Browse Articles

  • News & Views |

    Protease-enabled strand exchange to mediate assembly of type V pilus is confirmed using a combination of cryogenic electron microscopy and X-ray crystal structures.

    • Lori L. Burrows
  • News & Views |

    Multi-omics reveals how metabolites produced by pioneer bacterial species might alter the neonatal gut environment to an anaerobic state much earlier than was previously thought during the first hours of life.

    • Jincheng Wang
    •  & Maria Gloria Dominguez-Bello
  • 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 |

    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
  • Comment |

    How viruses are related, and how they have evolved and spread over time, can be investigated using phylogenetics. Here, we set out how genomic analyses should be used during an epidemic and propose that phylogenetic insights from the early stages of an outbreak should heed all of the available epidemiological information.

    • Ch. Julián Villabona-Arenas
    • , William P. Hanage
    •  & Damien C. Tully
  • 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
  • Article |

    A CRISPR–Cas9 screening identifies cellular genes that regulate Epstein–Barr virus latency type I–III transition. The authors identify UHRF1 and DNMT1 as major regulators of this pathway. They also show that components of the polycomb repressor complex contribute to this regulation.

    • Rui Guo
    • , Yuchen Zhang
    • , Mingxiang Teng
    • , Chang Jiang
    • , Molly Schineller
    • , Bo Zhao
    • , John G. Doench
    • , Richard J. O’Reilly
    • , Ethel Cesarman
    • , Lisa Giulino-Roth
    •  & Benjamin E. Gewurz
  • Comment |

    A precision approach to probiotics could address the heterogeneity inherent to probiotic strains, the hosts and their microbiomes. Here, we discuss the steps required to develop precision probiotics: mechanistic studies, phenotypic and target-based discovery strategies, and person-centric trials.

    • Patrick Veiga
    • , Jotham Suez
    • , Muriel Derrien
    •  & Eran Elinav
  • Letter |

    In rhizosphere microbial communities, iron competition via secreted siderophores can be used as a predictor of commensal–pathogen interactions and plant protection against infection with the pathogen Ralstonia solanacearum.

    • Shaohua Gu
    • , Zhong Wei
    • , Zhengying Shao
    • , Ville-Petri Friman
    • , Kehao Cao
    • , Tianjie Yang
    • , Jos Kramer
    • , Xiaofang Wang
    • , Mei Li
    • , Xinlan Mei
    • , Yangchun Xu
    • , Qirong Shen
    • , Rolf Kümmerli
    •  & Alexandre Jousset
  • Article |

    Porphyromonas gingivalis, an oral anaerobe involved in the pathogenesis of periodontitis, relies on extracellular proteases to degrade proteins into peptides for growth, but how these peptides enter the cell is unknown. Here, the authors identify RagAB as the outer-membrane importer for these peptides and solve its structure, elucidating that it works via a ‘pedal bin’ mechanism of nutrient uptake.

    • Mariusz Madej
    • , Joshua B. R. White
    • , Zuzanna Nowakowska
    • , Shaun Rawson
    • , Carsten Scavenius
    • , Jan J. Enghild
    • , Grzegorz P. Bereta
    • , Karunakar Pothula
    • , Ulrich Kleinekathoefer
    • , Arnaud Baslé
    • , Neil A. Ranson
    • , Jan Potempa
    •  & Bert van den Berg
  • Review Article |

    Recent advances in genome sequencing have started to reveal an increasing diversity and distribution of archaeal genomes across multiple ecosystems. In this Review, Baker and colleagues discuss how these genomes elucidate the metabolic capabilities of the Archaea and their ecological roles, while also expanding our view of the tree of life and of eukaryogenesis.

    • Brett J. Baker
    • , Valerie De Anda
    • , Kiley W. Seitz
    • , Nina Dombrowski
    • , Alyson E. Santoro
    •  & Karen G. Lloyd
  • Letter |

    Here, using RNA sequencing and data from several cohorts, the authors find an association of the presence of inherited, chromosomally integrated human herpesvirus 6 in the placenta with a clinical diagnosis of pre-eclampsia in the mother.

    • Francesca Gaccioli
    • , Susanne Lager
    • , Marcus C. de Goffau
    • , Ulla Sovio
    • , Justyna Dopierala
    • , Sungsam Gong
    • , Emma Cook
    • , Andrew Sharkey
    • , Ashley Moffett
    • , Wai Kwong Lee
    • , Christian Delles
    • , Cristina Venturini
    • , Judith Breuer
    • , Julian Parkhill
    • , Sharon J. Peacock
    • , D. Stephen Charnock-Jones
    •  & Gordon C. S. Smith
  • Review Article |

    Flaviviruses, a group of vector-borne RNA viruses that includes dengue virus, West Nile virus, Zika virus and several lesser-known species, often emerge in human populations and cause epidemics. Here, Pierson and Diamond review the basic biology of these viruses, their life cycles, the diseases they cause and available therapeutic options. They also discuss the global distribution of flaviviruses, with a focus on lesser-known species that have the potential to emerge more broadly in human populations.

