Browse Articles

  • News & Views |

    Severe fever with thrombocytopenia virus is an emerging, highly lethal tick-borne pathogen with growing impact. In this issue of Nature Microbiology, two papers make major progress towards a better understanding of its so far incompletely understood mechanisms of virulence.

    • Jennifer Deborah Wuerth
    •  & Friedemann Weber
  • News & Views |

    Bacteria have previously been assumed to cope with environmental stress by tuning their total number of active ribosomes. Instead, a study in this issue of Nature Microbiology shows that from a heterogeneous pool of ribosomes, Vibrio vulnificus uses ribosomes with a particular ribosomal RNA variant to translate upregulated stress response mRNAs.

    • Kathrin Leppek
    •  & Maria Barna
  • News & Views |

    Molecular players involved in systemic and acute infections are relatively easy to pinpoint, whereas bacterial resilience during chronic infections remains less well understood. Pseudomonas aeruginosa encodes a quorum-regulated virulence factor, TesG, that promotes chronic lung infection by suppressing host inflammatory responses.

    • Alain Filloux
    •  & Jane C. Davies
  • News & Views |

    Klebsiella pneumoniae isolated from patients with primary sclerosing cholangitis was found to cause intestinal barrier dysfunction resulting in T-helper-17-cell-mediated hepatobiliary injury, providing evidence for specific gut-derived, pore-forming pathogens as triggers for immune-mediated liver disease.

    • Peter Fickert
    •  & Hanns-Ulrich Marschall
  • Editorial |

    When accurate and thoughtfully presented, reporting of good science in the popular press should be celebrated and encouraged by researchers. In return, tabloid headline writers should dial down their hyperbolic rhetoric and avoid sensationalism when reporting scientific discoveries.

  • Article |

    Near-atomic resolution structure of bluetongue virus non-structural protein 1 (NS1) provides insights into its dynamic tubular assemblies and their contribution to NS1 function in viral protein synthesis.

    • Adeline Kerviel
    • , Peng Ge
    • , Mason Lai
    • , Jonathan Jih
    • , Mark Boyce
    • , Xing Zhang
    • , Z. Hong Zhou
    •  & Polly Roy
  • Article |

    The structure of adeno-associated virus (AAV) type 2 in complex with its receptor, AAVR, provides new insights on the molecular mechanism of AAV entry into host cells and will serve to optimize the design of AAV vectors for gene therapy.

    • Ran Zhang
    • , Lin Cao
    • , Mengtian Cui
    • , Zixian Sun
    • , Mingxu Hu
    • , Rouxuan Zhang
    • , William Stuart
    • , Xiaochu Zhao
    • , Zirui Yang
    • , Xueming Li
    • , Yuna Sun
    • , Shentao Li
    • , Wei Ding
    • , Zhiyong Lou
    •  & Zihe Rao
  • Letter |

    Selenoproteins—proteins that contain the twenty-first amino acid selenocysteine—were previously thought to be lacking in fungi. Analysis of genomes from early-branching fungal phyla identified selenocysteine machinery and selenoproteins, indicating that these proteins are present in all kingdoms of life.

    • Marco Mariotti
    • , Gustavo Salinas
    • , Toni Gabaldón
    •  & Vadim N. Gladyshev
  • Article |

    Assessment of metagenomic sequencing of cell-free DNA directly from patient samples as a diagnostic for infections.

    • Timothy A. Blauwkamp
    • , Simone Thair
    • , Michael J. Rosen
    • , Lily Blair
    • , Martin S. Lindner
    • , Igor D. Vilfan
    • , Trupti Kawli
    • , Fred C. Christians
    • , Shivkumar Venkatasubrahmanyam
    • , Gregory D. Wall
    • , Anita Cheung
    • , Zoë N. Rogers
    • , Galit Meshulam-Simon
    • , Liza Huijse
    • , Sanjeev Balakrishnan
    • , James V. Quinn
    • , Desiree Hollemon
    • , David K. Hong
    • , Marla Lay Vaughn
    • , Mickey Kertesz
    • , Sivan Bercovici
    • , Judith C. Wilber
    •  & Samuel Yang
  • Publisher Correction |

