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  • Structural basis for placental malaria mediated by Plasmodium falciparum VAR2CSA
    Nat. Microbiol. (IF 15.54) Pub Date : 2021-01-15
    Rui Ma; Tengfei Lian; Rick Huang; Jonathan P. Renn; Jennifer D. Petersen; Joshua Zimmerberg; Patrick E. Duffy; Niraj H. Tolia

    Plasmodium falciparum VAR2CSA binds to chondroitin sulfate A (CSA) on the surface of the syncytiotrophoblast during placental malaria. This interaction facilitates placental sequestration of malaria parasites resulting in severe health outcomes for both the mother and her offspring. Furthermore, CSA is presented by diverse cancer cells and specific targeting of cells by VAR2CSA may become a viable

    更新日期:2021-01-16
  • Bacteriophage-resistant Acinetobacter baumannii are resensitized to antimicrobials
    Nat. Microbiol. (IF 15.54) Pub Date : 2021-01-11
    Fernando Gordillo Altamirano; John H. Forsyth; Ruzeen Patwa; Xenia Kostoulias; Michael Trim; Dinesh Subedi; Stuart K. Archer; Faye C. Morris; Cody Oliveira; Luisa Kielty; Denis Korneev; Moira K. O’Bryan; Trevor J. Lithgow; Anton Y. Peleg; Jeremy J. Barr

    We characterized two bacteriophages, ΦFG02 and ΦCO01, against clinical isolates of Acinetobacter baumannii and established that the bacterial capsule is the receptor for these phages. Phage-resistant mutants harboured loss-of-function mutations in genes responsible for capsule biosynthesis, resulting in capsule loss and disruption of phage adsorption. The phage-resistant strains were resensitized to

    更新日期:2021-01-11
  • Comparative proteomics identifies Schlafen 5 (SLFN5) as a herpes simplex virus restriction factor that suppresses viral transcription
    Nat. Microbiol. (IF 15.54) Pub Date : 2021-01-11
    Eui Tae Kim; Joseph M. Dybas; Katarzyna Kulej; Emigdio D. Reyes; Alexander M. Price; Lisa N. Akhtar; Ann Orr; Benjamin A. Garcia; Chris Boutell; Matthew D. Weitzman

    Intrinsic antiviral host factors confer cellular defence by limiting virus replication and are often counteracted by viral countermeasures. We reasoned that host factors that inhibit viral gene expression could be identified by determining proteins bound to viral DNA (vDNA) in the absence of key viral antagonists. Herpes simplex virus 1 (HSV-1) expresses E3 ubiquitin-protein ligase ICP0 (ICP0), which

    更新日期:2021-01-11
  • Spatial integration of transcription and splicing in a dedicated compartment sustains monogenic antigen expression in African trypanosomes
    Nat. Microbiol. (IF 15.54) Pub Date : 2021-01-11
    Joana Faria; Vanessa Luzak; Laura S. M. Müller; Benedikt G. Brink; Sebastian Hutchinson; Lucy Glover; David Horn; T. Nicolai Siegel

    Highly selective gene expression is a key requirement for antigenic variation in several pathogens, allowing evasion of host immune responses and maintenance of persistent infections1. African trypanosomes—parasites that cause lethal diseases in humans and livestock—employ an antigenic variation mechanism that involves monogenic antigen expression from a pool of >2,600 antigen-coding genes2. In other

    更新日期:2021-01-11
  • Bifidobacterium bifidum strains synergize with immune checkpoint inhibitors to reduce tumour burden in mice
    Nat. Microbiol. (IF 15.54) Pub Date : 2021-01-11
    Se-Hoon Lee; Sung-Yup Cho; Youngmin Yoon; Changho Park; Jinyoung Sohn; Jin-Ju Jeong; Bu-Nam Jeon; Mongjoo Jang; Choa An; Suro Lee; Yun Yeon Kim; Gihyeon Kim; Sujeong Kim; Yunjae Kim; Gwang Bin Lee; Eun Ju Lee; Sang Gyun Kim; Hong Sook Kim; Yeongmin Kim; Hyun Kim; Hyun-Suk Yang; Sarang Kim; Seonggon Kim; Hayung Chung; Myeong Hee Moon; Myung Hee Nam; Jee Young Kwon; Sungho Won; Joon-Suk Park; George

    The gut microbiome can influence the development of tumours and the efficacy of cancer therapeutics1,2,3,4,5; however, the multi-omics characteristics of antitumour bacterial strains have not been fully elucidated. In this study, we integrated metagenomics, genomics and transcriptomics of bacteria, and analyses of mouse intestinal transcriptome and serum metabolome data to reveal an additional mechanism

    更新日期:2021-01-11
  • Escherichia coli Rho GTPase-activating toxin CNF1 mediates NLRP3 inflammasome activation via p21-activated kinases-1/2 during bacteraemia in mice
    Nat. Microbiol. (IF 15.54) Pub Date : 2021-01-11
    Océane Dufies; Anne Doye; Johan Courjon; Cédric Torre; Gregory Michel; Celine Loubatier; Arnaud Jacquel; Paul Chaintreuil; Alissa Majoor; Rodolphe R. Guinamard; Alexandre Gallerand; Pedro H. V. Saavedra; Els Verhoeyen; Amaury Rey; Sandrine Marchetti; Raymond Ruimy; Dorota Czerucka; Mohamed Lamkanfi; Bénédicte F. Py; Patrick Munro; Orane Visvikis; Laurent Boyer

