Latest Research

  • Publisher Correction |

    • Nicole C. Howard
    • , Nancy D. Marin
    • , Mushtaq Ahmed
    • , Bruce A. Rosa
    • , John Martin
    • , Monika Bambouskova
    • , Alexey Sergushichev
    • , Ekaterina Loginicheva
    • , Natalia Kurepina
    • , Javier Rangel-Moreno
    • , Liang Chen
    • , Barry N. Kreiswirth
    • , Robyn S. Klein
    • , Joan-Miquel Balada-Llasat
    • , Jordi B. Torrelles
    • , Gaya K. Amarasinghe
    • , Makedonka Mitreva
    • , Maxim N. Artyomov
    • , Fong-Fu Hsu
    • , Barun Mathema
    •  & Shabaana A. Khader
  • Letter |

    The effects of multidrug antimicrobial combinations follow a null model in which inhibitory effects are additive and where drug dosage is orthogonal, leading to a square-root scaling of potency with the number of drugs.

    • D. Russ
    •  & R. Kishony
  • Article |

    The phage phi3T peptide SAIRGA directs the lysis–lysogeny decision by modulating conformational changes in phAimR, whereas the SPbeta peptide GMPRGA regulates the lysis–lysogeny pathway by stabilizing spAimR in the dimeric state.

    • Chao Dou
    • , Jie Xiong
    • , Yijun Gu
    • , Kun Yin
    • , Jinjing Wang
    • , Yuehong Hu
    • , Dan Zhou
    • , Xianghui Fu
    • , Shiqian Qi
    • , Xiaofeng Zhu
    • , Shaohua Yao
    • , Heng Xu
    • , Chunlai Nie
    • , Zongan Liang
    • , Shengyong Yang
    • , Yuquan Wei
    •  & Wei Cheng
  • Article |

    The cryo-EM structure of the TssKFGE baseplate wedge complex of the type VI secretion system (T6SS) from enteroaggregative Escherichia coli helps to elucidate the molecular architecture of the whole T6SS baseplate, and its assembly and mode of action.

    • Yassine Cherrak
    • , Chiara Rapisarda
    • , Riccardo Pellarin
    • , Guillaume Bouvier
    • , Benjamin Bardiaux
    • , Fabrice Allain
    • , Christian Malosse
    • , Martial Rey
    • , Julia Chamot-Rooke
    • , Eric Cascales
    • , Rémi Fronzes
    •  & Eric Durand
  • Article |

    Bacillus subtilis mutants lacking either of the biofilm extracellular matrix components, exopolysaccharide or the fibre protein TasA, can evolve compensatory mutations that act on the residual matrix component to restore biofilm formation.

    • Anna Dragoš
    • , Marivic Martin
    • , Carolina Falcón Garcia
    • , Lara Kricks
    • , Patrick Pausch
    • , Thomas Heimerl
    • , Balázs Bálint
    • , Gergely Maróti
    • , Gert Bange
    • , Daniel López
    • , Oliver Lieleg
    •  & Ákos T. Kovács
  • Article | | open

    Single-cell genome sequencing of eight uncultured fungal species provides insights into the phylogenetic placement of early-diverging lineages, highlights metabolic deficiencies and identifies gene expansions correlated with parasitism and unculturability.

    • Steven R. Ahrendt
    • , C. Alisha Quandt
    • , Doina Ciobanu
    • , Alicia Clum
    • , Asaf Salamov
    • , Bill Andreopoulos
    • , Jan-Fang Cheng
    • , Tanja Woyke
    • , Adrian Pelin
    • , Bernard Henrissat
    • , Nicole K. Reynolds
    • , Gerald L. Benny
    • , Matthew E. Smith
    • , Timothy Y. James
    •  & Igor V. Grigoriev
  • Article |

    The adaptation of APEX2-dependent proximity biotinylation for use in bacteria enables the identification of binding partners of TssA, which controls T6SS sheath assembly. This approach identifies TagA as a TssA partner that stops sheath polymerization and clamps the extended sheath to the membrane.