    • Tommi Vatanen
    • , Damian R. Plichta
    • , Juhi Somani
    • , Philipp C. Münch
    • , Timothy D. Arthur
    • , Andrew Brantley Hall
    • , Sabine Rudolf
    • , Edward J. Oakeley
    • , Xiaobo Ke
    • , Rachel A. Young
    • , Henry J. Haiser
    • , Raivo Kolde
    • , Moran Yassour
    • , Kristiina Luopajärvi
    • , Heli Siljander
    • , Suvi M. Virtanen
    • , Jorma Ilonen
    • , Raivo Uibo
    • , Vallo Tillmann
    • , Sergei Mokurov
    • , Natalya Dorshakova
    • , Jeffrey A. Porter
    • , Alice C. McHardy
    • , Harri Lähdesmäki
    • , Hera Vlamakis
    • , Curtis Huttenhower
    • , Mikael Knip
    •  & Ramnik J. Xavier
  • Article |

    Combining the plaque assay with mass spectrometry imaging allowed high spatiotemporal resolution mapping of metabolites produced during viral infection of the alga Emiliania huxleyi, and revealed a shift in lipid metabolism towards odd-chain fatty acid lipids.

    • Guy Schleyer
    • , Nir Shahaf
    • , Carmit Ziv
    • , Yonghui Dong
    • , Roy A. Meoded
    • , Eric J. N. Helfrich
    • , Daniella Schatz
    • , Shilo Rosenwasser
    • , Ilana Rogachev
    • , Asaph Aharoni
    • , Jörn Piel
    •  & Assaf Vardi
  • Article |

    In Vibrio vulnificus, ribosomes containing variable rRNAs encoded by the rrnI operon (I-ribosomes) preferentially translate a subset of mRNAs involved in bacterial adaptation of environmental changes, establishing divergent rRNAs as regulators of gene expression.

    • Wooseok Song
    • , Minju Joo
    • , Ji-Hyun Yeom
    • , Eunkyoung Shin
    • , Minho Lee
    • , Hyung-Kyoon Choi
    • , Jihwan Hwang
    • , Yong-In Kim
    • , Ramin Seo
    • , J. Eugene Lee
    • , Christopher J. Moore
    • , Yong-Hak Kim
    • , Seong-il Eyun
    • , Yoonsoo Hahn
    • , Jeehyeon Bae
    •  & Kangseok Lee
  • Article |

    Correlation of microbiome features with host quality of life and depression identified specific taxa and microbial pathways in two independent, large population cohorts, identifying links between microbial neuroactive potential and depression.

    • Mireia Valles-Colomer
    • , Gwen Falony
    • , Youssef Darzi
    • , Ettje F. Tigchelaar
    • , Jun Wang
    • , Raul Y. Tito
    • , Carmen Schiweck
    • , Alexander Kurilshikov
    • , Marie Joossens
    • , Cisca Wijmenga
    • , Stephan Claes
    • , Lukas Van Oudenhove
    • , Alexandra Zhernakova
    • , Sara Vieira-Silva
    •  & Jeroen Raes
  • Article |

    By combining imaging and single-cell RNA sequencing, the authors identify genes regulated during cell growth and division and further analyse the heterogeneity of gene expression during adaptive and acute responses to changing environments.

    • Malika Saint
    • , François Bertaux
    • , Wenhao Tang
    • , Xi-Ming Sun
    • , Laurence Game
    • , Anna Köferle
    • , Jürg Bähler
    • , Vahid Shahrezaei
    •  & Samuel Marguerat
  • Article |

    Suppressive combination antiretroviral therapy fails to eradicate HIV-1 latent reservoirs in poorly characterized cell compartments. Here, urethral macrophages, but not urethral T cells, are shown to contain integrated HIV-1 DNA and to be able to release infectious HIV-1 following reactivation with lipopolysaccharide.

    • Yonatan Ganor
    • , Fernando Real
    • , Alexis Sennepin
    • , Charles-Antoine Dutertre
    • , Lisa Prevedel
    • , Lin Xu
    • , Daniela Tudor
    • , Bénédicte Charmeteau
    • , Anne Couedel-Courteille
    • , Sabrina Marion
    • , Ali-Redha Zenak
    • , Jean-Pierre Jourdain
    • , Zhicheng Zhou
    • , Alain Schmitt
    • , Claude Capron
    • , Eliseo A Eugenin
    • , Rémi Cheynier
    • , Marc Revol
    • , Sarra Cristofari
    • , Anne Hosmalin
    •  & Morgane Bomsel
  • Article |

    By combining a yeast single-cell RNA-seq method that counts transcript start sites in a strand- and isoform-specific manner with index sorting, the authors uncover a linear relationship between cell size and RNA content and extreme cell heterogeneity in the expression of metabolic genes.