    Inflammasomes are signalling platforms that are assembled in response to infection or sterile inflammation by cytosolic pattern recognition receptors. The consequent inflammasome-triggered caspase-1 activation is critical for the host defence against pathogens. During infection, NLRP3, which is a pattern recognition receptor that is also known as cryopyrin, triggers the assembly of the inflammasome-activating

    更新日期:2021-01-11
  • Structure and mechanism of the proton-driven motor that powers type 9 secretion and gliding motility
    Nat. Microbiol. (IF 15.54) Pub Date : 2021-01-11
    Rory Hennell James; Justin C. Deme; Andreas Kjӕr; Felicity Alcock; Augustinas Silale; Frédéric Lauber; Steven Johnson; Ben C. Berks; Susan M. Lea

    Three classes of ion-driven protein motors have been identified to date: ATP synthase, the bacterial flagellar motor and a proton-driven motor that powers gliding motility and the type 9 protein secretion system in Bacteroidetes bacteria. Here, we present cryo-electron microscopy structures of the gliding motility/type 9 protein secretion system motors GldLM from Flavobacterium johnsoniae and PorLM

    更新日期:2021-01-11
  • Publisher Correction: Quantitative image analysis of microbial communities with BiofilmQ
    Nat. Microbiol. (IF 15.54) Pub Date : 2021-01-08
    Raimo Hartmann; Hannah Jeckel; Eric Jelli; Praveen K. Singh; Sanika Vaidya; Miriam Bayer; Daniel K. H. Rode; Lucia Vidakovic; Francisco Díaz-Pascual; Jiunn C. N. Fong; Anna Dragoš; Olga Lamprecht; Janne G. Thöming; Niklas Netter; Susanne Häussler; Carey D. Nadell; Victor Sourjik; Ákos T. Kovács; Fitnat H. Yildiz; Knut Drescher

    A Correction to this paper has been published: https://doi.org/10.1038/s41564-021-00863-6.

    更新日期:2021-01-08
  • RNA antitoxin SprF1 binds ribosomes to attenuate translation and promote persister cell formation in Staphylococcus aureus
    Nat. Microbiol. (IF 15.54) Pub Date : 2021-01-04
    Marie-Laure Pinel-Marie; Régine Brielle; Camille Riffaud; Noëlla Germain-Amiot; Norbert Polacek; Brice Felden

    Persister cells are a subpopulation of transiently antibiotic-tolerant bacteria associated with chronic infection and antibiotic treatment failure. Toxin–antitoxin systems have been linked to persister cell formation but the molecular mechanisms leading to bacterial persistence are mostly unknown. Here, we show that SprF1, a type I antitoxin, associates with translating ribosomes from the major human

    更新日期:2021-01-04
  • Dinoflagellates alter their carbon and nutrient metabolic strategies across environmental gradients in the central Pacific Ocean
    Nat. Microbiol. (IF 15.54) Pub Date : 2021-01-04
    Natalie R. Cohen; Matthew R. McIlvin; Dawn M. Moran; Noelle A. Held; Jaclyn K. Saunders; Nicholas J. Hawco; Michael Brosnahan; Giacomo R. DiTullio; Carl Lamborg; John P. McCrow; Chris L. Dupont; Andrew E. Allen; Mak A. Saito

    Marine microeukaryotes play a fundamental role in biogeochemical cycling through the transfer of energy to higher trophic levels and vertical carbon transport. Despite their global importance, microeukaryote physiology, nutrient metabolism and contributions to carbon cycling across offshore ecosystems are poorly characterized. Here, we observed the prevalence of dinoflagellates along a 4,600-km meridional

    更新日期:2021-01-04
  • Quantitative image analysis of microbial communities with BiofilmQ
    Nat. Microbiol. (IF 15.54) Pub Date : 2021-01-04
    Raimo Hartmann; Hannah Jeckel; Eric Jelli; Praveen K. Singh; Sanika Vaidya; Miriam Bayer; Daniel K. H. Rode; Lucia Vidakovic; Francisco Díaz-Pascual; Jiunn C. N. Fong; Anna Dragoš; Olga Lamprecht; Janne G. Thöming; Niklas Netter; Susanne Häussler; Carey D. Nadell; Victor Sourjik; Ákos T. Kovács; Fitnat H. Yildiz; Knut Drescher

    Biofilms are microbial communities that represent a highly abundant form of microbial life on Earth. Inside biofilms, phenotypic and genotypic variations occur in three-dimensional space and time; microscopy and quantitative image analysis are therefore crucial for elucidating their functions. Here, we present BiofilmQ—a comprehensive image cytometry software tool for the automated and high-throughput

    更新日期:2021-01-04
  • The Rcs stress response inversely controls surface and CRISPR–Cas adaptive immunity to discriminate plasmids and phages
    Nat. Microbiol. (IF 15.54) Pub Date : 2021-01-04
    Leah M. Smith; Simon A. Jackson; Lucia M. Malone; James E. Ussher; Paul P. Gardner; Peter C. Fineran

    Bacteria harbour multiple innate defences and adaptive CRISPR–Cas systems that provide immunity against bacteriophages and mobile genetic elements. Although some bacteria modulate defences in response to population density, stress and metabolic state, a lack of high-throughput methods to systematically reveal regulators has hampered efforts to understand when and how immune strategies are deployed

    更新日期:2021-01-04
  • Trace gas oxidizers are widespread and active members of soil microbial communities
    Nat. Microbiol. (IF 15.54) Pub Date : 2021-01-04
    Sean K. Bay; Xiyang Dong; James A. Bradley; Pok Man Leung; Rhys Grinter; Thanavit Jirapanjawat; Stefan K. Arndt; Perran L. M. Cook; Douglas E. LaRowe; Philipp A. Nauer; Eleonora Chiri; Chris Greening

