Microbial communities articles within Nature

Featured

  • Outlook |

    More than half of the world’s cases of liver cancer are due to viral liver infections. Detecting and treating hepatitis B could help to reverse the global increase in fatal liver cancer.

    • Kristina Campbell

  • Article |

    A survey of species-level genes from 13,174 publicly available metagenomes shows that most species-level genes are specific to a single habitat, encode a small number of protein families and are under low positive (adaptive) pressure.

    • Luis Pedro Coelho
    • , Renato Alves
    •  & Peer Bork

  • Article |

    Bacteria in the human gut and oral microbiome encode enzymes that selectively phosphorylate the antidiabetic drug acarbose—an inhibitor of both human and bacterial α-glucosidases—resulting in its inactivation and limiting the drug's effects on the ability of the host to metabolize complex carbohydrates.

    • Jared Balaich
    • , Michael Estrella
    •  & Mohamed S. Donia

  • Outlook |

    Christina Warinner explains what the microorganisms that lived in our ancestors’ mouths reveal about human evolution and health.

    • Kristina Campbell

  • Article |

    This study systematically profiles the activity of several classes of antibiotics on gut commensal bacteria and identifies drugs that mitigate their collateral damage on commensal bacteria without compromising their efficacy against pathogens.

    • Lisa Maier
    • , Camille V. Goemans
    •  & Athanasios Typas

  • Article |

    An analysis of the interactions between 15 drugs and 25 gut bacterial strains shows that bioaccumulation of drugs within bacterial cells is another mechanism through which gut microorganisms can alter drug availability and efficacy.

    • Martina Klünemann
    • , Sergej Andrejev
    •  & Kiran R. Patil

  • Article |

    The microbiota of centenarians (aged 100 years and older) comprise gut microorganisms that are capable of generating unique secondary bile acids, including isoallolithocholic acid, a bile acid with potent antimicrobial effects against Gram-positive—but not Gram-negative—multidrug-resistant pathogens.

    • Yuko Sato
    • , Koji Atarashi
    •  & Kenya Honda

  • News & Views |

    Small molecules produced and modified by gut microorganisms can influence human physiology. An atlas of metabolic outputs of diverse gut microbes offers new ways to decipher the microbial mechanisms behind their production.

    • William F. Kindschuh
    •  & Tal Korem

  • Article |

    Acetate—a major gut microbial metabolite—increases the production of IgA in the colon, alters the capacity of the IgA pool to bind to specific microorganisms and alters the localization of these bacteria within the colon.

    • Tadashi Takeuchi
    • , Eiji Miyauchi
    •  & Hiroshi Ohno

  • Article |

    Fibre snacks that target distinct features of the microbiomes of donors with obesity transplanted into gnotobiotic mice also lead to fibre-specific changes in the microbiome and physiology when used in controlled-diet human studies.

    • Omar Delannoy-Bruno
    • , Chandani Desai
    •  & Jeffrey I. Gordon

  • News & Views |

    Appreciation is growing of how our gut microbes shape health and disease. Now, a study of ancient human faeces sheds light on how microbial populations in the gut have changed during the past 2,000 years.

    • Matthew R. Olm
    •  & Justin L. Sonnenburg

  • Research Summary |

    The first viruses to colonize the infant gut are shown to arise from bacteria, with human-cell viruses colonizing the gut later, at around four months of age. Exclusive and partial breastfeeding were associated with fewer human viruses in the gut of infants compared with formula-feeding alone.

    • Frederic D. Bushman
    •  & Guanxiang Liang

  • Article
    | Open Access

    Ancient microbiomes from palaeofaeces are more similar to non-industrialized than industrialized human gut microbiomes regardless of geography, but 39% of their de novo reconstructed genomes represent previously undescribed microbial species.

    • Marsha C. Wibowo
    • , Zhen Yang
    •  & Aleksandar D. Kostic

  • Article |

    Absolute microbial abundances delineate longitudinal dynamics of bacteria, fungi and archaea in the infant gut microbiome, uncovering drivers of microbiome development masked by relative abundances and revealing notable parallels to macroscopic ecosystem assemblies.

    • Chitong Rao
    • , Katharine Z. Coyte
    •  & Seth Rakoff-Nahoum

  • News Feature |

    Scientists are starting to work out how the gut microbiome can affect brain health. That might lead to better and easier treatments for brain diseases.

    • Cassandra Willyard

  • Outline |

    The gut is not the only part of the human body that hosts an important microbiome. The surface of the skin is home to a sprawling and complex microbial ecosystem, which interacts with the immune system and influences dermatological health.

    • Michael Eisenstein

  • Outline |

    The skin supports a diverse community of microorganisms that train and support the immune system, and fend off pathogenic threats.

    • Michael Eisenstein

  • Outlook |

    The world’s population is estimated to reach 10 billion by 2050. Providing everyone with a nutritious diet and protecting the planet requires a global response.

    • Catherine Armitage

  • Outlook |

    ‘Itch-proof’ cosmetics, keeping inflammation-causing T cells in check, and other highlights from allergy and immunology studies.

    • Elizabeth Svoboda

  • Outlook |

    Early disruptions in the composition of the gut microbiome can directly influence digestive and immune function in ways that put children at greater risk.

    • Michael Eisenstein

  • Article |

    High-phylogenetic-resolution microbiome mapping by fluorescence in situ hybridization (HiPR-FISH) enables the spatial mapping of hundreds of species of microorganisms and shows how microbial networks in the mouse gut are affected by antibiotic treatment.

    • Hao Shi
    • , Qiaojuan Shi
    •  & Iwijn De Vlaminck

  • Article |

    Influence of the gut microbiome on the human immune system is revealed by systems analysis of vast clinical data from decades of electronic health records paired with massive longitudinal microbiome sequencing.

    • Jonas Schluter
    • , Jonathan U. Peled
    •  & Joao B. Xavier

  • News & Views |

    What determines the chemical make-up of human blood? Measurement of the contributions of factors ranging from genetics to lifestyle has now identified diet and gut microbes as key predictors of blood’s molecular composition.

    • Patrick H. Bradley
    •  & Katherine S. Pollard

  • News & Views |

    When determining whether gut microbes affect human health, it is hard to distinguish between a causal and a correlative relationship. Analysis of microbial links to human traits and habits correlated with disease offers a step forward.

    • Sigal Leviatan
    •  & Eran Segal

  • Article |

    Experiments using an ecologically realistic 185-member bacterial synthetic community in the root system of Arabidopsis reveal that Variovorax bacteria can influence plant hormone levels to reverse the inhibitory effect of the community on root growth.

    • Omri M. Finkel
    • , Isai Salas-González
    •  & Jeffery L. Dangl

  • Review Article |

    This Review describes the interplay between host genetics, host immunity and the gut microbiome in the modulation of colorectal cancer, and discusses the role of specific bacterial species and metabolites alongside technological advances that will facilitate more in-depth investigation of the microbiome in disease.

    • Alina Janney
    • , Fiona Powrie
    •  & Elizabeth H. Mann

  • Article |

    A combination of gnotobiotic mouse models, transcriptomics, circuit tracing and chemogenetic manipulations identifies neuronal circuits that integrate microbial signals in the gut with regulation of the sympathetic nervous system.

    • Paul A. Muller
    • , Marc Schneeberger
    •  & Daniel Mucida

  • Technology Feature |

    Researchers are developing technologies to find and grow microbes that biologists have struggled to culture in the lab.

    • Amber Dance

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