    • Mariona Nadal-Ribelles
    • , Saiful Islam
    • , Wu Wei
    • , Pablo Latorre
    • , Michelle Nguyen
    • , Eulàlia de Nadal
    • , Francesc Posas
    •  & Lars M. Steinmetz
  • Publisher Correction |

    • Yusuke Okuno
    • , Takayuki Murata
    • , Yoshitaka Sato
    • , Hideki Muramatsu
    • , Yoshinori Ito
    • , Takahiro Watanabe
    • , Tatsuya Okuno
    • , Norihiro Murakami
    • , Kenichi Yoshida
    • , Akihisa Sawada
    • , Masami Inoue
    • , Keisei Kawa
    • , Masao Seto
    • , Koichi Ohshima
    • , Yuichi Shiraishi
    • , Kenichi Chiba
    • , Hiroko Tanaka
    • , Satoru Miyano
    • , Yohei Narita
    • , Masahiro Yoshida
    • , Fumi Goshima
    • , Jun-ichi Kawada
    • , Tetsuya Nishida
    • , Hitoshi Kiyoi
    • , Seiichi Kato
    • , Shigeo Nakamura
    • , Satoko Morishima
    • , Tetsushi Yoshikawa
    • , Shigeyoshi Fujiwara
    • , Norio Shimizu
    • , Yasushi Isobe
    • , Masaaki Noguchi
    • , Atsushi Kikuta
    • , Keiji Iwatsuki
    • , Yoshiyuki Takahashi
    • , Seiji Kojima
    • , Seishi Ogawa
    •  & Hiroshi Kimura
  • Letter |

    A member of the importin-β protein family, transportin 1, binds to influenza A virus matrix protein M1 and promotes its removal from the viral ribonucleoproteins (vRNPs), enabling disassembly of vRNP bundles, vRNP interaction with importin-α/β and entry into the nucleus.

    • Yasuyuki Miyake
    • , Jeremy J. Keusch
    • , Laure Decamps
    • , Hung Ho-Xuan
    • , Sho Iketani
    • , Heinz Gut
    • , Ulrike Kutay
    • , Ari Helenius
    •  & Yohei Yamauchi
  • Article | | open

    Here the authors discover megaphages, or Lak phages, with genomes >540 kilobases in length in the gut microbiomes of a range of hosts, identify Prevotella as the bacterial host and suggest that these phages are common members of the mammalian gut microbiome.

    • Audra E. Devoto
    • , Joanne M. Santini
    • , Matthew R. Olm
    • , Karthik Anantharaman
    • , Patrick Munk
    • , Jenny Tung
    • , Elizabeth A. Archie
    • , Peter J. Turnbaugh
    • , Kimberley D. Seed
    • , Ran Blekhman
    • , Frank M. Aarestrup
    • , Brian C. Thomas
    •  & Jillian F. Banfield
  • Brief Communication |

    Adaptive laboratory evolution experiments in Escherichia coli show that the pseudogene efeU can be repaired to restore the bacterium’s iron uptake system, demonstrating that pseudogenes may serve as an ‘adaptive repertoire’ of selectable traits.

    • Amitesh Anand
    • , Connor A. Olson
    • , Laurence Yang
    • , Anand V. Sastry
    • , Edward Catoiu
    • , Kumari Sonal Choudhary
    • , Patrick V. Phaneuf
    • , Troy E. Sandberg
    • , Sibei Xu
    • , Ying Hefner
    • , Richard Szubin
    • , Adam M. Feist
    •  & Bernhard O. Palsson
  • Letter |

    Classically, peptidoglycan (PG) synthesis was thought to be mediated solely by class A penicillin-binding proteins (PBPs) and related enzymes, a view changed by the identification of RodA as a PG polymerase. Now FtsW is also shown to polymerize PG, in a process that requires complex formation with a partner class B PBP.