    Soil microorganisms globally are thought to be sustained primarily by organic carbon sources. Certain bacteria also consume inorganic energy sources such as trace gases, but they are presumed to be rare community members, except within some oligotrophic soils. Here we combined metagenomic, biogeochemical and modelling approaches to determine how soil microbial communities meet energy and carbon needs

    更新日期:2021-01-04
  • Metabolic cooperation and spatiotemporal niche partitioning in a kefir microbial community
    Nat. Microbiol. (IF 15.54) Pub Date : 2021-01-04
    Sonja Blasche; Yongkyu Kim; Ruben A. T. Mars; Daniel Machado; Maria Maansson; Eleni Kafkia; Alessio Milanese; Georg Zeller; Bas Teusink; Jens Nielsen; Vladimir Benes; Rute Neves; Uwe Sauer; Kiran Raosaheb Patil

    Microbial communities often undergo intricate compositional changes yet also maintain stable coexistence of diverse species. The mechanisms underlying long-term coexistence remain unclear as system-wide studies have been largely limited to engineered communities, ex situ adapted cultures or synthetic assemblies. Here, we show how kefir, a natural milk-fermenting community of prokaryotes (predominantly

    更新日期:2021-01-04
  • Nature Microbiology at 5
    Nat. Microbiol. (IF 15.54) Pub Date : 2020-12-21

    In the past five years Nature Microbiology has championed research and commentary across the breadth of the discipline. Going forwards, we will expand our scope to include the biology and applications of microorganisms that can help to address the pressing issues of global change and sustainable living.

    更新日期:2020-12-21
  • Make equity essential to expedite change in academia
    Nat. Microbiol. (IF 15.54) Pub Date : 2020-12-21
    Beronda L. Montgomery

    In response to COVID-19, universities and other education providers pivoted rapidly from in-class learning to digital course instruction. Student tuition was deemed essential, thus swift change ensued. Similarly, if equity, diversity and inclusion are truly deemed essential at those same institutions, change could occur now — not later.

    更新日期:2020-12-21
  • Commensal pneumococci go nuclear
    Nat. Microbiol. (IF 15.54) Pub Date : 2020-12-21
    Elaine I. Tuomanen

    Commensal pneumococci convert invasive diseases to peaceful colonizers by commandeering the host nuclear KDM6B demethylase to mark NF-κB sites of the IL-11 cytokine promoter and increase epithelium repair.

    更新日期:2020-12-21
  • Crosstalking second messengers
    Nat. Microbiol. (IF 15.54) Pub Date : 2020-12-21
    Regine Hengge

    By competing for the same binding site on SmbA, a regulatory nucleotide-binding protein, the bacterial second messengers c-di-GMP and (p)ppGpp inversely balance cell cycle re-entry of growth-arrested swarmer cells of Caulobacter crescentus.

    更新日期:2020-12-21
  • Community-led, integrated, reproducible multi-omics with anvi’o
    Nat. Microbiol. (IF 15.54) Pub Date : 2020-12-21
    A. Murat Eren; Evan Kiefl; Alon Shaiber; Iva Veseli; Samuel E. Miller; Matthew S. Schechter; Isaac Fink; Jessica N. Pan; Mahmoud Yousef; Emily C. Fogarty; Florian Trigodet; Andrea R. Watson; Özcan C. Esen; Ryan M. Moore; Quentin Clayssen; Michael D. Lee; Veronika Kivenson; Elaina D. Graham; Bryan D. Merrill; Antti Karkman; Daniel Blankenberg; John M. Eppley; Andreas Sjödin; Jarrod J. Scott; Xabier

    Big data abound in microbiology, but the workflows designed to enable researchers to interpret data can constrain the biological questions that can be asked. Five years after anvi’o was first published, this community-led multi-omics platform is maturing into an open software ecosystem that reduces constraints in ‘omics data analyses.

    更新日期:2020-12-21
  • Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland
    Nat. Microbiol. (IF 15.54) Pub Date : 2020-12-21
    Ana da Silva Filipe; James G. Shepherd; Thomas Williams; Joseph Hughes; Elihu Aranday-Cortes; Patawee Asamaphan; Shirin Ashraf; Carlos Balcazar; Kirstyn Brunker; Alasdair Campbell; Stephen Carmichael; Chris Davis; Rebecca Dewar; Michael D. Gallagher; Rory Gunson; Verity Hill; Antonia Ho; Ben Jackson; Edward James; Natasha Jesudason; Natasha Johnson; E. Carol McWilliam Leitch; Kathy Li; Alasdair MacLean;

    Coronavirus disease 2019 (COVID-19) was first diagnosed in Scotland on 1 March 2020. During the first month of the outbreak, 2,641 cases of COVID-19 led to 1,832 hospital admissions, 207 intensive care admissions and 126 deaths. We aimed to identify the source and number of introductions of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) into Scotland using a combined phylogenetic and

    更新日期:2020-12-21
  • Stepwise evolution of Salmonella Typhimurium ST313 causing bloodstream infection in Africa
    Nat. Microbiol. (IF 15.54) Pub Date : 2020-12-21
    Caisey V. Pulford; Blanca M. Perez-Sepulveda; Rocío Canals; Jessica A. Bevington; Rebecca J. Bengtsson; Nicolas Wenner; Ella V. Rodwell; Benjamin Kumwenda; Xiaojun Zhu; Rebecca J. Bennett; George E. Stenhouse; P. Malaka De Silva; Hermione J. Webster; Jose A. Bengoechea; Amy Dumigan; Alicia Tran-Dien; Reenesh Prakash; Happy C. Banda; Lovemore Alufandika; Mike P. Mautanga; Arthur Bowers-Barnard; Alexandra

