Latest Research

  • Article |

    Using single-particle analysis cryogenic electron microscopy, the authors determine the structures of the bacterial flagellum stator complexes from three diverse bacteria.

    • Justin C. Deme
    • , Steven Johnson
    • , Owen Vickery
    • , Amy Muellbauer
    • , Holly Monkhouse
    • , Thomas Griffiths
    • , Rory Hennell James
    • , Ben C. Berks
    • , James W. Coulton
    • , Phillip J. Stansfeld
    •  & Susan M. Lea
  • Article |

    Cryo-electron microscopy structures of three varicella-zoster virus (VZV) capsids show VZV-specific features of the capsid-associated tegument complex (CATC) and genome packaging. The authors conclude that the VZV capsid is less stable and the CATC binds more weakly than in the homologues in other herpesviruses, characteristics that are linked to the small genome size of VZV.

    • Wei Wang
    • , Qingbing Zheng
    • , Dequan Pan
    • , Hai Yu
    • , Wenkun Fu
    • , Jian Liu
    • , Maozhou He
    • , Rui Zhu
    • , Yuze Cai
    • , Yang Huang
    • , Zhenghui Zha
    • , Zhenqin Chen
    • , Xiangzhong Ye
    • , Jinle Han
    • , Yuqiong Que
    • , Ting Wu
    • , Jun Zhang
    • , Shaowei Li
    • , Hua Zhu
    • , Z. Hong Zhou
    • , Tong Cheng
    •  & Ningshao Xia
  • Article |

    Preclinical studies show that fluoxazolevir, which inhibits the fusion of hepatitis C virus (HCV) with hepatic cells by binding viral envelope protein 1, could be useful in drug cocktails to treat HCV.

    • Christopher D. Ma
    • , Michio Imamura
    • , Daniel C. Talley
    • , Adam Rolt
    • , Xin Xu
    • , Amy Q. Wang
    • , Derek Le
    • , Takuro Uchida
    • , Mitsutaka Osawa
    • , Yuji Teraoka
    • , Kelin Li
    • , Xin Hu
    • , Seung Bum Park
    • , Nishanth Chalasani
    • , Parker H. Irvin
    • , Andres E. Dulcey
    • , Noel Southall
    • , Juan J. Marugan
    • , Zongyi Hu
    • , Kazuaki Chayama
    • , Kevin J. Frankowski
    •  & Tsanyang Jake Liang
  • Article |

    Transcriptional and functional immune-cell profiling reveals that Candida auris is a strong inducer of innate host defence and identifies possible targets for adjuvant immunotherapy.

    • Mariolina Bruno
    • , Simone Kersten
    • , Judith M. Bain
    • , Martin Jaeger
    • , Diletta Rosati
    • , Michael D. Kruppa
    • , Douglas W. Lowman
    • , Peter J. Rice
    • , Bridget Graves
    • , Zuchao Ma
    • , Yue Ning Jiao
    • , Anuradha Chowdhary
    • , George Renieris
    • , Frank L. van de Veerdonk
    • , Bart-Jan Kullberg
    • , Evangelos J. Giamarellos-Bourboulis
    • , Alexander Hoischen
    • , Neil A. R. Gow
    • , Alistair J. P. Brown
    • , Jacques F. Meis
    • , David L. Williams
    •  & Mihai G. Netea
  • Article
    | Open Access

    Large freshwater phage genomes can encode the pmoC gene, an important subunit of the methane oxidation enzyme, methane monooxygenase. These genes are similar to bacterial homologues and are actively expressed in situ. Further work is needed to confirm whether these phages contribute to methane oxidation in the environment.

    • Lin-Xing Chen
    • , Raphaël Méheust
    • , Alexander Crits-Christoph
    • , Katherine D. McMahon
    • , Tara Colenbrander Nelson
    • , Gregory F. Slater
    • , Lesley A. Warren
    •  & Jillian F. Banfield
  • Article |

    The authors do a CRISPR-knockout selection to investigate host factors required for influenza replication. They identified IFIT2 as being repurposed by influenza to promote replication.

