Microbiology articles within Nature Communications

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  • Article
    | Open Access

    Aminoglycoside antibiotics target the ribosome but their limited selectivity for the bacterial ribosome can cause side effects in humans. Here, the authors synthesize 4′-O-ether or 4′,6′-O-acetal modifications and show that these compounds possess increased selectivity against bacterial ribosomes.

    • Déborah Perez-Fernandez
    • , Dmitri Shcherbakov
    •  & Erik C. Böttger

  • Article |

    An outbreak of diarrhoea and haemolytic uraemic syndrome in Germany in 2011 was caused by a Shiga toxin-producing enteroaggregative E. coli, which carried the aggregative adherence plasmid pAA. Here, the authors show that autotransporters, but not pAA, are required for intestinal colonization in an infant rabbit model.

    • Diana Munera
    • , Jennifer M. Ritchie
    •  & Matthew K. Waldor

  • Article |

    Antibiotics alter the intestinal microbiota and facilitate colonization of pathogens such as Clostridium difficile. Here, the authors show that antibiotic-induced shifts in the mouse gut microbiome are correlated with changes in levels of certain metabolites that C. difficilecan use for germination and growth.

    • Casey M. Theriot
    • , Mark J. Koenigsknecht
    •  & Vincent B. Young

  • Article |

    Synthetic gene circuits can be programmed in living cells to perform diverse cellular functions. Here, the authors program a genetic circuit that performs a Pavlovian-like learning and recall function in E. coli, and demonstrate the dynamic nature of this conditioning process at a population level.

    • Haoqian Zhang
    • , Min Lin
    •  & Qi Ouyang

  • Article
    | Open Access

    Horizontal gene transfers are known to play an important role in prokaryote evolution but their impact and prevalence in eukaryotes is less clear. Here, the authors sequence the genomes of cheese making fungi P. roqueforti and P. camemberti, and provide evidence for recent horizontal transfers of a large genomic region.

    • Kevin Cheeseman
    • , Jeanne Ropars
    •  & Yves Brygoo

  • Article |

    New classes of antitubercular drugs are in constant demand as drug-resistant strains of Mycobacterium tuberculosis become more prevalent. Here, the authors characterize a class of drugs that are active against various M. tuberculosisstrains, including those resistant to currently used antituberculars.

    • Shichun Lun
    • , Haidan Guo
    •  & William R. Bishai

  • Article |

    Many Gram-negative bacterial pathogens use the type III secretion system to translocate effectors into the host cell. Here, the authors characterize a bacterial phosphoinositide-binding domain, which is conserved in diverse type III effectors of both plant and animal pathogens and couples membrane localization with refolding.

    • Dor Salomon
    • , Yirui Guo
    •  & Kim Orth

  • Article |

    Bacterial persistence is one of the major causes of failure of antibiotic treatment, and several toxin–antitoxin modules have been linked to the persistent phenotype. Here, the authors show that HipA toxin causes growth arrest and persistence via phosphorylation of the glutamyl-tRNA-synthetase.

    • Ilana Kaspy
    • , Eitan Rotem
    •  & Gad Glaser

  • Article |

    Bacterial chemoreceptors regulate the kinase CheA via ligand-induced conformational changes. Using long molecular dynamics simulations, Ortega et al.show that these changes are associated with flipping of the stacked aromatic rings of highly conserved phenylalanine residues within the kinase-activating domain.

    • Davi R. Ortega
    • , Chen Yang
    •  & Igor B. Zhulin

  • Article
    | Open Access

    Some clinical isolates of influenza A(H7N9) virus encode a mutation within neuraminidase that could confer resistance to the only class of drugs active against H7N9. Here, the authors show that this mutation does not affect viral replication and pathogenicity while mediating resistance to antivirals in vivo.

    • Rong Hai
    • , Mirco Schmolke
    •  & Nicole M. Bouvier

  • Article |

    Efficient and pathogen-specific antifungal agents are required to mitigate drug resistance problems. Here the authors present a series of cationic small molecules, which are easy to isolate and characterize, and which can self-assemble to give polymer-like antifungal activity and specificity.

    • Kazuki Fukushima
    • , Shaoqiong Liu
    •  & James L. Hedrick

  • Article |

    The mitochondrial calcium uniporter supports oxidative phosphorylation in mammals; however, it is also present in blood-stage trypanosomes, which lack a functional respiratory chain. Huang et al. show that the mitochondrial calcium uniporter is essential for blood-stage survival and metabolism in Trypanosoma brucei.

    • Guozhong Huang
    • , Anibal E. Vercesi
    •  & Roberto Docampo

  • Article
    | Open Access

    Helicobacter pylori survives in the acidic environment of the stomach by taking up urea and converting it to ammonia and carbon dioxide, which buffer the bacterial periplasm. Using molecular dynamics simulations, McNulty et al. provide insight into the mechanism of urea uptake through the H. pyloriurea transporter.

    • Reginald McNulty
    • , Jakob P. Ulmschneider
    •  & Martin B. Ulmschneider

  • Article |

    Methane is a promising renewable carbon source for chemical synthesis, yet methane bio-gas is currently underutilised as a feedstock. Here the authors examine the metabolic processes of methanotrophic bacteria to assess their use for conversion of methane to value-added chemical products.