    Bloodstream infections caused by nontyphoidal Salmonella are a major public health concern in Africa, causing ~49,600 deaths every year. The most common Salmonella enterica pathovariant associated with invasive nontyphoidal Salmonella disease is Salmonella Typhimurium sequence type (ST)313. It has been proposed that antimicrobial resistance and genome degradation has contributed to the success of ST313

    更新日期:2020-12-21
  • The histone demethylase KDM6B fine-tunes the host response to Streptococcus pneumoniae
    Nat. Microbiol. (IF 15.54) Pub Date : 2020-12-21
    Michael G. Connor; Tiphaine M. N. Camarasa; Emma Patey; Orhan Rasid; Laura Barrio; Caroline M. Weight; Daniel P. Miller; Robert S. Heyderman; Richard J. Lamont; Jost Enninga; Melanie A. Hamon

    Streptococcus pneumoniae is a natural colonizer of the human respiratory tract and an opportunistic pathogen. Although epithelial cells are among the first to encounter pneumococci, the cellular processes and contribution of epithelial cells to the host response are poorly understood. Here, we show that a S. pneumoniae serotype 6B ST90 strain, which does not cause disease in a murine infection model

    更新日期:2020-12-21
  • The SARS-CoV-2 RNA–protein interactome in infected human cells
    Nat. Microbiol. (IF 15.54) Pub Date : 2020-12-21
    Nora Schmidt; Caleb A. Lareau; Hasmik Keshishian; Sabina Ganskih; Cornelius Schneider; Thomas Hennig; Randy Melanson; Simone Werner; Yuanjie Wei; Matthias Zimmer; Jens Ade; Luisa Kirschner; Sebastian Zielinski; Lars Dölken; Eric S. Lander; Neva Caliskan; Utz Fischer; Jörg Vogel; Steven A. Carr; Jochen Bodem; Mathias Munschauer

    Characterizing the interactions that SARS-CoV-2 viral RNAs make with host cell proteins during infection can improve our understanding of viral RNA functions and the host innate immune response. Using RNA antisense purification and mass spectrometry, we identified up to 104 human proteins that directly and specifically bind to SARS-CoV-2 RNAs in infected human cells. We integrated the SARS-CoV-2 RNA

    更新日期:2020-12-21
  • Responses to acute infection with SARS-CoV-2 in the lungs of rhesus macaques, baboons and marmosets
    Nat. Microbiol. (IF 15.54) Pub Date : 2020-12-18
    Dhiraj Kumar Singh; Bindu Singh; Shashank R. Ganatra; Michal Gazi; Journey Cole; Rajesh Thippeshappa; Kendra J. Alfson; Elizabeth Clemmons; Olga Gonzalez; Ruby Escobedo; Tae-Hyung Lee; Ayan Chatterjee; Yenny Goez-Gazi; Riti Sharan; Maya Gough; Cynthia Alvarez; Alyssa Blakley; Justin Ferdin; Carmen Bartley; Hilary Staples; Laura Parodi; Jessica Callery; Amanda Mannino; Benjamin Klaffke; Priscilla Escareno;

    Non-human primate models will expedite therapeutics and vaccines for coronavirus disease 2019 (COVID-19) to clinical trials. Here, we compare acute severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in young and old rhesus macaques, baboons and old marmosets. Macaques had clinical signs of viral infection, mild to moderate pneumonitis and extra-pulmonary pathologies, and both age

    更新日期:2020-12-18
  • Therapeutically administered ribonucleoside analogue MK-4482/EIDD-2801 blocks SARS-CoV-2 transmission in ferrets
    Nat. Microbiol. (IF 15.54) Pub Date : 2020-12-03
    Robert M. Cox; Josef D. Wolf; Richard K. Plemper

    The coronavirus disease 2019 (COVID-19) pandemic is having a catastrophic impact on human health1. Widespread community transmission has triggered stringent distancing measures with severe socio-economic consequences. Gaining control of the pandemic will depend on the interruption of transmission chains until vaccine-induced or naturally acquired protective herd immunity arises. However, approved antiviral

    更新日期:2020-12-03
  • A DNA-based vaccine protects against Crimean-Congo haemorrhagic fever virus disease in a Cynomolgus macaque model
    Nat. Microbiol. (IF 15.54) Pub Date : 2020-11-30
    David W. Hawman; Gustaf Ahlén; K. Sofia Appelberg; Kimberly Meade-White; Patrick W. Hanley; Dana Scott; Vanessa Monteil; Stephanie Devignot; Atsushi Okumura; Friedemann Weber; Heinz Feldmann; Matti Sällberg; Ali Mirazimi

    There is currently no specific prophylaxis or vaccine against Crimean-Congo haemorrhagic fever virus (CCHFV). Crimean-Congo haemorrhagic fever (CCHF) is a severe febrile illness transmitted by Hyalomma ticks in endemic areas, handling of infected livestock or care of infected patients. We report here the successful protection against CCHFV-mediated disease in a non-human primate disease model. Cynomolgus

    更新日期:2020-12-01
  • Getting a grip on blast
    Nat. Microbiol. (IF 15.54) Pub Date : 2020-11-19
    Andrew J. Foster; Nicholas J. Talbot

    Spermine is essential for adhesion to the hydrophobic rice leaf surface by the blast fungus Magnaporthe oryzae during infection.

