma lucidumis a macrofungus in traditional Chinese medicine known to produce different bioactive compounds. In this study, the genome ofG. lucidumis sequenced, making this organism a potential model system for future studies of secondary metabolic pathways and their regulation in medicinal fungi.

    • Shilin Chen
    • , Jiang Xu
    •  & Chao Sun

  • Article
    | Open Access

    Vascular plants with root systems evolved in the mid-Palaeozoic with symbiotic fungi. Fieldet al. show that in contrast to non-vascular plants lacking roots, the efficiency of plant–fungal symbiosis increased for vascular plants with root systems as carbon dioxide levels declined in the mid-Palaeozoic.

    • Katie J. Field
    • , Duncan D. Cameron
    •  & David J. Beerling

  • Article |

    Lamivudine treatment of hepatitis B is associated with drug-resistance mutations in the virus’ DNA polymerase. In this study, 11 patients with drug resistance are investigated and the primary mutation in the DNA polymerase shown to be essential but not sufficient for establishing drug resistance.

    • Hong Thai
    • , David S. Campo
    •  & Yury Khudyakov

  • Article |

    Microbial metabolism is usually considered to be phototrophic or chemotrophic. By showing that light-induced photoelectrons from metal oxide and metal sulfides can stimulate the growth of chemoautotrophic and heterotrophic bacteria, this study indicates that light may be involved in non-phototrophic microbial activity.

    • Anhuai Lu
    • , Yan Li
    •  & Hailiang Dong

  • Article |

    Graphene is characterized by unique physical properties that offer substantial promise, most notably for electronic applications. Mannooret al. present a wireless graphene-based sensor for detecting bacteria on a range of biological tissues.

    • Manu S. Mannoor
    • , Hu Tao
    •  & Michael C. McAlpine

  • Article |

    The treatment ofMycobacterium tuberculosis with drugs such as isoniazid often results in drug resistance, but the mechanisms leading to the resistance are not fully known. In this study, an M. tuberculosisstrain lacking the sigma factor I is shown to be resistant to isoniazid.

    • Jong-Hee Lee
    • , Nicole C. Ammerman
    •  & William R. Bishai

  • Article |

    It is unclear whether pathogens can advantageously exploit the host's immune response. UsingCandida albicans, the authors show that host IL-17A binds to the fungi and induces nutrient starvation and autophagy, which eventually leads to enhanced biofilm formation and resistance to the hosts' defence.

    • Teresa Zelante
    • , Rossana G. Iannitti
    •  & Luigina Romani

  • Article
    | Open Access

    GALgenes enhance their own transcription via the transcription factor Gal4p, and the number of Galp4 sites in a promoter is expected to strengthen the feedback. In this study, Hsuet al. show that instead the feedback loops are activated by genes that have frequent bursts of expression and fast RNA decay kinetics.

    • Chieh Hsu
    • , Simone Scherrer
    •  & Attila Becskei

  • Article
    | Open Access

    Myeloid cells are important in the response to severe infection by invasiveStreptococcusGroup A. In this study, a distinct population of immature myeloid cells with ring shaped nuclei that produce interferon-γ are shown to be important for protection of mice against the early stages of invasive infection.

    • Takayuki Matsumura
    • , Manabu Ato
    •  & Kazuo Kobayashi

  • Article
    | Open Access

    Epitopes presented by MHC-II molecules bind to T-cell receptors to activate CD4+ T cells. In this study, changes in the carboxy-terminal region of the influenza hemagglutinin epitope HA305-320alters the strength of binding to the T-cell receptor, thus modulating T-cell receptor usage and activation.

    • David K. Cole
    • , Kathleen Gallagher
    •  & Andrew Godkin

  • Article
    | Open Access

    The influenza A virus genome consists of eight RNA segments, which permits genetic reassortment and contributes to the emergence of novel strains with pandemic potential. Here, electron tomography is used to study the three-dimensional structure of ribonucleoprotein complexes within progeny virions.

    • Takeshi Noda
    • , Yukihiko Sugita
    •  & Yoshihiro Kawaoka

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