    • M. G. Kalyuzhnaya
    • , S. Yang
    •  & M. E. Lidstrom

  • Article
    | Open Access

    Plasmodium falciparum reticulocyte-binding protein homologue 1 (PfRH1) and erythrocyte-binding-like protein EBA175 are important for parasite invasion of host cells. Here, Gao et al.show that PfRH1 activates calcium signalling, which induces release of EBA175 and allows junction formation between host cell and parasite.

    • Xiaohong Gao
    • , Karthigayan Gunalan
    •  & Peter R. Preiser

  • 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 |

    Toxin–antitoxin systems have been implicated in the pathogenicity of Mycobacterium tuberculosis. Here, the authors study the function of the M. tuberculosistoxin VapC20 and show that it can impair protein translation and inhibit bacterial growth by cleaving the Sarcin–Ricin loop of 23S rRNA

    • Kristoffer S. Winther
    • , Ditlev E. Brodersen
    •  & Kenn Gerdes

  • Article |

    Influenza virus can enter host cells through endocytosis, but the molecular pathways involved in this process are not fully understood. Here, the authors dissect these pathways and identify Ca2+as a key regulator of influenza A virus entry via both clathrin-mediated and clathrin-independent endocytosis.

    • Yoichiro Fujioka
    • , Masumi Tsuda
    •  & Yusuke Ohba

  • Article |

    Mutations in the haemagglutinin of H5N1 avian influenza viruses confer transmissibility in ferrets. Here, Wilker et al. show that while within host variability is high, transmitted virus diversity is low suggesting a genetic bottleneck acts during transmission, driven by selection on haemagglutinin genes.

    • Peter R. Wilker
    • , Jorge M. Dinis
    •  & Thomas C. Friedrich

  • 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 |

    The locus of enterocyte effacement is a pathogenicity island essential for virulence of some Escherichia colipathogenic serotypes. Here, the authors solve the structure of a regulatory complex that optimizes regulation of this locus during the infection process.

    • Abhilash Padavannil
    • , Chacko Jobichen
    •  & J. Sivaraman

  • Article
    | Open Access

    Viruses contribute to the pathogenesis of certain cancers. Using massively parallel sequencing data from The Cancer Genome Atlas to analyse viral expression in 19 tumour types, Tang et al. both confirm and reject previously described viral associations and present new information on viral integration and host interaction.

    • Ka-Wei Tang
    • , Babak Alaei-Mahabadi
    •  & Erik Larsson

  • Article
    | Open Access

    During the initiation of bacterial DNA replication, loader proteins transfer the hexameric helicase ring onto replication origin DNA. Liu et al.report the crystal structure of a 570-kDa prepriming complex and suggest that the release of loader proteins is associated with the transition of the helicase ring to a spiral configuration.

    • Bin Liu
    • , William K. Eliason
    •  & Thomas A. Steitz

  • Article |

    Bacterial cell division requires the coordination of chromosome replication with cell growth and division but how these processes are coordinated in mycobacteria is largely unexplored. Santi et al. use single-cell technologies to describe the cell cycle dynamics of Mycobacterium smegmatisand outline important differences in comparison with other bacterial species.

    • Isabella Santi
    • , Neeraj Dhar
    •  & John D. McKinney

  • 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

    Mouse models of influenza infection that permit monitoring of infection in living animals are scarce. Here Pan et al. describe an engineered influenza virus expressing luciferase, which enables real-time in vivovisualization of viral infection and assessment of antiviral drugs.

    • Weiqi Pan
    • , Zhenyuan Dong
    •  & Ling Chen

  • 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

    Horizontal gene transfer of mobile genetic elements contributes to bacterial evolution and emergence of new pathogens. Here the authors demonstrate that the highly diverse structure of wall teichoic acid polymers governs horizontal gene transfer among Gram-positive pathogens, even across long phylogenetic distances.

    • Volker Winstel
    • , Chunguang Liang
    •  & Guoqing Xia

  • Article |

    Viral vectors can be used both to map and manipulate neural circuits in vivo; however, their use is limited by weak expression levels, especially when expression of more than one protein is required. Here, the authors overcome this limitation using deletion-mutant rabies viruses.

    • Ian R. Wickersham
    • , Heather A. Sullivan
    •  & H. Sebastian Seung

  • Article |

    Sequencing whole microbial genomes has become standard practice and methods to examine their phylogenetic relationships need to match the increasing demand. Segata et al. present a new computational pipeline that allows fast and accurate taxonomic assignment of microbial species.

    • Nicola Segata
    • , Daniela Börnigen
    •  & Curtis Huttenhower

  • Article |

    Actin normally polymerizes into filaments in a cooperative manner, with nucleation and elongation phases. Skillman et al. show that actin from the protozoan parasite Toxoplasma gondiipolymerizes in an isodesmic manner, without any evidence of nucleation, resulting in filaments that are very short and unstable.

    • Kristen M. Skillman
    • , Christopher I. Ma
    •  & L. David Sibley

  • Article |

    The potential evolutionary advantage associated with genome segmentation in multipartite viruses is not well established. Here Sicard et al. demonstrate that genome segmentation can allow a differential regulation of the copy number of each gene in a multipartite plant nanovirus during host infection.

    • Anne Sicard
    • , Michel Yvon
    •  & Stéphane Blanc

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