Microbial communities articles within Nature Communications

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  • Article
    | Open Access

    Diet is a major factor determining the composition of gut microbiota in mammals, while host evolutionary history seems to play an unclear role. Here, Sanderset al. show that baleen whales, which prey on animals, harbour a unique gut microbiome with similarities to those of terrestrial herbivores.

    • Jon G. Sanders
    • , Annabel C. Beichman
    •  & Peter R. Girguis

  • Article |

    There is growing evidence that the intestinal microbiota can affect host behaviour. Here, De Palma et al. show in mice that early-life stress (maternal separation) induces changes in host physiology that alter the gut microbiota, which then triggers anxiety-like and depression-like behaviour later in life.

    • G. De Palma
    • , P. Blennerhassett
    •  & P. Bercik

  • Article
    | Open Access

    The coffee berry borer, the main insect pest of coffee, feeds and lives on the caffeine-rich beans despite caffeine’s toxic effects. Here Ceja-Navarro et al. show that certain microbes, including Pseudomonasspecies, mediate caffeine detoxification in the insect’s gut.

    • Javier A. Ceja-Navarro
    • , Fernando E. Vega
    •  & Eoin L. Brodie

  • Article
    | Open Access

    Mucosal sialoglycans contribute to host–microbe interactions at mucosal surfaces and impact bacterial colonization of the digestive system. Here the authors identify and characterize an intramolecular trans-sialidase produced by the gut bacterium R. gnavusATCC 29149 that may contribute to adaptation to the mucosal environment.

    • Louise E. Tailford
    • , C. David Owen
    •  & Nathalie Juge

  • Article
    | Open Access

    The potential recovery of the human gut microbiota after an antibiotic treatment, and its effects on our health, are poorly understood. Here, the authors use a mouse model mimicking paediatric antibiotic use to shed new light into these processes.

    • Yael R. Nobel
    • , Laura M. Cox
    •  & Martin J. Blaser

  • Article
    | Open Access

    The human gut microbiota helps us to degrade complex dietary carbohydrates such as xylan and, in turn, the carbohydrate breakdown products control the structure of the microbiota. Here the authors characterize the xylan-degrading apparatus of a key member of the gut microbiota, Bacteroides ovatus.

    • Artur Rogowski
    • , Jonathon A. Briggs
    •  & David N. Bolam

  • Article
    | Open Access

    The gut microbiomes of urban-industrialized societies differ from those of traditional rural societies and hunter-gatherers. Here the authors perform a comparative analysis of available and new gut microbiome data to provide fresh insight into these differences.

    • Alexandra J. Obregon-Tito
    • , Raul Y. Tito
    •  & Cecil M. Lewis

  • Article |

    The gut microbiota is involved in the development of colorectal cancer. Here, the authors analyse the faecal microbiomes of healthy subjects and of patients with colorectal cancer or benign adenoma, revealing microbial genes, strains and functions enriched in each group.

    • Qiang Feng
    • , Suisha Liang
    •  & Jun Wang

  • Article |

    Some bacteria can form nanotubes to transfer proteins and plasmids between neighbouring cells. Here, the authors show that nanotubes can also mediate the exchange of cytoplasmic amino acids between cells of the same or different bacterial species.

    • Samay Pande
    • , Shraddha Shitut
    •  & Christian Kost

  • Article
    | Open Access

    Certain soil fungi form specialized cellular structures or 'traps' to feed on nematodes, which in turn eat bacteria. Here, the authors show that urea released from bacteria induces trap formation in the fungi and this promotes nematode elimination.

    • Xin Wang
    • , Guo-Hong Li
    •  & Ke-Qin Zhang

  • Article |

    Leaf-cutting ants cultivate fungi that have evolved inflated hyphal cells, known as gongylidia, on which the ants feed. Here, the authors perform genetic and transcriptomic analyses of gongylidia, supporting that these fungal structures provide the ants with essential amino acids and plant-degrading enzymes.

    • Henrik H. De Fine Licht
    • , Jacobus J. Boomsma
    •  & Anders Tunlid

  • Article
    | Open Access

    Within microbial communities, microorganisms adopt different lifestyle strategies to use the available resources. Here, the authors use an integrated ‘multi-omic’ approach to study niche breadth (generalist versus specialist lifestyles) in oleaginous microbial assemblages from an anoxic wastewater treatment tank.

    • Emilie E. L. Muller
    • , Nicolás Pinel
    •  & Paul Wilmes

  • Article |

    Vultures are scavengers with a high tolerance to bacterial toxins in decaying meat. Here, Roggenbuck et al.show that the vulture’s gut microbiome displays unique features and is dominated by Clostridia and Fusobacteria, two bacterial groups commonly associated with infectious disease in other animals.

    • Michael Roggenbuck
    • , Ida Bærholm Schnell
    •  & Lars H Hansen

  • Article |

    The effect of a host's genetic variation on the structure of its microbial community is poorly understood. Here, Horton et al. reveal associations between genetic variants in the plant model species Arabidopsis thalianaand the composition of the leaves' microbial communities.

    • Matthew W. Horton
    • , Natacha Bodenhausen
    •  & Joy Bergelson

  • Article |

    Assembly of the root surface microbiome varies according to soil type and plant species. Here, Ofek-Lalzar et al.use metagenome and metatranscriptome analysis to reveal distinct functional signatures of microbial communities associated with two diverse plant hosts.

    • Maya Ofek-Lalzar
    • , Noa Sela
    •  & Dror Minz

  • Article
    | Open Access

    Intestinal microbes can have important effects on our health. Here, the authors analyse the gut microbiota composition in 1,000 western adults and find that certain bacteria are either abundant or nearly absent, and that these alternative states are associated with ageing and overweight.