    更新日期:2020-11-19
  • A new spin on flagellar rotation
    Nat. Microbiol. (IF 15.54) Pub Date : 2020-11-19
    Natalie S. Al-Otaibi; Julien R. C. Bergeron

    Many bacteria rely on their flagella for motility, yet the molecular mechanism of flagellar rotation was previously unclear. Recently, multiple papers solved the atomic structure of the bacterial flagellum stator complex, elucidating how these intricate molecular machines operate.

    更新日期:2020-11-19
  • Our microbiology coverage in 2020
    Nat. Microbiol. (IF 15.54) Pub Date : 2020-11-19

    Microbiology has been front and centre during the ongoing SARS-CoV-2 pandemic. We reflect on the content we published this year and look ahead to aligning output with the Sustainable Development Goals in 2021.

    更新日期:2020-11-19
  • Spike-specific circulating T follicular helper cell and cross-neutralizing antibody responses in COVID-19-convalescent individuals
    Nat. Microbiol. (IF 15.54) Pub Date : 2020-11-16
    Jian Zhang; Qian Wu; Ziyan Liu; Qijie Wang; Jiajing Wu; Yabin Hu; Tingting Bai; Ting Xie; Mincheng Huang; Tiantian Wu; Danhong Peng; Weijin Huang; Kun Jin; Ling Niu; Wangyuan Guo; Dixian Luo; Dongzhu Lei; Zhijian Wu; Guicheng Li; Renbin Huang; Yingbiao Lin; Xiangping Xie; Shuangyan He; Yunfan Deng; Jianghua Liu; Weilang Li; Zhongyi Lu; Haifu Chen; Ting Zeng; Qingting Luo; Yi-Ping Li; Youchun Wang;

    Coronavirus disease 2019 (COVID-19) is caused by infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)1,2,3 and individuals with COVID-19 have symptoms that can be asymptomatic, mild, moderate or severe4,5. In the early phase of infection, T- and B-cell counts are substantially decreased6,7; however, IgM8,9,10,11 and IgG12,13,14 are detectable within 14 d after symptom onset.

    更新日期:2020-11-16
  • Transcriptional regulator-induced phenotype screen reveals drug potentiators in Mycobacterium tuberculosis
    Nat. Microbiol. (IF 15.54) Pub Date : 2020-11-16
    Shuyi Ma; Robert Morrison; Samuel J. Hobbs; Vijay Soni; Jessica Farrow-Johnson; Andrew Frando; Neil Fleck; Christoph Grundner; Kyu Y. Rhee; Tige R. Rustad; David R. Sherman

    Transposon-based strategies provide a powerful and unbiased way to study the bacterial stress response1,2,3,4,5,6,7,8, but these approaches cannot fully capture the complexities of network-based behaviour. Here, we present a network-based genetic screening approach: the transcriptional regulator-induced phenotype (TRIP) screen, which we used to identify previously uncharacterized network adaptations

    更新日期:2020-11-16
  • Author Correction: Roadmap for naming uncultivated Archaea and Bacteria
    Nat. Microbiol. (IF 15.54) Pub Date : 2020-11-12
    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;

    An amendment to this paper has been published and can be accessed via a link at the top of the paper.

    更新日期:2020-11-13
  • Author Correction: Structures of the stator complex that drives rotation of the bacterial flagellum
    Nat. Microbiol. (IF 15.54) Pub Date : 2020-11-09
    Justin C. Deme; Steven Johnson; Owen Vickery; Amy Aron; Holly Monkhouse; Thomas Griffiths; Rory Hennell James; Ben C. Berks; James W. Coulton; Phillip J. Stansfeld; Susan M. Lea

    An amendment to this paper has been published and can be accessed via a link at the top of the paper.

    更新日期:2020-11-09
  • Structure and reconstitution of a hydrolase complex that may release peptidoglycan from the membrane after polymerization
    Nat. Microbiol. (IF 15.54) Pub Date : 2020-11-09
    Kaitlin Schaefer; Tristan W. Owens; Julia E. Page; Marina Santiago; Daniel Kahne; Suzanne Walker

    Bacteria are encapsulated by a peptidoglycan cell wall that is essential for their survival1. During cell wall assembly, a lipid-linked disaccharide–peptide precursor called lipid II is polymerized and cross-linked to produce mature peptidoglycan. As lipid II is polymerized, nascent polymers remain membrane-anchored at one end, and the other end becomes cross-linked to the matrix2,3,4. How bacteria

    更新日期:2020-11-09
  • Reciprocal growth control by competitive binding of nucleotide second messengers to a metabolic switch in Caulobacter crescentus
    Nat. Microbiol. (IF 15.54) Pub Date : 2020-11-09
    Viktoriya Shyp; Badri Nath Dubey; Raphael Böhm; Johannes Hartl; Jutta Nesper; Julia A. Vorholt; Sebastian Hiller; Tilman Schirmer; Urs Jenal

    Bacteria use small signalling molecules such as (p)ppGpp or c-di-GMP to tune their physiology in response to environmental changes. It remains unclear whether these regulatory networks operate independently or whether they interact to optimize bacterial growth and survival. We report that (p)ppGpp and c-di-GMP reciprocally regulate the growth of Caulobacter crescentus by converging on a single small-molecule-binding

    更新日期:2020-11-09
  • β-Barrel proteins tether the outer membrane in many Gram-negative bacteria
    Nat. Microbiol. (IF 15.54) Pub Date : 2020-11-02
    Kelsi M. Sandoz; Roger A. Moore; Paul A. Beare; Ankur V. Patel; Robert E. Smith; Marshall Bern; Hyea Hwang; Connor J. Cooper; Suzette A. Priola; Jerry M. Parks; James C. Gumbart; Stéphane Mesnage; Robert A. Heinzen