    • Yoann G. Santin
    • , Thierry Doan
    • , Régine Lebrun
    • , Leon Espinosa
    • , Laure Journet
    •  & Eric Cascales
  • Article |

    Using millimetre-scale replicate granules from an enhanced biological phosphorus removal reactor, the authors observe strain-level variability providing insights into the intrinsic drivers of microbial assembly at relevant spatial scales.

    • Gabriel E. Leventhal
    • , Carles Boix
    • , Urs Kuechler
    • , Tim N. Enke
    • , Elzbieta Sliwerska
    • , Christof Holliger
    •  & Otto X. Cordero
  • Letter |

    A prevalent rifampicin resistance mutation in Mycobacterium tuberculosis alters bacterial virulence lipid expression and enables bypasses of a host immune axis that is critical for the control of drug-susceptible infections.

    • Nicole C. Howard
    • , Nancy D. Marin
    • , Mushtaq Ahmed
    • , Bruce A. Rosa
    • , John Martin
    • , Monika Bambouskova
    • , Alexey Sergushichev
    • , Ekaterina Loginicheva
    • , Natalia Kurepina
    • , Javier Rangel-Moreno
    • , Liang Chen
    • , Barry N. Kreiswirth
    • , Robyn S. Klein
    • , Joan-Miquel Balada-Llasat
    • , Jordi B. Torrelles
    • , Gaya K. Amarasinghe
    • , Makedonka Mitreva
    • , Maxim N. Artyomov
    • , Fong-Fu Hsu
    • , Barun Mathema
    •  & Shabaana A. Khader
  • Letter |

    Aberrant mini viral RNAs, which are produced by erroneous RNA polymerase activity during the replication of the viral RNA genome, act as the main agonists of RIG-I during influenza virus infection.

    • Aartjan J. W. te Velthuis
    • , Joshua C. Long
    • , David L. V. Bauer
    • , Rebecca L. Y. Fan
    • , Hui-Ling Yen
    • , Jane Sharps
    • , Jurre Y. Siegers
    • , Marian J. Killip
    • , Hollie French
    • , Maria José Oliva-Martín
    • , Richard E. Randall
    • , Emmie de Wit
    • , Debby van Riel
    • , Leo L. M. Poon
    •  & Ervin Fodor
  • Letter |

    Flavivirus replication at the endoplasmic reticulum (ER) is targeted by the interferon response through blocking of the formation of virus-induced ER membrane invaginations by the interferon-stimulated gene IFI6, encoding an ER-localized integral membrane effector.

    • R. Blake Richardson
    • , Maikke B. Ohlson
    • , Jennifer L. Eitson
    • , Ashwani Kumar
    • , Matthew B. McDougal
    • , Ian N. Boys
    • , Katrina B. Mar
    • , Pamela C. De La Cruz-Rivera
    • , Connor Douglas
    • , Genevieve Konopka
    • , Chao Xing
    •  & John W. Schoggins
  • Article |

    Autophagy-deficient murine hosts are protected from infection and injury at the intestinal barrier and this is driven by a microbiota-dependent type I interferon response, indicating that autophagy is important for limiting host responses to the microbiota.

    • Patricia K. Martin
    • , Amanda Marchiando
    • , Ruliang Xu
    • , Eugene Rudensky
    • , Frank Yeung
    • , Samantha L. Schuster
    • , Elisabeth Kernbauer
    •  & Ken Cadwell
  • Article |

    Male offspring of pregnant mice infected with a low dose of Zika virus infection have increased testosterone levels, an increased number of immature neurons in apical hippocampal dendrites and are less likely to survive in utero infection than female littermates.

