Microbiology articles within Nature

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  • 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

  • Letter |

    Much of the mammalian genome is derived from retroelements, a significant proportion of which are endogenous retroviruses (ERVs). ERVs are transcriptionally silenced during early embryogenesis by histone and DNA methylation, but the initiators of this process are largely unknown. Here, deletion of KAP1 is shown to lead to a marked upregulation of a range of ERVs in mouse embryonic stem cells and in early embryos.

    • Helen M. Rowe
    • , Johan Jakobsson
    •  & Didier Trono

  • Article |

    Although Archaea encode proteasomes highly related to those of eukaryotes, archaeal ubiquitin-like proteins are less conserved and not known to function in protein conjugation, complicating our understanding of the origins of ubiquitination. Two small archaeal modifier proteins, SAMP1 and SAMP2, structurally similar to ubiquitin, are now reported to form protein conjugates in the archaeon Haloferax volcanii.

    • Matthew A. Humbard
    • , Hugo V. Miranda
    •  & Julie A. Maupin-Furlow

  • News & Views |

    A survey of mammalian genomes has unexpectedly unearthed DNA derived from bornaviruses, leading to speculation about the role of these viruses in causing mutations with evolutionary and medical consequences.

    • Cédric Feschotte

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