    • Vy Tran
    • , Mitchell P. Ledwith
    • , Thiprampai Thamamongood
    • , Christina A. Higgins
    • , Shashank Tripathi
    • , Max W. Chang
    • , Christopher Benner
    • , Adolfo García-Sastre
    • , Martin Schwemmle
    • , Adrianus C. M. Boon
    • , Michael S. Diamond
    •  & Andrew Mehle
  • Article |

    Outer membrane vesicles from Neisseria gonorrhoeae and other Gram-negative pathogens can kill macrophages via induction of mitochondrial apoptosis and activation of the pro-apoptotic BCL-2 family member BAK, and activate the NLRP3 inflammasome.

    • Pankaj Deo
    • , Seong H. Chow
    • , Mei-Ling Han
    • , Mary Speir
    • , Cheng Huang
    • , Ralf B. Schittenhelm
    • , Subhash Dhital
    • , Jack Emery
    • , Jian Li
    • , Benjamin T. Kile
    • , James E. Vince
    • , Kate E. Lawlor
    •  & Thomas Naderer
  • Article |

    Dissimilatory sulfate reduction in archaeon ‘Candidatus Vulcanisaeta moutnovskia’ is distinct from bacterial sulfate reduction and sheds light on the evolution of sulfur metabolism.

    • Nikolay A. Chernyh
    • , Sinje Neukirchen
    • , Evgenii N. Frolov
    • , Filipa L. Sousa
    • , Margarita L. Miroshnichenko
    • , Alexander Y. Merkel
    • , Nikolay V. Pimenov
    • , Dimitry Y. Sorokin
    • , Sergio Ciordia
    • , María Carmen Mena
    • , Manuel Ferrer
    • , Peter N. Golyshin
    • , Alexander V. Lebedinsky
    • , Inês A. Cardoso Pereira
    •  & Elizaveta A. Bonch-Osmolovskaya
  • Letter |

    Identification of the entire set of genes needed for multi-drug plasmid IncC conjugation will inform efforts to prevent plasmid spread.

    • Steven J. Hancock
    • , Minh-Duy Phan
    • , Zhenyao Luo
    • , Alvin W. Lo
    • , Kate M. Peters
    • , Nguyen Thi Khanh Nhu
    • , Brian M. Forde
    • , Jason Whitfield
    • , Ji Yang
    • , Richard A. Strugnell
    • , David L. Paterson
    • , Timothy R. Walsh
    • , Bostjan Kobe
    • , Scott A. Beatson
    •  & Mark A. Schembri
  • Author Correction |

    • Thomas D. Otto
    • , Aude Gilabert
    • , Thomas Crellen
    • , Ulrike Böhme
    • , Céline Arnathau
    • , Mandy Sanders
    • , Samuel O. Oyola
    • , Alain Prince Okouga
    • , Larson Boundenga
    • , Eric Willaume
    • , Barthélémy Ngoubangoye
    • , Nancy Diamella Moukodoum
    • , Christophe Paupy
    • , Patrick Durand
    • , Virginie Rougeron
    • , Benjamin Ollomo
    • , François Renaud
    • , Chris Newbold
    • , Matthew Berriman
    •  & Franck Prugnolle
  • Article |

    This study describes design automation and predictable gene regulatory network engineering in a eukaryotic microorganism.

    • Ye Chen
    • , Shuyi Zhang
    • , Eric M. Young
    • , Timothy S. Jones
    • , Douglas Densmore
    •  & Christopher A. Voigt
  • Article |

    This study describes the mechanism by which Chlamydia trachomatis reprogrammes host glutamine metabolism in a c-Myc-dependent manner. The authors show that glutamine uptake via the SLC15A transporter and glutaminolysis are crucial for peptidoglycan synthesis and Chlamydia replication.

    • Karthika Rajeeve
    • , Nadine Vollmuth
    • , Sudha Janaki-Raman
    • , Thomas F. Wulff
    • , Apoorva Baluapuri
    • , Francesca R. Dejure
    • , Claudia Huber
    • , Julian Fink
    • , Maximilian Schmalhofer
    • , Werner Schmitz
    • , Rajeeve Sivadasan
    • , Elmar Wolf
    • , Wolfgang Eisenreich
    • , Almut Schulze
    • , Jürgen Seibel
    •  & Thomas Rudel
  • Article |

    In this manuscript, the authors address evolutionary questions on the emergence of SARS-CoV-2. They find that SARS-CoV-2 is not a recombinant of any sarbecoviruses detected to date, and that the bat and pangolin sequences most closely related to SARS-CoV-2 probably diverged several decades ago or possibly earlier from human SARS-CoV-2 samples.

