Microbiology articles within Nature

Featured

  • Letter |

    Almost 200 million people worldwide are chronically infected with hepatitis C virus. Current treatments are poorly tolerated and not wholly effective, so new drugs are needed. Here, a potent new inhibitor of hepatitis C virus is described. This inhibitor targets the viral protein NS5A, and shows potential as part of a therapeutic regimen based on a combination of viral inhibitors.

    • Min Gao
    • , Richard E. Nettles
    •  & Lawrence G. Hamann

  • Letter |

    It has been thought that ocean temperatures during the early Palaeoarchaean era (around 3.5 billion years ago) were 55–85 °C. But a recent study indicated that the temperatures might be no higher than 40 °C. Here, studies are reported of the oxygen isotope compositions of phosphates in sediments from the 3.2–3.5-billion-year-old Barberton Greenstone Belt in South Africa. The findings indicate a well-developed phosphorus cycle and evolved biological activity in an Archaean ocean with temperatures of 26–35 °C.

    • Ruth E. Blake
    • , Sae Jung Chang
    •  & Aivo Lepland

  • Letter |

    One of the roles of the human gut microbiota is to break down nutrients using bacterial enzymes that are lacking from the human genome. It is now shown that the gut microbiota of Japanese, but not American, individuals contains porphyranases, enzymes that digest sulphated polysaccharides which are present in the marine environment only. These findings indicate that diet can select for gene content of the human microbiota.

    • Jan-Hendrik Hehemann
    • , Gaëlle Correc
    •  & Gurvan Michel

  • News & Views |

    Without the trillions of microbes that inhabit our gut, we can't fully benefit from the components of our diet. But cultural differences in diet may, in part, dictate what food our gut microbiota can digest.

    • Justin L. Sonnenburg

  • Letter |

    'Horizontal gene transfer' refers to the passage of genetic material between non-mating species. Transposable elements (transposons) may be especially prone to horizontal gene transfer, but the mechanisms by which they can spread across diverged species have been elusive. Here it is shown that transposons can spread by hitchhiking in the genomes of parasites. The amount of DNA that can be transferred in this way underscores the impact of horizontal gene transfer on genome evolution.

    • Clément Gilbert
    • , Sarah Schaack
    •  & Cédric Feschotte

  • News & Views |

    The addition of a fatty acid to certain proteins is vital for the survival of protozoa that cause sleeping sickness and of their mammalian hosts. Compounds that target this process in the protozoa are now reported.

    • George A. M. Cross

  • Letter
    | Open Access

    The genome of the black truffle - one of the most popular truffles on the market - has been sequenced. This is the first genome of a symbiotic ascomycete to be analysed. Comparison with the genome of another ectomycorrhizal symbiotic fungus indicates that a genetic predisposition to symbiosis evolved differently in ascomycetes and basidiomycetes. The study also offers insight into fungal sex and fruiting.

    • Francis Martin
    • , Annegret Kohler
    •  & Patrick Wincker

  • Letter |

    Thermophilic bacteria and archaea use carbon dioxide or carbon monoxide as a starting material for making the organic substances used in cellular molecules. A central enzyme in this pathway has now been discovered, namely fructose 1,6-bisphosphate aldolase/phosphatase. This enzyme might represent the ancestral gluconeogenic enzyme.

    • Rafael F. Say
    •  & Georg Fuchs

  • Article |

    In certain microbes, the anaerobic oxidation of methane can be linked to the reduction of nitrates and nitrites. Here it is shown that this occurs through the intermediate production of oxygen. This brings the number of known biological pathways for oxygen production to four, with implications for our understanding of life on the early Earth.

    • Katharina F. Ettwig
    • , Margaret K. Butler
    •  & Marc Strous

  • News & Views |

    Microorganisms that grow by oxidizing methane come in two basic types, aerobic and anaerobic. Now we have something in between that generates its own supply of molecular oxygen by metabolizing nitric oxide.

    • Ronald S. Oremland

  • News |

    Atomically thin carbon sheets offer bacteria a protective shell in electron microscopes.