    • Stephanie Stanelle-Bertram
    • , Kerstin Walendy-Gnirß
    • , Thomas Speiseder
    • , Swantje Thiele
    • , Ivy Asantewaa Asante
    • , Carola Dreier
    • , Nancy Mounogou Kouassi
    • , Annette Preuß
    • , Gundula Pilnitz-Stolze
    • , Ursula Müller
    • , Stefanie Thanisch
    • , Melanie Richter
    • , Robin Scharrenberg
    • , Vanessa Kraus
    • , Ronja Dörk
    • , Lynn Schau
    • , Vanessa Herder
    • , Ingo Gerhauser
    • , Vanessa Maria Pfankuche
    • , Christopher Käufer
    • , Inken Waltl
    • , Thais Moraes
    • , Julie Sellau
    • , Stefan Hoenow
    • , Jonas Schmidt-Chanasit
    • , Stephanie Jansen
    • , Benjamin Schattling
    • , Harald Ittrich
    • , Udo Bartsch
    • , Thomas Renné
    • , Ralf Bartenschlager
    • , Petra Arck
    • , Daniel Cadar
    • , Manuel A. Friese
    • , Olli Vapalahti
    • , Hanna Lotter
    • , Sany Benites
    • , Lane Rolling
    • , Martin Gabriel
    • , Wolfgang Baumgärtner
    • , Fabio Morellini
    • , Sabine M. Hölter
    • , Oana Amarie
    • , Helmut Fuchs
    • , Martin Hrabe de Angelis
    • , Wolfgang Löscher
    • , Froylan Calderon de Anda
    •  & Gülsah Gabriel
  • Letter |

    CD153 expression by CD4 T cells is required for control of pulmonary Mycobacterium tuberculosis infection.

    • Michelle A. Sallin
    • , Keith D. Kauffman
    • , Catherine Riou
    • , Elsa Du Bruyn
    • , Taylor W. Foreman
    • , Shunsuke Sakai
    • , Stella G. Hoft
    • , Timothy G. Myers
    • , Paul J. Gardina
    • , Alan Sher
    • , Rashida Moore
    • , Temeri Wilder-Kofie
    • , Ian N. Moore
    • , Alessandro Sette
    • , Cecilia S. Lindestam Arlehamn
    • , Robert J. Wilkinson
    •  & Daniel L. Barber
  • Letter |

    The conditional overexpression of the transcription factor AP2-G in Plasmodium berghei enables the large-scale conversion of parasite populations into gametocytes, facilitating analysis of the sexual commitment stage of the parasite life cycle.

    • Robyn S. Kent
    • , Katarzyna K. Modrzynska
    • , Rachael Cameron
    • , Nisha Philip
    • , Oliver Billker
    •  & Andrew P. Waters
  • Publisher Correction |

    • Angelino T. Tromp
    • , Michiel Van Gent
    • , Pauline Abrial
    • , Amandine Martin
    • , Joris P. Jansen
    • , Carla J. C. De Haas
    • , Kok P. M. Van Kessel
    • , Bart W. Bardoel
    • , Elisabeth Kruse
    • , Emilie Bourdonnay
    • , Michael Boettcher
    • , Michael T. McManus
    • , Christopher J. Day
    • , Michael P. Jennings
    • , Gérard Lina
    • , François Vandenesch
    • , Jos A. G. Van Strijp
    • , Robert Jan Lebbink
    • , Pieter-Jan A. Haas
    • , Thomas Henry
    •  & András N. Spaan
  • Article |

    Genomic analysis uncovers global prevalence of three multidrug-resistant Staphylococcus epidermidis lineages encoding rifampicin resistance and reduced susceptibility to glycopeptide antibiotics.

    • Jean Y. H. Lee
    • , Ian R. Monk
    • , Anders Gonçalves da Silva
    • , Torsten Seemann
    • , Kyra Y. L. Chua
    • , Angela Kearns
    • , Robert Hill
    • , Neil Woodford
    • , Mette D. Bartels
    • , Birgit Strommenger
    • , Frederic Laurent
    • , Magali Dodémont
    • , Ariane Deplano
    • , Robin Patel
    • , Anders R. Larsen
    • , Tony M. Korman
    • , Timothy P. Stinear
    •  & Benjamin P. Howden
  • Article |

    A combination of cryo-EM structures and experiments using liposomes and lipid nanodiscs elucidates how the Tse6 effector is loaded into the type VI secretion system and travels across membranes to intoxicate target cells.