    Gram-negative bacteria have a cell envelope that comprises an outer membrane (OM), a peptidoglycan (PG) layer and an inner membrane (IM)1. The OM and PG are load-bearing, selectively permeable structures that are stabilized by cooperative interactions between IM and OM proteins2,3. In Escherichia coli, Braun’s lipoprotein (Lpp) forms the only covalent tether between the OM and PG and is crucial for

    更新日期:2020-11-02
  • Bacterial–fungal interactions revealed by genome-wide analysis of bacterial mutant fitness
    Nat. Microbiol. (IF 15.54) Pub Date : 2020-11-02
    Emily C. Pierce; Manon Morin; Jessica C. Little; Roland B. Liu; Joanna Tannous; Nancy P. Keller; Kit Pogliano; Benjamin E. Wolfe; Laura M. Sanchez; Rachel J. Dutton

    Microbial interactions are expected to be major determinants of microbiome structure and function. Although fungi are found in diverse microbiomes, their interactions with bacteria remain largely uncharacterized. In this work, we characterize interactions in 16 different bacterial–fungal pairs, examining the impacts of 8 different fungi isolated from cheese rind microbiomes on 2 bacteria (Escherichia

    更新日期:2020-11-02
  • β-Barrels covalently link peptidoglycan and the outer membrane in the α-proteobacterium Brucella abortus
    Nat. Microbiol. (IF 15.54) Pub Date : 2020-11-02
    Pierre Godessart; Adélie Lannoy; Marc Dieu; Sander E. Van der Verren; Patrice Soumillion; Jean-François Collet; Han Remaut; Patricia Renard; Xavier De Bolle

    Gram-negative bacteria are surrounded by a cell envelope that comprises an outer membrane (OM) and an inner membrane that, together, delimit the periplasmic space, which contains the peptidoglycan (PG) sacculus. Covalent anchoring of the OM to the PG is crucial for envelope integrity in Escherichia coli. When the OM is not attached to the PG, the OM forms blebs and detaches from the cell. The Braun

    更新日期:2020-11-02
  • Roles of bacteriophages, plasmids and CRISPR immunity in microbial community dynamics revealed using time-series integrated meta-omics
    Nat. Microbiol. (IF 15.54) Pub Date : 2020-11-02
    Susana Martínez Arbas; Shaman Narayanasamy; Malte Herold; Laura A. Lebrun; Michael R. Hoopmann; Sujun Li; Tony J. Lam; Benoît J. Kunath; Nathan D. Hicks; Cindy M. Liu; Lance B. Price; Cedric C. Laczny; John D. Gillece; James M. Schupp; Paul S. Keim; Robert L. Moritz; Karoline Faust; Haixu Tang; Yuzhen Ye; Alexander Skupin; Patrick May; Emilie E. L. Muller; Paul Wilmes

    Viruses and plasmids (invasive mobile genetic elements (iMGEs)) have important roles in shaping microbial communities, but their dynamic interactions with CRISPR-based immunity remain unresolved. We analysed generation-resolved iMGE–host dynamics spanning one and a half years in a microbial consortium from a biological wastewater treatment plant using integrated meta-omics. We identified 31 bacterial

    更新日期:2020-11-02
  • Symbiosis, virulence and natural-product biosynthesis in entomopathogenic bacteria are regulated by a small RNA
    Nat. Microbiol. (IF 15.54) Pub Date : 2020-11-02
    Nick Neubacher; Nicholas J. Tobias; Michaela Huber; Xiaofeng Cai; Timo Glatter; Sacha J. Pidot; Timothy P. Stinear; Anna Lena Lütticke; Kai Papenfort; Helge B. Bode

    Photorhabdus and Xenorhabdus species have mutualistic associations with nematodes and an entomopathogenic stage1,2 in their life cycles. In both stages, numerous specialized metabolites are produced that have roles in symbiosis and virulence3,4. Although regulators have been implicated in the regulation of these specialized metabolites3,4, how small regulatory RNAs (sRNAs) are involved in this process

    更新日期:2020-11-02
  • Modifying bacterial flagellin to evade Nod-like Receptor CARD 4 recognition enhances protective immunity against Salmonella
    Nat. Microbiol. (IF 15.54) Pub Date : 2020-10-26
    Panagiotis Tourlomousis; John A. Wright; Alessandra S. Bittante; Lee J. Hopkins; Steven J. Webster; Owain J. Bryant; Pietro Mastroeni; Duncan J. Maskell; Clare E. Bryant

    Pattern recognition receptors (PRRs) expressed in antigen-presenting cells are thought to shape pathogen-specific immunity by inducing secretion of costimulatory cytokines during T-cell activation, yet data to support this notion in vivo are scarce. Here, we show that the cytosolic PRR Nod-like Receptor CARD 4 (NLRC4) suppresses, rather than facilitates, effector and memory CD4+ T-cell responses against

    更新日期:2020-10-28
  • Quantifying acquisition and transmission of Enterococcus faecium using genomic surveillance
    Nat. Microbiol. (IF 15.54) Pub Date : 2020-10-26
    Theodore Gouliouris; Francesc Coll; Catherine Ludden; Beth Blane; Kathy E. Raven; Plamena Naydenova; Charles Crawley; Mili Estée Török; David A. Enoch; Nicholas M. Brown; Ewan M. Harrison; Julian Parkhill; Sharon J. Peacock

    Nosocomial acquisition and transmission of vancomycin-resistant Enterococcus faecium (VREfm) is the driver for E. faecium carriage in hospitalized patients, which, in turn, is a risk factor for invasive infection in immunocompromised patients. In the present study, we provide a comprehensive picture of E. faecium transmission in an entire sampled patient population using a sequence-driven approach