    • Maciej F. Boni
    • , Philippe Lemey
    • , Xiaowei Jiang
    • , Tommy Tsan-Yuk Lam
    • , Blair W. Perry
    • , Todd A. Castoe
    • , Andrew Rambaut
    •  & David L. Robertson
  • Article |

    This study reveals features of Epstein–Barr virus that are similar but not identical to the closely related Kaposi’s sarcoma-associated herpesvirus. The authors provide locations of protein components within the viral capsid and reveal different conformers of protein components by revealing variations in links between capsid proteins and exploiting approaches with relaxation of symmetry. The capsid-associated tegument complex is loaded on to the capsid with long-range asymmetry, relative to the location of the portal vertex (the site of genome entry and egress).

    • Wei Liu
    • , Yanxiang Cui
    • , Caiyan Wang
    • , Zihang Li
    • , Danyang Gong
    • , Xinghong Dai
    • , Guo-Qiang Bi
    • , Ren Sun
    •  & Z. Hong Zhou
  • Article |

    This study reveals that prion-like domains support the assembly of transcription factor complexes that control fungal cell identity and highlights parallels with the ‘super-enhancers’ that regulate mammalian cell fate.

    • Corey Frazer
    • , Mae I. Staples
    • , Yoori Kim
    • , Matthew Hirakawa
    • , Maureen A. Dowell
    • , Nicole V. Johnson
    • , Aaron D. Hernday
    • , Veronica H. Ryan
    • , Nicolas L. Fawzi
    • , Ilya J. Finkelstein
    •  & Richard J. Bennett
  • Letter |

    Subinhibitory levels of sulfamethoxazole, an antibiotic used to treat Escherichia coli infections, trigger a previously undescribed metabolic pathway in E. coli that comprises a family of hybrid pterin–phenylpyruvate conjugates called colipterins. These metabolites are antioxidants, have immunomodulatory properties and improve colitis in a murine model.

    • Hyun Bong Park
    • , Zheng Wei
    • , Joonseok Oh
    • , Hao Xu
    • , Chung Sub Kim
    • , Rurun Wang
    • , Thomas P. Wyche
    • , Grazia Piizzi
    • , Richard A. Flavell
    •  & Jason M. Crawford
  • Letter |

    Here, the authors identify lymphocyte antigen 6E (LY6E) as a coronavirus (CoV) restriction factor that prevents infection of B cells and dendritic cells. LY6E inhibits both human and mouse CoV entry into cells by interfering with viral spike protein-mediated membrane fusion. It facilitates an antiviral immune response that prevents liver disease and reduces death in the mouse model of MHV-A59 CoV infection.

    • Stephanie Pfaender
    • , Katrina B. Mar
    • , Eleftherios Michailidis
    • , Annika Kratzel
    • , Ian N. Boys
    • , Philip V’kovski
    • , Wenchun Fan
    • , Jenna N. Kelly
    • , Dagny Hirt
    • , Nadine Ebert
    • , Hanspeter Stalder
    • , Hannah Kleine-Weber
    • , Markus Hoffmann
    • , Hans-Heinrich Hoffmann
    • , Mohsan Saeed
    • , Ronald Dijkman
    • , Eike Steinmann
    • , Mary Wight-Carter
    • , Matthew B. McDougal
    • , Natasha W. Hanners
    • , Stefan Pöhlmann
    • , Tom Gallagher
    • , Daniel Todt
    • , Gert Zimmer
    • , Charles M. Rice
    • , John W. Schoggins
    •  & Volker Thiel
  • Article
    | Open Access

    Metagenomic analysis of a single RNA virome from the Yangshan Deep-Water Harbour in China enabled the recovery of more than 4,500 distinct RNA viruses, doubling the known set of RNA viruses to date, and provided insights into their biology.

    • Yuri I. Wolf
    • , Sukrit Silas
    • , Yongjie Wang
    • , Shuang Wu
    • , Michael Bocek
    • , Darius Kazlauskas
    • , Mart Krupovic
    • , Andrew Fire
    • , Valerian V. Dolja
    •  & Eugene V. Koonin
  • Article |

    Vpu prevents HIV superinfection and immune activation by modulating DNA repair mechanisms, particularly by inhibiting homologous repair. Vpu achieves this by disrupting the RanBP2–RanGAP1*SUMO1–Ubc9 complex at the nuclear pore to reduce PML SUMOylation and consequent PML nuclear body formation, which hampers the homologous recombination factors Rad52 and BLM.