    • Dennis Quentin
    • , Shehryar Ahmad
    • , Premy Shanthamoorthy
    • , Joseph D. Mougous
    • , John C. Whitney
    •  & Stefan Raunser
  • Letter |

    Cryo-electron-microscopy imaging of hibernating ribosomes from Escherichia coli elucidates the molecular composition of these complexes and their mode of assembly, reveals how translation initiation is inhibited, and identifies a role for the ribosomal protein S1 in ribosome inactivation.

    • Bertrand Beckert
    • , Martin Turk
    • , Andreas Czech
    • , Otto Berninghausen
    • , Roland Beckmann
    • , Zoya Ignatova
    • , Jürgen M. Plitzko
    •  & Daniel N. Wilson
  • Brief Communication |

    Genomic characterization of a new ebolavirus, detected in free-tailed bats in Sierra Leone, whose viral glycoprotein can mediate entry into human cells.

    • Tracey Goldstein
    • , Simon J. Anthony
    • , Aiah Gbakima
    • , Brian H. Bird
    • , James Bangura
    • , Alexandre Tremeau-Bravard
    • , Manjunatha N. Belaganahalli
    • , Heather L. Wells
    • , Jasjeet K. Dhanota
    • , Eliza Liang
    • , Michael Grodus
    • , Rohit K. Jangra
    • , Veronica A. DeJesus
    • , Gorka Lasso
    • , Brett R. Smith
    • , Amara Jambai
    • , Brima O. Kamara
    • , Sorie Kamara
    • , William Bangura
    • , Corina Monagin
    • , Sagi Shapira
    • , Christine K. Johnson
    • , Karen Saylors
    • , Edward M. Rubin
    • , Kartik Chandran
    • , W. Ian Lipkin
    •  & Jonna A. K. Mazet
  • Letter |

    A combination of regulated gene expression, mutagenesis and electrophysiology experiments shows that EXP2, in addition to its role as part of the Plasmodium translocon of exported proteins (PTEX), functions as a nutrient-permeable channel in the vacuolar membrane of the parasite.

    • Matthias Garten
    • , Armiyaw S. Nasamu
    • , Jacquin C. Niles
    • , Joshua Zimmerberg
    • , Daniel E. Goldberg
    •  & Josh R. Beck
  • Review Article |

    This Review Article discusses the importance of considering known microbial processes to inform our understanding of the role of microbial communities in ecosystem processes, and a move away from approaches based solely on correlation analyses.

    • Ed K. Hall
    • , Emily S. Bernhardt
    • , Raven L. Bier
    • , Mark A. Bradford
    • , Claudia M. Boot
    • , James B. Cotner
    • , Paul A. del Giorgio
    • , Sarah E. Evans
    • , Emily B. Graham
    • , Stuart E. Jones
    • , Jay T. Lennon
    • , Kenneth J. Locey
    • , Diana Nemergut
    • , Brooke B. Osborne
    • , Jennifer D. Rocca
    • , Joshua P. Schimel
    • , Mark P. Waldrop
    •  & Matthew D. Wallenstein
  • Author Correction |

    • Patrick Munk
    • , Berith Elkær Knudsen
    • , Oksana Lukjancenko
    • , Ana Sofia Ribeiro Duarte
    • , Liese Van Gompel
    • , Roosmarijn E. C. Luiken
    • , Lidwien A. M. Smit
    • , Heike Schmitt
    • , Alejandro Dorado Garcia
    • , Rasmus Borup Hansen
    • , Thomas Nordahl Petersen
    • , Alex Bossers
    • , Etienne Ruppé
    • , Ole Lund
    • , Tine Hald
    • , Sünje Johanna Pamp
    • , Håkan Vigre
    • , Dick Heederik
    • , Jaap A. Wagenaar
    • , Dik Mevius
    • , Frank M. Aarestrup
    • , Haitske Graveland
    • , Alieda van Essen
    • , Bruno Gonzalez-Zorn
    • , Gabriel Moyano
    • , Pascal Sanders
    • , Claire Chauvin
    • , Julie David
    • , Antonio Battisti
    • , Andrea Caprioli
    • , Jeroen Dewulf
    • , Thomas Blaha
    • , Katharina Wadepohl
    • , Maximiliane Brandt
    • , Dariusz Wasyl
    • , Magdalena Skarzyńska
    • , Magdalena Zajac
    • , Hristo Daskalov
    • , Helmut W. Saatkamp
    •  & Katharina D. C. Stärk
  • Article |

    A donor strain (XPORT) that can transfer a miniature integrative and conjugative element from Bacillus subtilis (ICEBs1) enables DNA delivery into a broad range of bacterial strains isolated from human skin and gut, and soil.