    更新日期:2020-10-28
  • Longitudinal observation and decline of neutralizing antibody responses in the three months following SARS-CoV-2 infection in humans
    Nat. Microbiol. (IF 15.54) Pub Date : 2020-10-26
    Jeffrey Seow; Carl Graham; Blair Merrick; Sam Acors; Suzanne Pickering; Kathryn J. A. Steel; Oliver Hemmings; Aoife O’Byrne; Neophytos Kouphou; Rui Pedro Galao; Gilberto Betancor; Harry D. Wilson; Adrian W. Signell; Helena Winstone; Claire Kerridge; Isabella Huettner; Jose M. Jimenez-Guardeño; Maria Jose Lista; Nigel Temperton; Luke B. Snell; Karen Bisnauthsing; Amelia Moore; Adrian Green; Lauren Martinez;

    Antibody responses to SARS-CoV-2 can be detected in most infected individuals 10–15 d after the onset of COVID-19 symptoms. However, due to the recent emergence of SARS-CoV-2 in the human population, it is not known how long antibody responses will be maintained or whether they will provide protection from reinfection. Using sequential serum samples collected up to 94 d post onset of symptoms (POS)

    更新日期:2020-10-28
  • Language matters in a pandemic
    Nat. Microbiol. (IF 15.54) Pub Date : 2020-10-21

    Do you ‘beat’ or ‘treat’ a virus infection? Are you strong if you survive SARS-CoV-2 but weak if you don’t? Language matters if we are to galvanize people to follow public health guidance during the COVID-19 pandemic.

    更新日期:2020-10-28
  • Phase separation and cell fate in Candida
    Nat. Microbiol. (IF 15.54) Pub Date : 2020-10-21
    Haoping Liu

    Epigenetic switching between white and opaque cell types in Candida is mediated by transcription factors that undergo liquid–liquid phase separation.

    更新日期:2020-10-28
  • Stressed-out gut bacteria are pterin up gut inflammation
    Nat. Microbiol. (IF 15.54) Pub Date : 2020-10-21
    Margaret Alexander; Peter J. Turnbaugh

    Sub-inhibitory levels of an antibiotic switch on cryptic stress pathways in Escherichia coli that result in the production of immunomodulatory molecules.

    更新日期:2020-10-28
  • Crowdsourcing virtual summer research opportunities to support minorities in microbiology
    Nat. Microbiol. (IF 15.54) Pub Date : 2020-10-19
    Michael D. L. Johnson; David A. Baltrus; Jennifer Gardy

    Summer research programmes are renowned for encouraging underrepresented minorities (URMs) to pursue STEM careers, but COVID-19 left many students in the United States unable to participate. We created the National Summer Undergraduate Research Project to matchmake students with mentors, enabling 250 URM students to do summer research.

    更新日期:2020-10-19
  • Extracellular SQSTM1 mediates bacterial septic death in mice through insulin receptor signalling
    Nat. Microbiol. (IF 15.54) Pub Date : 2020-10-19
    Borong Zhou; Jiao Liu; Ling Zeng; Shan Zhu; Haichao Wang; Timothy R. Billiar; Guido Kroemer; Daniel J. Klionsky; Herbert J. Zeh; Jianxin Jiang; Daolin Tang; Rui Kang

    Sepsis is the most common cause of death for patients in intensive care worldwide due to a dysregulated host response to infection. Here, we investigate the role of sequestosome-1 (SQSTM1/p62), an autophagy receptor that functions as a regulator of innate immunity, in sepsis. We find that lipopolysaccharide elicits gasdermin D-dependent pyroptosis to enable passive SQSTM1 release from macrophages and

    更新日期:2020-10-19
  • Metallodrug ranitidine bismuth citrate suppresses SARS-CoV-2 replication and relieves virus-associated pneumonia in Syrian hamsters
    Nat. Microbiol. (IF 15.54) Pub Date : 2020-10-07
    Shuofeng Yuan; Runming Wang; Jasper Fuk-Woo Chan; Anna Jinxia Zhang; Tianfan Cheng; Kenn Ka-Heng Chik; Zi-Wei Ye; Suyu Wang; Andrew Chak-Yiu Lee; Lijian Jin; Hongyan Li; Dong-Yan Jin; Kwok-Yung Yuen; Hongzhe Sun

    SARS-CoV-2 is causing a pandemic of COVID-19, with high infectivity and significant mortality1. Currently, therapeutic options for COVID-19 are limited. Historically, metal compounds have found use as antimicrobial agents, but their antiviral activities have rarely been explored. Here, we test a set of metallodrugs and related compounds, and identify ranitidine bismuth citrate, a commonly used drug

    更新日期:2020-10-07
  • Escherichia coli is engineered to grow on CO 2 and formic acid
    Nat. Microbiol. (IF 15.54) Pub Date : 2020-09-28
    Junho Bang; Chang Hun Hwang; Jung Ho Ahn; Jong An Lee; Sang Yup Lee

    We engineered Escherichia coli to grow on CO2 and formic acid alone by introducing the synthetic CO2 and formic acid assimilation pathway, expressing two formate dehydrogenase genes, fine-tuning metabolic fluxes and optimizing the levels of cytochrome bo3 and bd-I ubiquinol oxidase. Our engineered strain can grow to an optical density at 600 nm of 7.38 in 450 h, and shows promise as a platform strain

    更新日期:2020-09-28
  • Staphylcoccus aureus metabolites promote IL-10.
    Nat. Microbiol. (IF 15.54) Pub Date : 2020-09-22
    Alice Prince

    Glycolytic Staphylococcus aureus generate lactate that targets specific histone deacetylases to stimulate the production of IL-10 and enable biofilm formation.