    • Geoff Brumfiel

  • Article
    | Open Access

    Fungi from the genus Fusarium are important pathogens of animals and crop plants. Some have a wide host range, whereas others are more specific in the organisms they infect. Here, clues are provided as to how differences in specificity come about. The genomes of two Fusarium fungi with differing host ranges have been sequenced, and compared with the genome of a third species. Experiments show that transferring two whole chromosomes turns a non-pathogenic Fusarium strain into a pathogenic one.

    • Li-Jun Ma
    • , H. Charlotte van der Does
    •  & Martijn Rep

  • Opinion |

    Translational-research programmes supported by flexible, long-term, large-scale grants are needed to turn advances in basic science into successful vaccines to halt the AIDS epidemic, says Wayne C. Koff.

    • Wayne C. Koff

  • News & Views |

    Every machine is made of parts. But, as the new structure of the HIV integrase enzyme in complex with viral DNA shows, one could not have predicted from the individual parts just how this machine works.

    • Robert Craigie

  • Article
    | Open Access

    Deep metagenomic sequencing and characterization of the human gut microbiome from healthy and obese individuals, as well as those suffering from inflammatory bowel disease, provide the first insights into this gene set and how much of it is shared among individuals. The minimal gut metagenome as well as the minimal gut bacterial genome is also described.

    • Junjie Qin
    • , Ruiqiang Li
    •  & Jun Wang

  • News & Views |

    Redox reactions in widely spatially separated layers of marine sediments are coupled to each other. This suggests that bacteria mediate the flow of electrons between the layers — an idea that would previously have been dismissed.

    • Kenneth H. Nealson

  • News |

    Nanowires growing from bacteria might link up distant chemical reactions in sediments.

    • Katharine Sanderson

  • Letter |

    The Red Queen hypothesis predicts that coevolution should increase the rate of evolution at the molecular level. Here, genome sequencing in an experimental phage–bacteria system is used to show that this is true, but the effect is concentrated on specific loci, and also that coevolution drives greater diversification of phage populations.

    • Steve Paterson
    • , Tom Vogwill
    •  & Michael A. Brockhurst

  • Letter |

    UCYN–A is a recently discovered nitrogen-fixing cyanobacterium with unusual metabolic features. The complete genome of this uncultivated organism is now presented, revealing a photofermentative metabolism and dependency on other organisms for essential compounds.

    • H. James Tripp
    • , Shellie R. Bench
    •  & Jonathan P. Zehr

  • Letter |

    Endogenous retroviruses (ERVs) are widely dispersed in mammalian genomes, and are silenced in somatic cells by DNA methylation. Here, an ERV silencing pathway independent of DNA methylation is shown to operate in embryonic stem cells. The pathway involves the histone H3K9 methyltransferase ESET and might be important for ERV silencing during the stages in embryogenesis when DNA methylation is reprogrammed.

    • Toshiyuki Matsui
    • , Danny Leung
    •  & Yoichi Shinkai

  • Letter |

    The increasing cost of energy and concerns about the environment have emphasized the need to find new sources of fuel, with the microbial production of high-energy fuels a promising approach. Here, Escherichia coli is engineered to produce more complex biofuels — fatty esters (biodiesel), fatty alcohols and waxes — directly from simple sugars. Some cells are further engineered to express hemicellulases, a step towards producing these compounds directly from hemicellulose.

    • Eric J. Steen
    • , Yisheng Kang
    •  & Jay D. Keasling

  • News & Views |

    By synchronizing clocks, humans make more efficient use of their time and orchestrate their activities in different places. Bacteria have now been engineered that similarly coordinate their molecular timepieces.

    • Martin Fussenegger

  • Letter |

    High mutation rates in the influenza A virus facilitate the generation of viral escape mutants, rendering vaccines and drugs potentially ineffective, but targeting host cell determinants could prevent viral escape. Here, 287 human host cell genes influencing influenza A virus replication are found using a genome-wide RNA interference screen. An independent assay is then used to investigate overlap between genes necessary for different viral strains.

    • Alexander Karlas
    • , Nikolaus Machuy
    •  & Thomas F. Meyer

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