    • Jennifer A. N. Brophy
    • , Alexander J. Triassi
    • , Bryn L. Adams
    • , Rebecca L. Renberg
    • , Dimitra N. Stratis-Cullum
    • , Alan D. Grossman
    •  & Christopher A. Voigt
  • Article |

    The Plasmodium falciparum protease plasmepsin V forms a complex for the translocation of PEXEL effector proteins into the endoplasmic reticulum that is distinct from the Sec61–signal peptidase complex that regulates the translocation of proteins destined for the classical secretory pathway.

    • Danushka S. Marapana
    • , Laura F. Dagley
    • , Jarrod J. Sandow
    • , Thomas Nebl
    • , Tony Triglia
    • , Michał Pasternak
    • , Benjamin K. Dickerman
    • , Brendan S. Crabb
    • , Paul R. Gilson
    • , Andrew I. Webb
    • , Justin A. Boddey
    •  & Alan F. Cowman
  • Article |

    A genome-wide association study of Mycobacterium tuberculosis clinical isolates finds mutations in prpR that alter propionate metabolism and mediate multidrug tolerance.

    • Nathan D. Hicks
    • , Jian Yang
    • , Xiaobing Zhang
    • , Bing Zhao
    • , Yonatan H. Grad
    • , Liguo Liu
    • , Xichao Ou
    • , Zhili Chang
    • , Hui Xia
    • , Yang Zhou
    • , Shengfen Wang
    • , Jie Dong
    • , Lilian Sun
    • , Yafang Zhu
    • , Yanlin Zhao
    • , Qi Jin
    •  & Sarah M. Fortune
  • Perspective |

    This Perspective argues that microbiome research needs to consider the different philosophical definitions of function to avoid confusion in the field, and uses the hologenome concept as an example.

    • Jonathan L. Klassen
  • Article |

    Different nutrient limitations slow down Escherichia coli translation via distinct mechanisms: P limitation leads to fewer ribosomes; N limitation reduces translation elongation via ribosome stalling; and C limitation is characterized by inactive ribosomes not bound to mRNA.

    • Sophia Hsin-Jung Li
    • , Zhiyuan Li
    • , Junyoung O. Park
    • , Christopher G. King
    • , Joshua D. Rabinowitz
    • , Ned S. Wingreen
    •  & Zemer Gitai
  • Article |

    Quantitative metagenomics reveals an altered bacteriophage community in a mouse model of colitis, which overlaps with that observed in humans with inflammatory bowel disease (IBD), providing a tool for interrogating phage dynamics in IBD.

    • Breck A. Duerkop
    • , Manuel Kleiner
    • , David Paez-Espino
    • , Wenhan Zhu
    • , Brian Bushnell
    • , Brian Hassell
    • , Sebastian E. Winter
    • , Nikos C. Kyrpides
    •  & Lora V. Hooper
  • Article |

    MCR-1-positive Escherichia coli carriage in humans across China is associated with anthropogenic factors, including meat consumption and aquatic food production.

    • Yingbo Shen
    • , Hongwei Zhou
    • , Jiao Xu
    • , Yongqiang Wang
    • , Qijing Zhang
    • , Timothy R. Walsh
    • , Bing Shao
    • , Congming Wu
    • , Yanyan Hu
    • , Lu Yang
    • , Zhangqi Shen
    • , Zuowei Wu
    • , Qiaoling Sun
    • , Yanran Ou
    • , Yueling Wang
    • , Shaolin Wang
    • , Yongning Wu
    • , Chang Cai
    • , Juan Li
    • , Jianzhong Shen
    • , Rong Zhang
    •  & Yang Wang
  • Article |

    Metagenomic analyses of European pig and poultry farms show differing resistome profiles and an association with country-level antibiotic use.