    • Meta Volcic
    • , Konstantin M. J. Sparrer
    • , Lennart Koepke
    • , Dominik Hotter
    • , Daniel Sauter
    • , Christina M. Stürzel
    • , Myriam Scherer
    • , Thomas Stamminger
    • , Thomas G. Hofmann
    • , Nathalie J. Arhel
    • , Lisa Wiesmüller
    •  & Frank Kirchhoff
  • Article |

    The AcP10 protein—an active uridine kinase, encoded by the beluga whale coronavirus SW1—is an antagonist of the integrated stress response that acts downstream of phosphorylation of the translation initiation factor eIF2, irrespective of which eIF2 kinase is activated. AcP10 acts as a competitive inhibitor of the eIF2[P]–eIF2B interaction by binding to eIF2B. A protein with a similar function is also encoded by Aichivirus, a picornavirus.

    • Huib H. Rabouw
    • , Linda J. Visser
    • , Tim C. Passchier
    • , Martijn A. Langereis
    • , Fan Liu
    • , Piero Giansanti
    • , Arno L. W. van Vliet
    • , José G. Dekker
    • , Susanne G. van der Grein
    • , Jesús G. Saucedo
    • , Aditya A. Anand
    • , Mikael E. Trellet
    • , Alexandre M. J. J. Bonvin
    • , Peter Walter
    • , Albert J. R. Heck
    • , Raoul J. de Groot
    •  & Frank J. M. van Kuppeveld
  • Article |

    The authors propose a nomenclature of SARS-CoV-2 lineages to assist research on epidemiology and decision-making during the COVID-19 pandemic. This nomenclature is based on the SARS-CoV-2 phylogeny and designed to provide a real-time bird’s-eye view of the diversity of the hundreds of thousands of genome sequences collected worldwide. The authors develop a set of rules to produce a hierarchical four-level nomenclature of labels that is flexible and dynamic.

    • Andrew Rambaut
    • , Edward C. Holmes
    • , Áine O’Toole
    • , Verity Hill
    • , John T. McCrone
    • , Christopher Ruis
    • , Louis du Plessis
    •  & Oliver G. Pybus
  • Article |

    This study highlights a unique drug target for trypanosomatid parasitic protozoa and a new chemical tool for investigating the function of their divergent kinetochores.

    • Manuel Saldivia
    • , Eric Fang
    • , Xiaolei Ma
    • , Elmarie Myburgh
    • , Juliana B. T. Carnielli
    • , Christopher Bower-Lepts
    • , Elaine Brown
    • , Ryan Ritchie
    • , Suresh B. Lakshminarayana
    • , Yen-Liang Chen
    • , Debjani Patra
    • , Elizabeth Ornelas
    • , Hazel X. Y. Koh
    • , Sarah L. Williams
    • , Frantisek Supek
    • , Daniel Paape
    • , Richard McCulloch
    • , Marcel Kaiser
    • , Michael P. Barrett
    • , Jan Jiricek
    • , Thierry T. Diagana
    • , Jeremy C. Mottram
    •  & Srinivasa P. S. Rao
  • Article |

    In this Article, the authors report the discovery of a small molecule (GHP-88309) that is a new class of allosteric viral polymerase inhibitor that works against two different genera of paramyxoviruses.

    • Robert M. Cox
    • , Julien Sourimant
    • , Mart Toots
    • , Jeong-Joong Yoon
    • , Satoshi Ikegame
    • , Mugunthan Govindarajan
    • , Ruth E. Watkinson
    • , Patricia Thibault
    • , Negar Makhsous
    • , Michelle J. Lin
    • , Jose R. Marengo
    • , Zachary Sticher
    • , Alexander A. Kolykhalov
    • , Michael G. Natchus
    • , Alexander L. Greninger
    • , Benhur Lee
    •  & Richard K. Plemper
  • Article |

    Adenovirus produces two early proteins, E1B55K and E4orf6, that become components of the host cell ubiquitin ligase complex comprising elongin-B and C, cullin-5 and RBX1. The authors identified new protein substrates that are ubiquitinated by the E1B55K–E4orf6 complex and find that hnRNP-C and RALY play an inhibitory role on late viral RNA transcripts and that this is counteracted by ubiquitination due to a reduction on the capacity of these proteins to interact with viral RNA.