    • Theodore C. Pierson
    •  & Michael S. Diamond
  • Article |

    Monkeypox is caused by an emerging zoonotic virus. This study describes a detailed investigation into monkeypox outbreaks in chimpanzees through non-invasive environmental sampling, virus genomics, pathology, behavioural ecology and dietary metabarcoding.

    • Livia V. Patrono
    • , Kamilla Pléh
    • , Liran Samuni
    • , Markus Ulrich
    • , Caroline Röthemeier
    • , Andreas Sachse
    • , Silvia Muschter
    • , Andreas Nitsche
    • , Emmanuel Couacy-Hymann
    • , Christophe Boesch
    • , Roman M. Wittig
    • , Sébastien Calvignac-Spencer
    •  & Fabian H. Leendertz
  • Consensus Statement
    | Open Access

    Here, the International Committee on Taxonomy of Viruses describe a new, expanded virus classification scheme with 15 ranks that closely aligns with the Linnaean taxonomic system and better encompasses viral diversity.

    • Alexander E. Gorbalenya
    • , Mart Krupovic
    • , Arcady Mushegian
    • , Andrew M. Kropinski
    • , Stuart G. Siddell
    • , Arvind Varsani
    • , Michael J. Adams
    • , Andrew J. Davison
    • , Bas E. Dutilh
    • , Balázs Harrach
    • , Robert L. Harrison
    • , Sandra Junglen
    • , Andrew M. Q. King
    • , Nick J. Knowles
    • , Elliot J. Lefkowitz
    • , Max L. Nibert
    • , Luisa Rubino
    • , Sead Sabanadzovic
    • , Hélène Sanfaçon
    • , Peter Simmonds
    • , Peter J. Walker
    • , F. Murilo Zerbini
    •  & Jens H. Kuhn
  • Article |

    The authors present the full-length structure of the polymerase (L protein) from the severe fever with thrombocytopenia syndrome virus (SFTSV)—a segmented, negative-stranded RNA virus. The structure reveals important details with implications for the understanding of viral transcription and replication, and provides information on the organization of the polymerase core domain, entrance and exit tunnels, as well as the cap-binding and endonuclease domains.

    • Panpan Wang
    • , Lu Liu
    • , Aijun Liu
    • , Liming Yan
    • , Yong He
    • , Shu Shen
    • , Mingxu Hu
    • , Yu Guo
    • , Haiguang Liu
    • , Chuang Liu
    • , Yinying Lu
    • , Peiyi Wang
    • , Fei Deng
    • , Zihe Rao
    •  & Zhiyong Lou
  • Article |

    A comparison of the evolutionary history and geographical spread of the antimicrobial-resistant pathogen Staphylococcus capitis in neonatal intensive care units indicates that acquisition of antibiotic resistance and increased competitiveness have led to the success of the NRCS-A S. capitis clone.

    • Thierry Wirth
    • , Marine Bergot
    • , Jean-Philippe Rasigade
    • , Bruno Pichon
    • , Maxime Barbier
    • , Patricia Martins-Simoes
    • , Laurent Jacob
    • , Rachel Pike
    • , Pierre Tissieres
    • , Jean-Charles Picaud
    • , Angela Kearns
    • , Philip Supply
    • , Marine Butin
    • , Frédéric Laurent
    • , Vaclava Adamkova
    • , Timothy Barkham
    • , Karsten Becker
    • , Desiree Bennett
    • , Olivier Claris
    • , Clarence Buddy Creech
    • , Herminia De Lencastre
    • , Margaret Deighton
    • , Olivier Denis
    • , John Ferguson
    • , Yhu-Chering Huang
    • , Claus Klingenberg
    • , Andre Ingebretsen
    • , Celine Laferrière
    • , Katia Regina Netto dos Santos
    • , Jacques Schrenzel
    • , Iris Spiliopoulou
    • , Stefania Stefani
    • , Kim TaekSoo
    • , Eveliina Tarkka
    • , Alex Friedrich
    • , Christina Vandenbroucke-Grauls
    • , James Ussher
    • , Francois Vandenesch
    • , Lars Westblade
    • , Jodi Lindsay
    • , Francois Vandenesch
    • , Anders Rhod Larsen
    • , Philipp Zanger
    • , Barbara C. Kahl
    •  & Cristina Prat Aymerich
  • Perspective |

    In this Perspective, Lopez-Garcia and Moreira update the Syntrophy hypothesis for the origin of eukaryotes, considering recent advances in the archaeal field about the physiology, metabolism, ecology and evolution of these microbes. They also compare and contrast their model with alternative ones, such as the classical Searcy’s and Hydrogen hypotheses and the more recent Reverse Flow and Entangle–Engulf–Endogenize models, and discuss model predictions and ways to test these.