    • Patrick Munk
    • , Berith Elkær Knudsen
    • , Oksana Lukjancenko
    • , Ana Sofia Ribeiro Duarte
    • , Liese Van Gompel
    • , Roosmarijn E. C. Luiken
    • , Lidwien A. M. Smit
    • , Heike Schmitt
    • , Alejandro Dorado Garcia
    • , Rasmus Borup Hansen
    • , Thomas Nordahl Petersen
    • , Alex Bossers
    • , Etienne Ruppé
    • , Haitske Graveland
    • , Alieda van Essen
    • , Bruno Gonzalez-Zorn
    • , Gabriel Moyano
    • , Pascal Sanders
    • , Claire Chauvin
    • , Julie David
    • , Antonio Battisti
    • , Andrea Caprioli
    • , Jeroen Dewulf
    • , Thomas Blaha
    • , Katharina Wadepohl
    • , Maximiliane Brandt
    • , Dariusz Wasyl
    • , Magdalena Skarzyńska
    • , Magdalena Zajac
    • , Hristo Daskalov
    • , Helmut W. Saatkamp
    • , Katharina D. C. Stärk
    • , Ole Lund
    • , Tine Hald
    • , Sünje Johanna Pamp
    • , Håkan Vigre
    • , Dick Heederik
    • , Jaap A. Wagenaar
    • , Dik Mevius
    •  & Frank M. Aarestrup
  • Article |

    The type VI secretion system of Serratia marcescens can deliver effector proteins that target fungi, including pathogenic Candida species, via disruption of nutrient uptake and metabolism or loss of plasma membrane potential.

    • Katharina Trunk
    • , Julien Peltier
    • , Yi-Chia Liu
    • , Brian D. Dill
    • , Louise Walker
    • , Neil A. R. Gow
    • , Michael J. R. Stark
    • , Janet Quinn
    • , Henrik Strahl
    • , Matthias Trost
    •  & Sarah J. Coulthurst
  • Article |

    Natural product biosynthesis gene clusters were identified in bacterial isolates from the Arabidopsis phyllosphere, including inhibitory products with antibiotic activity, demonstrating the potential of the phyllosphere as a resource for antibiotics.

    • Eric J. N. Helfrich
    • , Christine M. Vogel
    • , Reiko Ueoka
    • , Martin Schäfer
    • , Florian Ryffel
    • , Daniel B. Müller
    • , Silke Probst
    • , Markus Kreuzer
    • , Jörn Piel
    •  & Julia A. Vorholt
  • Article |

    A combination of genetics, microscopy and modelling identifies FrzX as a target of the Frz kinase that controls cell polarity in Myxococcus xanthus by serving as a gate that regulates the MglA–MglB–RomR relaxation oscillator.

    • Mathilde Guzzo
    • , Seán M. Murray
    • , Eugénie Martineau
    • , Sébastien Lhospice
    • , Grégory Baronian
    • , Laetitia My
    • , Yong Zhang
    • , Leon Espinosa
    • , Renaud Vincentelli
    • , Benjamin P. Bratton
    • , Joshua W. Shaevitz
    • , Virginie Molle
    • , Martin Howard
    •  & Tâm Mignot
  • Letter | | open

    The recovery of viral populations from peatland soils across a permafrost thaw gradient provides insights into soil viral diversity, their hosts and the potential impacts on carbon cycling in this environment.

    • Joanne B. Emerson
    • , Simon Roux
    • , Jennifer R. Brum
    • , Benjamin Bolduc
    • , Ben J. Woodcroft
    • , Ho Bin Jang
    • , Caitlin M. Singleton
    • , Lindsey M. Solden
    • , Adrian E. Naas
    • , Joel A. Boyd
    • , Suzanne B. Hodgkins
    • , Rachel M. Wilson
    • , Gareth Trubl
    • , Changsheng Li
    • , Steve Frolking
    • , Phillip B. Pope
    • , Kelly C. Wrighton
    • , Patrick M. Crill
    • , Jeffrey P. Chanton
    • , Scott R. Saleska
    • , Gene W. Tyson
    • , Virginia I. Rich
    •  & Matthew B. Sullivan