Microbial communities articles within Nature

Featured

  • News & Views |

    The epithelial cells that line the intestine have been found to sense tight attachment of bacteria, and to respond by producing proteins that shape the effector functions of the immune system's TH17 cells.

    • Shai Bel
    •  & Lora V. Hooper

  • Article |

    The anaerobic oxidation of methane in marine sediments is performed by consortia of methane-oxidizing archaea and sulfate-reducing bacteria; an examination of the role of interspecies spatial positioning on single cell activity reveals that interspecies electron transfer may overcome the requirement for close spatial proximity, a proposition supported by large multi-haem cytochromes in ANME-2 genomes as well as redox-active electron microscopy staining.

    • Shawn E. McGlynn
    • , Grayson L. Chadwick
    •  & Victoria J. Orphan

  • Letter |

    The ammonia-oxidizing archaeon Nitrososphaera gargensis can utilize cyanate as the only source of energy for growth due to the presence of a cyanase enzyme, and cyanase-encoding nitrite-oxidizing bacteria can work together with cyanase-negative ammonia oxidizers to collectively grow on cyanate via reciprocal feeding; cyanases are widespread in the environment according to metagenomic data sets, pointing to the potential importance of cyanate in the nitrogen cycle.

    • Marton Palatinszky
    • , Craig Herbold
    •  & Michael Wagner

  • Outlook |

    By analysing bacteria that live in the digestive tracts of bees, researchers hope to learn about the role of microbes in insect health.

    • Alla Katsnelson

  • Outlook |

    Gut bacteria have an important but elusive role in the formation of colorectal cancer.

    • Sarah DeWeerdt

  • Innovations In |

    Evidence that genes shape the microbiome may point to new treatments for common diseases

    • Ruth E. Ley

  • Innovations In |

    Synthetic biology may lead to the creation of smart microbes that can detect and treat disease

    • Justin L. Sonnenburg

  • Innovations In |

    The microbiome may yield a new class of psychobiotics for the treatment of anxiety, depression and other mood disorders

    • Charles Schmidt

  • Innovations In |

    Amid the trillions of microbes that live in the intestines, scientists have found a few species that seem to play a key role in keeping us healthy

    • Moises Velasquez-Manoff

  • Article |

    Previous work has shown that human skin is home to a rich and varied microbiota; here a metagenomic approach for samples from physiologically diverse body sites illuminates that the skin microbiota, including bacterial, fungal and viral members, is shaped by the local biogeography and yet marked by strong individuality.

    • Julia Oh
    • , Allyson L. Byrd
    •  & Julia A. Segre

  • Letter |

    Recovery from cholera is characterized by a pattern of accumulation of bacterial taxa that shows similarities to the pattern of maturation of the gut microbiota in healthy children, raising the possibility that some of these taxa may be useful for ‘repair’ of the gut microbiota in individuals whose gut communities have been ‘wounded’ through a variety of insults.

    • Ansel Hsiao
    • , A. M. Shamsir Ahmed
    •  & Jeffrey I. Gordon

  • Article |

    Non-caloric artificial sweeteners (NAS), widely used food additives considered to be safe and beneficial alternatives to sugars, are shown here to lead to the development of glucose intolerance through compositional and functional changes in the gut microbiota of mice, and the deleterious metabolic effects are transferred to germ-free mice by faecal transplant; NAS-induced dysbiosis and glucose intolerance are also demonstrated in healthy human subjects.

    • Jotham Suez
    • , Tal Korem
    •  & Eran Elinav

  • Letter |

    Bacterial species whose representation defines healthy postnatal assembly of the gut microbiota in Bangladeshi children during their first 2 years are identified, and a model is constructed to compare healthy children to those with severe acute malnutrition (SAM); results show that SAM is associated with microbiota immaturity that is only partially ameliorated by existing nutritional interventions.

    • Sathish Subramanian
    • , Sayeeda Huq
    •  & Jeffrey I. Gordon

  • Outlook |

    • Tony Scully

  • Letter |

    The microbiome composition of 300 individuals sampled over 12–18 months was partitioned into microbial community types, which could be associated with the type found at other body sites, as well as with whether individuals were breastfed as an infant, their gender and their level of education.

    • Tao Ding
    •  & Patrick D. Schloss

  • Letter |

    Consuming diets rich in plant versus animal products changes the microbes found in the human gut within days, with important implications for our health and evolution.

    • Lawrence A. David
    • , Corinne F. Maurice
    •  & Peter J. Turnbaugh

  • Letter |

    This work identifies a role for intestinal epithelial cell (IEC)-intrinsic expression of histone deacetylase 3 in regulating commensal-bacteria-dependent gene expression and intestinal homeostasis; IEC-specific HDAC3 deficiency gives rise to Paneth cell abnormalities, impaired intestinal barrier function, and increased DSS-induced intestinal inflammation in commensal-bacteria-containing, but not germ-free, mice.

    • Theresa Alenghat
    • , Lisa C. Osborne
    •  & David Artis

  • Letter |

    Antibiotic treatment disturbs the commensal microbiota and is often followed by infection with enteric pathogens such as Salmonella typhimurium and Clostridium difficile; pathogen expansion is fuelled by antibiotic-driven accumulation of commensal-liberated host mucosal carbohydrates.

    • Katharine M. Ng
    • , Jessica A. Ferreyra
    •  & Justin L. Sonnenburg

  • Outlook |

    Our skin is home to thousands of species of bacteria — and when these microscopic societies are disrupted, skin infections can arise.

    • Bijal Trivedi

  • 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 |

    The nuclear genomes of two of nature's most complex cells have been sequenced. The data will help to determine the evolutionary path from symbioses between species to a multi-compartmental unicellular organism. See Article p.59

    • Sven B. Gould

  • Letter |

    Novel pathogenic infectious retroviruses, generated by recombination between replication-defective endogenous retroviruses in the absence of a functional antibody response, are identified; these recombinant retroviruses establish infection of mouse colonies and ultimately cause cancer.

    • George R. Young
    • , Urszula Eksmond
    •  & George Kassiotis

  • 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 |

    Treatment of young mice with low levels of antibiotics results in increases in adiposity and causes both a change in the composition of the intestinal microbial community and an alteration in the activity of microbial metabolic pathways, leading to increased short-chain fatty acid production.

    • Ilseung Cho
    • , Shingo Yamanishi
    •  & Martin J. Blaser

  • Letter |

    Roots of land plants are populated by a specific microbiota capable of modulating plant growth and development; here large-scale sequencing analysis shows that the bacterial community inhabiting Arabidopsis roots is influenced by soil type and plant genotype, and that plant cell-wall features serve as colonization cue for a subcommunity of the root microbiota.

    • Davide Bulgarelli
    • , Matthias Rott
    •  & Paul Schulze-Lefert

  • Letter |

    Sequencing of the Arabidopsis thaliana root microbiome shows that its composition is strongly influenced by location, inside or outside the root, and by soil type.

    • Derek S. Lundberg
    • , Sarah L. Lebeis
    •  & Jeffery L. Dangl

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