    • Purificación López-García
    •  & David Moreira
  • Letter |

    This paper shows that the parasite Trypanosoma brucei is able to establish infection in flies by penetrating the protective peritrophic matrix in the fly midgut at the place of matrix secretion in the proventriculus. Such early proventricular colonization is potentiated by factors that are present in trypanosome-infected blood ingested by the flies.

    • Clair Rose
    • , Aitor Casas-Sánchez
    • , Naomi A. Dyer
    • , Carla Solórzano
    • , Alison J. Beckett
    • , Ben Middlehurst
    • , Marco Marcello
    • , Lee R. Haines
    • , Jaime Lisack
    • , Markus Engstler
    • , Michael J. Lehane
    • , Ian A. Prior
    •  & Álvaro Acosta-Serrano
  • Article |

    The oxysterol 25-hydroxycholesterol reduces the levels of plasma membrane accessible cholesterol via acyl-CoA cholesterol acyltransferase to inhibit infection and dissemination of intracellular bacterial pathogens, including Listeria monocytogenes.

    • Michael E. Abrams
    • , Kristen A. Johnson
    • , Sofya S. Perelman
    • , Li-shu Zhang
    • , Shreya Endapally
    • , Katrina B. Mar
    • , Bonne M. Thompson
    • , Jeffrey G. McDonald
    • , John W. Schoggins
    • , Arun Radhakrishnan
    •  & Neal M. Alto
  • Article |

    Using a multi-omics approach to analyse meconium and stool samples from babies during the first few days of life, the authors show that the gut is detectably colonized within 16 h of birth, with Escherichia coli dominating, and that this correlates with proteome and metabolome changes including the fermentation of amino acids.

    • Kyle Bittinger
    • , Chunyu Zhao
    • , Yun Li
    • , Eileen Ford
    • , Elliot S. Friedman
    • , Josephine Ni
    • , Chiraag V. Kulkarni
    • , Jingwei Cai
    • , Yuan Tian
    • , Qing Liu
    • , Andrew D. Patterson
    • , Debolina Sarkar
    • , Siu. H. J. Chan
    • , Costas Maranas
    • , Anumita Saha-Shah
    • , Peder Lund
    • , Benjamin A. Garcia
    • , Lisa M. Mattei
    • , Jeffrey S. Gerber
    • , Michal A. Elovitz
    • , Andrea Kelly
    • , Patricia DeRusso
    • , Dorothy Kim
    • , Casey E. Hofstaedter
    • , Mark Goulian
    • , Hongzhe Li
    • , Frederic D. Bushman
    • , Babette S. Zemel
    •  & Gary D. Wu
  • Article |

    Using macroecological approaches and human and murine gut microbiota datasets, the authors demonstrate that the dynamics of these complex microbial communities can be characterized similarly to other ecological systems by multiple quantitative relationships. The observed macroecological relationships were then used to identify specific taxa that are impacted by environmental changes.

    • Brian W. Ji
    • , Ravi U. Sheth
    • , Purushottam D. Dixit
    • , Konstantine Tchourine
    •  & Dennis Vitkup
  • Letter |

    Structures of the FimA pilin from Porphyromonas gingivalis in monomeric and polymerized states reveal the protease-mediated strand-exchange assembly mechanism of type V pili, which is a key virulence factor of this periodontal pathogen.

    • Satoshi Shibata
    • , Mikio Shoji
    • , Kodai Okada
    • , Hideyuki Matsunami
    • , Melissa M. Matthews
    • , Katsumi Imada
    • , Koji Nakayama
    •  & Matthias Wolf
  • Letter |

    Streptomyces bacteria make volatile compounds such as geosmin and 2-methylisoborneol that attract springtails to bacterial colonies. The soil arthropods feed on the bacteria and help to disseminate spores via faecal pellets and through adherence to their surface.

    • Paul G. Becher
    • , Vasiliki Verschut
    • , Maureen J. Bibb
    • , Matthew J. Bush
    • , Béla P. Molnár
    • , Elisabeth Barane
    • , Mahmoud M. Al-Bassam
    • , Govind Chandra
    • , Lijiang Song
    • , Gregory L. Challis
    • , Mark J. Buttner
    •  & Klas Flärdh
  • Article |

    SspABCD–SspE is a widespread bacterial defence system against phage infection, in which SspABCD is responsible for introducing phosphorothioate modifications and SspE serves as a nickase that cleaves foreign DNA.