    更新日期:2020-09-22
  • Author Correction: A nonlinear time-series analysis approach to identify thresholds in associations between population antibiotic use and rates of resistance.
    Nat. Microbiol. (IF 15.54) Pub Date : 2020-09-21
    José-María López-Lozano,Timothy Lawes,César Nebot,Arielle Beyaert,Xavier Bertrand,Didier Hocquet,Mamoon Aldeyab,Michael Scott,Geraldine Conlon-Bingham,David Farren,Gábor Kardos,Adina Fésűs,Jesús Rodríguez-Baño,Pilar Retamar,Nieves Gonzalo-Jiménez,Ian M Gould,

    An amendment to this paper has been published and can be accessed via a link at the top of the paper.

    更新日期:2020-09-22
  • Discovery of broad-spectrum fungicides that block septin-dependent infection processes of pathogenic fungi.
    Nat. Microbiol. (IF 15.54) Pub Date : 2020-09-21
    Min He,Jia Su,Youpin Xu,Jinhua Chen,Mawsheng Chern,Mingliang Lei,Tuo Qi,Zongkuan Wang,Lauren S Ryder,Bozeng Tang,Míriam Osés-Ruiz,Keke Zhu,Yuyan Cao,Xia Yan,Iris Eisermann,Yuan Luo,Weitao Li,Jing Wang,Junjie Yin,Sin Man Lam,Guoxiong Peng,Xiaofang Sun,Xiaobo Zhu,Bingtian Ma,Jichun Wang,Jiali Liu,Hai Qing,Li Song,Long Wang,Qingqing Hou,Peng Qin,Yan Li,Jing Fan,Deqiang Li,Yuping Wang,Xiue Wang,Ling Jiang

    Many pathogenic fungi depend on the development of specialized infection structures called appressoria to invade their hosts and cause disease. Impairing the function of fungal infection structures therefore provides a potential means by which diseases could be prevented. In spite of this extraordinary potential, however, relatively few anti-penetrant drugs have been developed to control fungal diseases

    更新日期:2020-09-22
  • Spermine-mediated tight sealing of the Magnaporthe oryzae appressorial pore-rice leaf surface interface.
    Nat. Microbiol. (IF 15.54) Pub Date : 2020-09-14
    Raquel O Rocha,Christian Elowsky,Ngoc T T Pham,Richard A Wilson

    Cellular adhesion mediates many important plant–microbe interactions. In the devastating blast fungus Magnaporthe oryzae1, powerful glycoprotein-rich mucilage adhesives2 cement melanized and pressurized dome-shaped infection cells—appressoria—to host rice leaf surfaces. Enormous internal turgor pressure is directed onto a penetration peg emerging from the unmelanized, thin-walled pore at the appressorial

    更新日期:2020-09-14
  • Structures of the stator complex that drives rotation of the bacterial flagellum.
    Nat. Microbiol. (IF 15.54) Pub Date : 2020-09-14
    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

    The bacterial flagellum is the prototypical protein nanomachine and comprises a rotating helical propeller attached to a membrane-embedded motor complex. The motor consists of a central rotor surrounded by stator units that couple ion flow across the cytoplasmic membrane to generate torque. Here, we present the structures of the stator complexes from Clostridium sporogenes, Bacillus subtilis and Vibrio

    更新日期:2020-09-14
  • Antibody-dependent enhancement and SARS-CoV-2 vaccines and therapies.
    Nat. Microbiol. (IF 15.54) Pub Date : 2020-09-09
    Wen Shi Lee,Adam K Wheatley,Stephen J Kent,Brandon J DeKosky

    Antibody-based drugs and vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are being expedited through preclinical and clinical development. Data from the study of SARS-CoV and other respiratory viruses suggest that anti-SARS-CoV-2 antibodies could exacerbate COVID-19 through antibody-dependent enhancement (ADE). Previous respiratory syncytial virus and dengue virus vaccine

    更新日期:2020-09-10
  • Near-atomic cryo-electron microscopy structures of varicella-zoster virus capsids.
    Nat. Microbiol. (IF 15.54) Pub Date : 2020-09-07
    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

    Varicella-zoster virus (VZV) is a medically important human herpesvirus that causes chickenpox and shingles, but its cell-associated nature has hindered structure studies. Here we report the cryo-electron microscopy structures of purified VZV A-capsid and C-capsid, as well as of the DNA-containing capsid inside the virion. Atomic models derived from these structures show that, despite enclosing a genome

    更新日期:2020-09-08
  • Anthrax lethal factor cleaves regulatory subunits of phosphoinositide-3 kinase to contribute to toxin lethality.
    Nat. Microbiol. (IF 15.54) Pub Date : 2020-09-07
    Megan A Mendenhall,Shihui Liu,Makayla K Portley,Danielle O'Mard,Rasem Fattah,Roman Szabo,Thomas H Bugge,Jaspal S Khillan,Stephen H Leppla,Mahtab Moayeri

    Anthrax lethal toxin (LT), produced by Bacillus anthracis, comprises a receptor-binding moiety, protective antigen and the lethal factor (LF) protease1,2. Although LF is known to cleave mitogen-activated protein kinase kinases (MEKs/MKKs) and some variants of the NLRP1 inflammasome sensor, targeting of these pathways does not explain the lethality of anthrax toxin1,2. Here we report that the regulatory

    更新日期:2020-09-08