Microbial communities articles within Nature

Featured

  • Article |

    Mutations in genes involved in immune signalling and vesicle trafficking cause defects in the leaf microbiome of Arabidopsis thaliana that result in damage to leaf tissues, suggesting mechanisms by which terrestrial plants control the level and diversity of endophytic phyllosphere microbiota.

    • Tao Chen
    • , Kinya Nomura
    •  & Sheng Yang He

  • Article |

    Analyses of microbial communities that live 10–750 m below the seafloor at Atlantis Bank, Indian Ocean, provide insights into how these microorganisms survive by coupling energy sources to organic and inorganic carbon resources.

    • Jiangtao Li
    • , Paraskevi Mara
    •  & Virginia P. Edgcomb

  • Article |

    Microbial nucleic acids are detected in samples of tissues and blood from more than 10,000 patients with cancer, and machine learning is used to show that these can be used to discriminate between and among different types of cancer, suggesting a new microbiome-based diagnostic approach.

    • Gregory D. Poore
    • , Evguenia Kopylova
    •  & Rob Knight

  • Article |

    Metabolomics data from germ-free and specific-pathogen-free mice reveal effects of the microbiome on host chemistry, identifying conjugations of bile acids that are also enriched in patients with inflammatory bowel disease or cystic fibrosis.

    • Robert A. Quinn
    • , Alexey V. Melnik
    •  & Pieter C. Dorrestein

  • Article
    | Open Access

    Genomic analyses of major clades of huge phages sampled from across Earth’s ecosystems show that they have diverse genetic inventories, including a variety of CRISPR–Cas systems and translation-relevant genes.

    • Basem Al-Shayeb
    • , Rohan Sachdeva
    •  & Jillian F. Banfield

  • Outlook |

    Microorganisms live in the human digestive system and affect our health — scientists are trying to work out how.

    • Herb Brody

  • Outlook |

    Modified bacteria and carefully formulated microbial communities could form the basis of new living treatments.

    • Claire Ainsworth

  • Outlook |

    Despite evidence of the gut microbiome’s role in human health, researchers are still working out what shapes the community of microbes.

    • Michael Eisenstein

  • Outlook |

    Targeting the microbiome could hold the key to combating a range of malignant diseases.

    • Elie Dolgin

  • Technology Feature |

    Thought leaders predict the tech developments that could have a big impact in the coming year.

    • Esther Landhuis

  • Article |

    Neonatal mice are protected against infection with the enteric pathogen enterotoxigenic Escherichia coli by maternally derived natural antibodies as well as by maternal commensal microbiota that induce antibodies that recognize antigens expressed by  Enterobacteriaceae.

    • Wen Zheng
    • , Wenjing Zhao
    •  & Dennis L. Kasper

  • Article |

    An interbacterial defence strategy, involving clusters of immunity genes against toxins released by the type VI secretion system of the same or different species, is widespread among Bacteroides species, and transfer of these gene clusters confers resistance to toxins in vitro and in the mammalian gut.

    • Benjamin D. Ross
    • , Adrian J. Verster
    •  & Joseph D. Mougous

  • News & Views |

    The impact of fungi on human health is under-studied and underappreciated. One genus of fungus, Malassezia, has now been linked to the progression of pancreatic cancer.

    • Ivy M. Dambuza
    •  & Gordon D. Brown

  • Technology Feature |

    The tools of chemical biology, genomics and data mining can yield insights into the metabolites of the microbiome.

    • Esther Landhuis

  • News |

    UK study provides the best evidence yet that the way infants are born can alter their microbiomes — but the health effects are unclear.

    • Ewen Callaway

  • News & Views |

    Analysis of hundreds of placentas provides convincing evidence that this organ does not harbour microorganisms that can enter the fetal gut — a key finding for research into how the human microbiota is established.

    • Nicola Segata

  • Article |

    The human placenta does not have a microbiota, suggesting that bacterial infection of the placenta is not a common cause of adverse pregnancy outcome, but group B Streptococcus is found in approximately 5% of placental samples.

    • Marcus C. de Goffau
    • , Susanne Lager
    •  & Gordon C. S. Smith

  • News & Views |

    The Human Microbiome Project put the health-associated microbes found in humans on centre stage. The project’s second phase shows how microbial disturbance in disease is linked to host processes.

    • Verónica Lloréns-Rico
    •  & Jeroen Raes

  • Perspective
    | Open Access

    Over ten years, the Human Microbiome Project has provided resources for studying the microbiome and its relationship to disease; this Perspective summarizes the key achievements and findings of the project and its relationship to the broader field.

    • Lita M. Proctor
    • , Heather H. Creasy
    •  & Curtis Huttenhower

  • Article
    | Open Access

    The Inflammatory Bowel Disease Multi’omics Database includes longitudinal data encompassing a multitude of analyses of stool, blood and biopsies of more than 100 individuals, and provides a comprehensive description of host and microbial activities in inflammatory bowel diseases.

    • Jason Lloyd-Price
    • , Cesar Arze
    •  & Curtis Huttenhower

  • Article |

    The authors systematically characterize structural variation in the genomes of gut microbiota and show that they are associated with bacterial fitness and with host risk factors, and that examining genes coded in these regions facilitates investigation of mechanisms that may underlie these associations.

    • David Zeevi
    • , Tal Korem
    •  & Eran Segal

  • Article
    | Open Access

    The known species repertoire of the collective human gut microbiota is substantially expanded with the discovery of 1,952 uncultured bacterial species that greatly improve classification of understudied African and South American samples.

    • Alexandre Almeida
    • , Alex L. Mitchell
    •  & Robert D. Finn

  • Article |

    A consortium of 11 bacterial strains from the healthy human gut microbiota can strongly induce interferon-γ-producing CD8 T cells in the intestine, and enhance both resistance to bacterial infection and the therapeutic efficacy of immune checkpoint inhibitors.

    • Takeshi Tanoue
    • , Satoru Morita
    •  & Kenya Honda

  • Outlook |

    Each person’s skin carries a unique population of microbes that might help to protect skin from infection, or increase its vulnerability.

    • Emily Sohn

  • Outline |

    Existing treatments bring only temporary relief to people with ulcerative colitis, a common form of inflammatory bowel disease. Insights into the immunobiology of the condition are driving the development of therapies that could lead to prolonged periods of remission.

    • Michael Eisenstein

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