Microbiota articles within Nature

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  • Outlook |

    Transplants of faecal matter have done wonders for the treatment of certain gastrointestinal infections. Will they ever work for inflammatory bowel disease?

    • Liam Drew

  • Outlook |

    Studies of gut bacteria are beginning to untangle how diet affects health in old age — but determining cause and effect is tricky.

    • Virginia Hughes

  • Article |

    A framework for metagenomic variation analysis to explore variation in the human microbiome is developed; the study describes SNPs, short indels and structural variants in 252 faecal metagenomes of 207 individuals from Europe and North America.

    • Siegfried Schloissnig
    • , Manimozhiyan Arumugam
    •  & Peer Bork

  • News & Views |

    An innovative method for probing the genomes of the vast community of microorganisms that inhabit the human gut provides an alternative approach to identifying risk factors for type 2 diabetes. See Letter p.55

    • Julia Oh
    •  & Julia A. Segre

  • Article |

    The authors have developed a new method, metagenome-wide association study (MGWAS), to compare the combined genetic content of the faecal microbiota of healthy people versus patients with type 2 diabetes; they identify multiple microbial species and metabolic pathways that are associated with either cohort and show that some of these may be used as biomarkers.

    • Junjie Qin
    • , Yingrui Li
    •  & Jun Wang

  • News & Views |

    Mice receiving low doses of certain antibiotics gain weight and accumulate fat. This could be because some gut bacteria survive the treatment better than others, shifting digestion towards greater energy provision. See Article p.621

    • Harry J. Flint

  • News & Views |

    Dietary lack of a single amino acid impairs intestinal immunity in mice, altering the guts microbial community and leaving it vulnerable to damage. The finding helps to explain how malnutrition favours gut inflammation. See Letter p.477

    • Ana Izcue
    •  & Fiona Powrie

  • News & Views |

    Western-style diets could be contributing to the rapid increase in inflammatory bowel disease. New research suggests that dietary fat can alter bile composition and so favour the growth of pro-inflammatory gut microbes. See Letter p.104

    • Peter J. Turnbaugh

  • Letter |

    Selective impairment of peripheral regulatory T-cell differentiation is found to result in spontaneous allergic TH2-type inflammation in the intestine and lungs, demonstrating the functional heterogeneity of regulatory T cells generated in the thymus and extrathymically in controlling immune mediated inflammation and disease.

    • Steven Z. Josefowicz
    • , Rachel E. Niec
    •  & Alexander Y. Rudensky

  • Outlook |

    Many ingredients in traditional herbal medicines cannot be absorbed by the human gut. Could our microbial inhabitants do for us what we can't do ourselves?

    • James Mitchell Crow

  • Outlook |

    Microbes are under the spotlight in efforts to unravel — and combat — allergies.

    • Cassandra Willyard

  • News & Views |

    Humans must maintain a balanced composition for the trillions of commensal microbes that inhabit their gut, but how they do this is largely unclear. It now emerges that one factor is a molecular pathway in gut epithelial cells.

    • Menno van Lookeren Campagne
    •  & Vishva M. Dixit

  • Article |

    This paper shows that gut flora can influence cardiovascular disease, by metabolizing a dietary phospholipid. Using a metabolomics approach it is found that plasma levels of three metabolites of dietary phosphatidylcholine—choline, betaine and TMAO—are associated with increased risk of cardiovascular disease in humans. The gut flora is known to have a role in TMAO formation from choline, and this paper shows that dietary choline supplementation enhances macrophage foam cell formation and lesion formation in atherosclerosis-prone mice, but not if the gut flora are depleted with antibiotics.

    • Zeneng Wang
    • , Elizabeth Klipfell
    •  & Stanley L. Hazen

  • Letter |

    This paper shows that the activity of human beta-defensin 1 is regulated by its redox status, with enhanced antibiotic killing activity under reducing conditions as they are found in the distal colon. This is believed to serve to protect the healthy intestinal epithelium against potentially harmful colonization by commensal bacteria and opportunistic fungi. In vitro evidence implicates thioredoxin as the likely reducing agent.

    • Bjoern O. Schroeder
    • , Zhihong Wu
    •  & Jan Wehkamp

  • Article |

    Salmonella enterica serotype Typhimurium causes acute gut inflammation, which promotes the growth of the pathogen through unknown mechanisms. It is now shown that the reactive oxygen species generated during inflammation react with host-derived sulphur compounds to produce tetrathionate, which the pathogen uses as a terminal electron acceptor to support its growth. The ability to use tetrathionate provides the pathogen with a competitive advantage over bacteria that lack this property.

    • Sebastian E. Winter
    • , Parameth Thiennimitr
    •  & Andreas J. Bäumler

  • Article |

    The microbial content of the human gut has been the focus of much research interest recently. Now another layer of complexity has been added: the viral content of the gut. Virus-like particles were isolated from faecal samples from four sets of identical twins and their mothers, at three time points over a one-year period. The viromes (metagenomes) of these particles were then sequenced. The results show that there is high interpersonal variation in viromes, but that intrapersonal diversity was very low over this time period.

    • Alejandro Reyes
    • , Matthew Haynes
    •  & Jeffrey I. Gordon

  • 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

  • News & Views |

    Metabolic disorders such as obesity are characterized by long-term, low-grade inflammation. Under certain conditions, the resident microorganisms of the gut might contribute to this inflammation, resulting in disease.

    • Ping Li
    •  & Gökhan S. Hotamisligil

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