    • Christin Herrmann
    • , Joseph M. Dybas
    • , Jennifer C. Liddle
    • , Alexander M. Price
    • , Katharina E. Hayer
    • , Richard Lauman
    • , Caitlin E. Purman
    • , Matthew Charman
    • , Eui Tae Kim
    • , Benjamin A. Garcia
    •  & Matthew D. Weitzman
  • Article |

    Bacteria-derived lactate mediates inhibition of HDAC11 during Staphylococcus aureus biofilm infections, resulting in epigenetic changes that reprogramme the host immune response.

    • Cortney E. Heim
    • , Megan E. Bosch
    • , Kelsey J. Yamada
    • , Amy L. Aldrich
    • , Sujata S. Chaudhari
    • , David Klinkebiel
    • , Casey M. Gries
    • , Abdulelah A. Alqarzaee
    • , Yixuan Li
    • , Vinai C. Thomas
    • , Edward Seto
    • , Adam R. Karpf
    •  & Tammy Kielian
  • Analysis |

    This is a comparative analysis of the performance of the primer–probe sets from four open-source molecular diagnostic assays for SARS-CoV-2 recommended by the World Health Organization.

    • Chantal B. F. Vogels
    • , Anderson F. Brito
    • , Anne L. Wyllie
    • , Joseph R. Fauver
    • , Isabel M. Ott
    • , Chaney C. Kalinich
    • , Mary E. Petrone
    • , Arnau Casanovas-Massana
    • , M. Catherine Muenker
    • , Adam J. Moore
    • , Jonathan Klein
    • , Peiwen Lu
    • , Alice Lu-Culligan
    • , Xiaodong Jiang
    • , Daniel J. Kim
    • , Eriko Kudo
    • , Tianyang Mao
    • , Miyu Moriyama
    • , Ji Eun Oh
    • , Annsea Park
    • , Julio Silva
    • , Eric Song
    • , Takehiro Takahashi
    • , Manabu Taura
    • , Maria Tokuyama
    • , Arvind Venkataraman
    • , Orr-El Weizman
    • , Patrick Wong
    • , Yexin Yang
    • , Nagarjuna R. Cheemarla
    • , Elizabeth B. White
    • , Sarah Lapidus
    • , Rebecca Earnest
    • , Bertie Geng
    • , Pavithra Vijayakumar
    • , Camila Odio
    • , John Fournier
    • , Santos Bermejo
    • , Shelli Farhadian
    • , Charles S. Dela Cruz
    • , Akiko Iwasaki
    • , Albert I. Ko
    • , Marie L. Landry
    • , Ellen F. Foxman
    •  & Nathan D. Grubaugh
  • Article |

    Productive influenza infection can be improved by cooperation and this varies between viral strains and hosts. By quantifying the rates of reassortment and virus production using several methods, including single-cell sequencing, the authors find that isolates of the avian H9N2 influenza subtype are dependent on infections with a second virus, but only in mammalian cells and not in avian cells. These findings are supported by in vivo experiments in guinea pigs and quail. The authors find indications that this type of cooperation between influenza A viruses depends on the RNA polymerase subunit PA.

    • Kara L. Phipps
    • , Ketaki Ganti
    • , Nathan T. Jacobs
    • , Chung-Young Lee
    • , Silvia Carnaccini
    • , Maria C. White
    • , Miglena Manandhar
    • , Brett E. Pickett
    • , Gene S. Tan
    • , Lucas M. Ferreri
    • , Daniel R. Perez
    •  & Anice C. Lowen
  • Article |

    Isolation of phages associated with the gut commensal Bacteroides thetaiotaomicron reveals a link between cell surface structures, including phase-variable capsular polysaccharides, lipoproteins and S-layer proteins, and susceptibility to phage infection.

    • Nathan T. Porter
    • , Andrew J. Hryckowian
    • , Bryan D. Merrill
    • , Jaime J. Fuentes
    • , Jackson O. Gardner
    • , Robert W. P. Glowacki
    • , Shaleni Singh
    • , Ryan D. Crawford
    • , Evan S. Snitkin
    • , Justin L. Sonnenburg
    •  & Eric C. Martens
  • Letter |

    A microbiome genome-wide association study using three large European cohorts identified several significant study-wide and genome-wide correlations between human genetic variants and microbial traits, and used Mendelian randomization to estimate causal relationships between microbial traits and disease.