    • Xiaolin Xiong
    • , Geng Wu
    • , Yue Wei
    • , Liqiong Liu
    • , Yubing Zhang
    • , Rui Su
    • , Xianyue Jiang
    • , Mengxue Li
    • , Haiyan Gao
    • , Xihao Tian
    • , Yizhou Zhang
    • , Li Hu
    • , Si Chen
    • , You Tang
    • , Susu Jiang
    • , Ruolin Huang
    • , Zhiqiang Li
    • , Yunfu Wang
    • , Zixin Deng
    • , Jiawei Wang
    • , Peter C. Dedon
    • , Shi Chen
    •  & Lianrong Wang
  • News & Views |

    The combined selective pressures of residing in different protozoan hosts in the environment drives the evolution of virulence in the opportunistic pathogen Legionella pneumophila.

    • Diane McDougald
    •  & Sharon R. Longford
  • News & Views |

    N6-methyladenosine (m6A) is a widespread modification on cellular RNA that is dynamically regulated involving m6A writers, erasers and readers, and can impact many cellular processes and pathways. A recent study demonstrates that viruses can use m6A to ensure their RNA avoids innate immune sensing.

    • Volker Thiel
  • News & Views |

    Two studies now identify bradyzoite-formation deficient 1 and microrchidia as ‘master regulators’ of the transcriptional events that control developmental life cycle transitions in the protozoan parasite Toxoplasma gondii.

    • William J. Sullivan Jr
  • Article |

    A search for genes encoding anti-CRISPR (Acr) proteins on plasmids and other conjugative elements identifies new Acrs that regulate plasmid dissemination and are broad-spectrum inhibitors of Cas9 in human cells.

    • Caroline Mahendra
    • , Kathleen A. Christie
    • , Beatriz A. Osuna
    • , Rafael Pinilla-Redondo
    • , Benjamin P. Kleinstiver
    •  & Joseph Bondy-Denomy
  • Article |

    Using single-cell imaging of the cyanobacterium Synechococcus, the authors show that confinement or mechanical perturbations result in altered photosynthetic activity.

    • Kristin A. Moore
    • , Sabina Altus
    • , Jian W. Tay
    • , Janet B. Meehl
    • , Evan B. Johnson
    • , David M. Bortz
    •  & Jeffrey C. Cameron
  • Letter |

    The identification of the KinB–AlgB two-component system, known to modulate alginate biosynthesis, together with downstream proteins that repress the Type I-F CRISPR–Cas system in Pseudomonas aeruginosa, elucidates how bacteria control the expression of nucleolytic host defence systems to minimize the potential risks of self-targeting.

    • Adair L. Borges
    • , Bardo Castro
    • , Sutharsan Govindarajan
    • , Tina Solvik
    • , Veronica Escalante
    •  & Joseph Bondy-Denomy
  • Article |

    In this Article, the authors identify the mechanism of influenza virus transcription in viral ribonucleoproteins (vRNPs). This processive helical track mechanism is enabled by the extreme flexibility of the helical part of the vRNP, which allows the polymerase to move over the genome while bound to both RNA ends.

    • Rocío Coloma
    • , Rocío Arranz
    • , José M. de la Rosa-Trevín
    • , Carlos O. S. Sorzano
    • , Sandie Munier
    • , Diego Carlero
    • , Nadia Naffakh
    • , Juan Ortín
    •  & Jaime Martín-Benito
  • Letter |

    The crystal structure of the RodA–PBP2 complex from Thermus thermophilus elucidates how binding between these two proteins regulates their abilities to polymerize and crosslink peptidoglycan during bacterial cell wall synthesis.

    • Megan Sjodt
    • , Patricia D. A. Rohs
    • , Morgan S. A. Gilman
    • , Sarah C. Erlandson
    • , Sanduo Zheng
    • , Anna G. Green
    • , Kelly P. Brock
    • , Atsushi Taguchi
    • , Daniel Kahne
    • , Suzanne Walker
    • , Debora S. Marks
    • , David Z. Rudner
    • , Thomas G. Bernhardt
    •  & Andrew C. Kruse
  • Article |

    The replication of hepatitis B virus involves the formation of covalently closed circular DNA (cccDNA), which relies on a set of undefined host factors. Here, the authors use a cell-free system to reconstitute cccDNA formation and identify the minimal set of host factors required, which are components of the lagging-DNA-strand replication machinery.

    • Lei Wei
    •  & Alexander Ploss