    • Leo Lahti
    • , Jarkko Salojärvi
    •  & Willem M. de Vos

  • Article |

    Microbial community function depends on metabolic interdependencies between individual species, some of which include electron transfer. Nagarajan et al. use genomic, transcriptomic and modelling approaches to describe the mechanisms supporting the syntrophic relationship between Geobacter metallireducens and Geobacter sulfurreducens.

    • Harish Nagarajan
    • , Mallory Embree
    •  & Karsten Zengler

  • Article |

    Persistence of cooperation requires limited spread of defectors, but it is unclear how evolutionary history affects the spread of these individuals. Here, Jousset et al.show that microbial cooperators can only inhibit defectors that are closely related to them, suggesting that evolutionary history can predict the stability of cooperation.

    • Alexandre Jousset
    • , Nico Eisenhauer
    •  & Stefan Scheu

  • Article
    | Open Access

    The structure of the human gut microbiota has been shown to vary between populations. Tyakht et al.analyse the gut microbiota assembly from Russian individuals living in urban and rural areas, and compare these with previously studied populations.

    • Alexander V. Tyakht
    • , Elena S. Kostryukova
    •  & Vadim M. Govorun

  • Article |

    The social amoeba Dictyostelium discoideum displays a primitive form of agriculture with some clones carrying bacteria to seed out food crops. Brock et al. now demonstrate that these farmers also carry non-food bacteria that harm competing non-farmer amoeba clones, protecting the crop from exploitation.

    • Debra A. Brock
    • , Silven Read
    •  & Joan E. Strassmann

  • Article
    | Open Access

    Turnover of sediment organic matter contributes to global carbon cycling, yet the microorganisms involved are largely unknown. Castelleet al.reveal that an aquifer sediment core hosts a ‘zoo’ of organisms, including representatives of a previously undescribed phylum (Zixibacteria).

    • Cindy J. Castelle
    • , Laura A. Hug
    •  & Jillian F. Banfield

  • Article
    | Open Access

    Bacterial infections can influence disease outcome in influenza infection; however, the mechanisms mediating these complex interactions remain unclear. Wang et al. reveal how infection with a component of the airway microbiota enhances survival during influenza infection via induction of anti-inflammatory macrophages.

    • Jian Wang
    • , Fengqi Li
    •  & Zhigang Tian

  • Article
    | Open Access

    Deep subsurface formations are potential sites for carbon capture and storage but how subsurface microbial communities may respond to this is not clear. Here, Mayumi et al. construct microcosms and show that increasing CO2partial pressure via carbon capture and storage more than doubles the rate of methanogenesis.

    • Daisuke Mayumi
    • , Jan Dolfing
    •  & Yoichi Kamagata

  • Article |

    Microbes living in human skin are known to influence the immune system; however, the deeper layers in which immune cells reside were thought to be largely impervious to bacteria. Nakatsuji et al.show that the skin microbiome extends into the dermis, enabling contact with cells below the basement membrane.

    • Teruaki Nakatsuji
    • , Hsin-I. Chiang
    •  & Richard L. Gallo

  • Article |

    Biological invasion varies under different environmental stressors. Here, using a fully controlled system of bacterial communities, De Roy et al. find that community evenness affects the level of invasion, and that the community’s response depends on specific environmental conditions as well as the community evenness.

    • Karen De Roy
    • , Massimo Marzorati
    •  & Nico Boon

  • Article |

    Natural populations are complex systems where interactions can lead to chaotic dynamics. This study tests how cyclic and chaotic microbial predator–prey communities synchronize, showing different phase-locking responses for cyclic and chaotic systems.

    • Lutz Becks
    •  & Hartmut Arndt

  • Article
    | Open Access

    The gut microbiota has emerged as an environmental factor that can influence the development of obesity and diabetes. Here, Karlsson et al. report compositional and functional alterations of the gut metagenome in patients with symptomatic atherosclerosis.

    • Fredrik H. Karlsson
    • , Frida Fåk
    •  & Jens Nielsen

  • Article |

    Species coexistence can be explained by the competition–colonization trade-off theory. Here, Livingston et al. illustrate this theory in a metacommunity experiment using two bacterial strains, finding a negative correlation between diversity and productivity when scaled to full metacommunities.

    • George Livingston
    • , Miguel Matias
    •  & Nicolas Mouquet

  • Article |

    Large-scale sequencing techniques have helped to understand the genetic diversity of little-known microbial communities. These authors demonstrate a cheaper alternative to direct sequencing—the construction of virtual metagenomes using gel electrophoresis and related genome sequences.

    • Shujiro Okuda
    • , Yuki Tsuchiya
    •  & Hisao Morisaki

  • Article |

    Humans tend to adopt one of a limited number of different bacterial community structures in the gut, known as enterotypes. Moeller et al.now show that these microbial fingerprints are conserved in chimpanzees, and that individuals can switch between enterotypes over periods of several years.

    • Andrew H. Moeller
    • , Patrick H. Degnan
    •  & Howard Ochman

  • Article
    | Open Access

    Vascular plants with root systems evolved in the mid-Palaeozoic with symbiotic fungi. Fieldet al. show that in contrast to non-vascular plants lacking roots, the efficiency of plant–fungal symbiosis increased for vascular plants with root systems as carbon dioxide levels declined in the mid-Palaeozoic.

    • Katie J. Field
    • , Duncan D. Cameron
    •  & David J. Beerling

  • Article |

    Genome-scale metabolic models for bacterial species allow a systematic study of inter-species interactions. Here, competitive and cooperative potential is predicted between 6,903 pairs of species, to explore the role of these interactions in shaping coexistence patterns in natural communities.

    • Shiri Freilich
    • , Raphy Zarecki
    •  & Eytan Ruppin

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