    • David A. Hughes
    • , Rodrigo Bacigalupe
    • , Jun Wang
    • , Malte C. Rühlemann
    • , Raul Y. Tito
    • , Gwen Falony
    • , Marie Joossens
    • , Sara Vieira-Silva
    • , Liesbet Henckaerts
    • , Leen Rymenans
    • , Chloë Verspecht
    • , Susan Ring
    • , Andre Franke
    • , Kaitlin H. Wade
    • , Nicholas J. Timpson
    •  & Jeroen Raes
  • Article |

    This study describes the mechanisms of FOXO1-mediated repression of endoplasmic reticulum (ER) stress in HIV-1 latency. The authors propose a model where inhibition of FOXO1 activity promotes protein accumulation in the ER leading to ER stress signalling and calcium release, which mobilizes ATF4 and NFAT and activates HIV-1 transcription.

    • Albert Vallejo-Gracia
    • , Irene P. Chen
    • , Rosalba Perrone
    • , Emilie Besnard
    • , Daniela Boehm
    • , Emilie Battivelli
    • , Tugsan Tezil
    • , Karsten Krey
    • , Kyle A. Raymond
    • , Philip A. Hull
    • , Marius Walter
    • , Ireneusz Habrylo
    • , Andrew Cruz
    • , Steven Deeks
    • , Satish Pillai
    • , Eric Verdin
    •  & Melanie Ott
  • Article |

    Using the proteome-wide pSILAC-AHA labelling approach, the authors resolve the host proteome spatiotemporal dynamics during macrophage infection with Salmonella enterica Typhimurium and reveal the active role of cathepsins in cell death via the non-canonical inflammasome.

    • Joel Selkrig
    • , Nan Li
    • , Annika Hausmann
    • , Matthew S. J. Mangan
    • , Matylda Zietek
    • , André Mateus
    • , Jacob Bobonis
    • , Anna Sueki
    • , Haruna Imamura
    • , Bachir El Debs
    • , Gianluca Sigismondo
    • , Bogdan I. Florea
    • , Herman S. Overkleeft
    • , Nataša Kopitar-Jerala
    • , Boris Turk
    • , Pedro Beltrao
    • , Mikhail M. Savitski
    • , Eicke Latz
    • , Wolf-Dietrich Hardt
    • , Jeroen Krijgsveld
    •  & Athanasios Typas
  • Article |

    In this Article, using a nutrient-limited, media-based compound screening, the authors discover that the old antibiotic rifabutin is highly active against extensively drug-resistant Acinetobacter baumannii.

    • Brian Luna
    • , Vincent Trebosc
    • , Bosul Lee
    • , Malina Bakowski
    • , Amber Ulhaq
    • , Jun Yan
    • , Peggy Lu
    • , Jiaqi Cheng
    • , Travis Nielsen
    • , Juhyeon Lim
    • , Warisa Ketphan
    • , Hyungjin Eoh
    • , Case McNamara
    • , Nicholas Skandalis
    • , Rosemary She
    • , Christian Kemmer
    • , Sergio Lociuro
    • , Glenn E. Dale
    •  & Brad Spellberg
  • Consensus Statement
    | Open Access

    In this Consensus Statement, the authors discuss the issue of naming uncultivated prokaryotic microorganisms, which currently do not have a formal nomenclature system due to a lack of type material or cultured representatives, and propose two recommendations including the recognition of DNA sequences as type material.

    • Alison E. Murray
    • , John Freudenstein
    • , Simonetta Gribaldo
    • , Roland Hatzenpichler
    • , Philip Hugenholtz
    • , Peter Kämpfer
    • , Konstantinos T. Konstantinidis
    • , Christopher E. Lane
    • , R. Thane Papke
    • , Donovan H. Parks
    • , Ramon Rossello-Mora
    • , Matthew B. Stott
    • , Iain C. Sutcliffe
    • , J. Cameron Thrash
    • , Stephanus N. Venter
    • , William B. Whitman
    • , Silvia G. Acinas
    • , Rudolf I. Amann
    • , Karthik Anantharaman
    • , Jean Armengaud
    • , Brett J. Baker
    • , Roman A. Barco
    • , Helge B. Bode
    • , Eric S. Boyd
    • , Carrie L. Brady
    • , Paul Carini
    • , Patrick S. G. Chain
    • , Daniel R. Colman
    • , Kristen M. DeAngelis
    • , Maria Asuncion de los Rios
    • , Paulina Estrada-de los Santos
    • , Christopher A. Dunlap
    • , Jonathan A. Eisen
    • , David Emerson
    • , Thijs J. G. Ettema
    • , Damien Eveillard
    • , Peter R. Girguis
    • , Ute Hentschel
    • , James T. Hollibaugh
    • , Laura A. Hug
    • , William P. Inskeep
    • , Elena P. Ivanova
    • , Hans-Peter Klenk
    • , Wen-Jun Li
    • , Karen G. Lloyd
    • , Frank E. Löffler
    • , Thulani P. Makhalanyane
    • , Duane P. Moser
    • , Takuro Nunoura
    • , Marike Palmer
    • , Victor Parro
    • , Carlos Pedrós-Alió
    • , Alexander J. Probst
    • , Theo H. M. Smits
    • , Andrew D. Steen
    • , Emma T. Steenkamp
    • , Anja Spang
    • , Frank J. Stewart
    • , James M. Tiedje
    • , Peter Vandamme
    • , Michael Wagner
    • , Feng-Ping Wang
    • , Brian P. Hedlund
    •  & Anna-Louise Reysenbach
  • Letter |

    This study describes the development of prokaryotic expression profiling by tagging RNA in situ and sequencing (PETRI-seq)—a high-throughput prokaryotic scRNA-seq method capable of sequencing tens of thousands of cells in a single experiment.

    • Sydney B. Blattman
    • , Wenyan Jiang
    • , Panos Oikonomou
    •  & Saeed Tavazoie
  • Letter |

    A genome-wide CRISPR screen identifies gangliosides as receptors for hepatitis A virus that facilitate a post-entry step in infection.

    • Anshuman Das
    • , Rodell Barrientos
    • , Tomoyuki Shiota
    • , Victoria Madigan
    • , Ichiro Misumi
    • , Kevin L. McKnight
    • , Lu Sun
    • , Zhucui Li
    • , Rita M. Meganck
    • , You Li
    • , Ewelina Kaluzna
    • , Aravind Asokan
    • , Jason K. Whitmire
    • , Maryna Kapustina
    • , Qibin Zhang
    •  & Stanley M. Lemon
  • Perspective |

    Urban informal settlements, more commonly known as slums, are hotspots for the environmental transmission of antimicrobial resistance (AMR). Here, the authors discuss the behavioural, environmental and structural reasons for this and propose that improvements in water and waste infrastructure, as well as legal and economic incentives, could limit environmental AMR dissemination.

    • Maya L. Nadimpalli
    • , Sara J. Marks
    • , Maria Camila Montealegre
    • , Robert H. Gilman
    • , Monica J. Pajuelo
    • , Mayuko Saito
    • , Pablo Tsukayama
    • , Sammy M. Njenga
    • , John Kiiru
    • , Jenna Swarthout
    • , Mohammad Aminul Islam
    • , Timothy R. Julian
    •  & Amy J. Pickering
  • Article |

    Lentimonas’—a marine microorganism from the Verrucomicrobia phylum—has >200 different glycoside hydrolase and sulfatase enzymes enabling digestion of the algal polysaccharide fucoidan, which was thought to be a recalcitrant source of carbon in our oceans.

    • Andreas Sichert
    • , Christopher H. Corzett
    • , Matthew S. Schechter
    • , Frank Unfried
    • , Stephanie Markert
    • , Dörte Becher
    • , Antonio Fernandez-Guerra
    • , Manuel Liebeke
    • , Thomas Schweder
    • , Martin F. Polz
    •  & Jan-Hendrik Hehemann
  • Letter |

    Here, the authors report the discovery of prophages in cultured SAR11 and show that lysogenic SAR11 produce virions by prophage induction of up to 2.3% of infected cells under carbon-replete growth conditions and up to 30.6% of infected cells under carbon-deplete conditions.

    • Robert M. Morris
    • , Kelsy R. Cain
    • , Kelli L. Hvorecny
    •  & Justin M. Kollman