    • Atsushi Taguchi
    • , Michael A. Welsh
    • , Lindsey S. Marmont
    • , Wonsik Lee
    • , Megan Sjodt
    • , Andrew C. Kruse
    • , Daniel Kahne
    • , Thomas G. Bernhardt
    •  & Suzanne Walker
  • Article |

    Leishmania exosomes function as viral envelopes for Leishmania RNA virus 1 (LRV1) and facilitate LRV1 transmission, resulting in more aggressive mucocutaneous disease triggered in response to the double-stranded RNA virus in the mammalian host.

    • Vanessa Diniz Atayde
    • , Alonso da Silva Lira Filho
    • , Visnu Chaparro
    • , Aude Zimmermann
    • , Caroline Martel
    • , Maritza Jaramillo
    •  & Martin Olivier
  • News & Views |

    Sterols are a hallmark of eukaryotes. So how do hordes of primitive eukaryotes survive and thrive without a key enzyme for making these crucial lipids? We now learn what solution evolution arrived at — invention of an alternative enzyme that does the same job.

    • Matthew A. B. Baker
    •  & Andrew J. Brown
  • News & Views |

    A secreted effector from the plant pathogenic fungus Ustilago maydis has evolved to acquire a new function that contributes to the unique lifestyle of this species, highlighting the utility of using comparative genetic analyses to address current questions in plant–microorganism interactions.

    • Erin K. Zess
    • , Aleksandra Białas
    •  & Sophien Kamoun
  • Editorial |

    Researchers can be expected to employ a vast range of experimental techniques in pursuit of a scientific question. Making efforts to seek expert advice and develop the competency to generate, store and analyse high-quality data when first using an approach will save time in the long run.

  • News & Views |

    Only a tiny fraction of bacterial species can be cultured and engineered in the laboratory, limiting our ability to deploy bacteria in harsh environments or use them to produce important compounds. Recent work has opened this frontier by developing new methods to characterize and engineer diverse, undomesticated bacterial species.

    • Elizabeth A. Libby
    •  & Pamela A. Silver
  • Letter |

    Genome sequencing of fractionated T-, B- and natural killer cells from patients with chronic active Epstein–Barr virus (EBV) infection sheds light on the nature of the EBV-infected progenitor and suggests a link between intragenic EBV deletions and EBV-associated neoplastic proliferations.

    • Yusuke Okuno
    • , Takayuki Murata
    • , Yoshitaka Sato
    • , Hideki Muramatsu
    • , Yoshinori Ito
    • , Takahiro Watanabe
    • , Tatsuya Okuno
    • , Norihiro Murakami
    • , Kenichi Yoshida
    • , Akihisa Sawada
    • , Masami Inoue
    • , Keisei Kawa
    • , Masao Seto
    • , Koichi Ohshima
    • , Yuichi Shiraishi
    • , Kenichi Chiba
    • , Hiroko Tanaka
    • , Satoru Miyano
    • , Yohei Narita
    • , Masahiro Yoshida
    • , Fumi Goshima
    • , Jun-ichi Kawada
    • , Tetsuya Nishida
    • , Hitoshi Kiyoi
    • , Seiichi Kato
    • , Shigeo Nakamura
    • , Satoko Morishima
    • , Tetsushi Yoshikawa
    • , Shigeyoshi Fujiwara
    • , Norio Shimizu
    • , Yasushi Isobe
    • , Masaaki Noguchi
    • , Atsushi Kikuta
    • , Keiji Iwatsuki
    • , Yoshiyuki Takahashi
    • , Seiji Kojima
    • , Seishi Ogawa
    •  & Hiroshi Kimura
  • Article |

    Klebsiella pneumoniae from the gut microbiota of patients with primary sclerosing cholangitis (PSC) can damage the intestinal epithelial barrier, resulting in bacterial translocation and T helper 17 cell responses in the liver, indicating a role in PSC pathogenesis.

    • Nobuhiro Nakamoto
    • , Nobuo Sasaki
    • , Ryo Aoki
    • , Kentaro Miyamoto
    • , Wataru Suda
    • , Toshiaki Teratani
    • , Takahiro Suzuki
    • , Yuzo Koda
    • , Po-Sung Chu
    • , Nobuhito Taniki
    • , Akihiro Yamaguchi
    • , Mitsuhiro Kanamori
    • , Nobuhiko Kamada
    • , Masahira Hattori
    • , Hiroshi Ashida
    • , Michiie Sakamoto
    • , Koji Atarashi
    • , Seiko Narushima
    • , Akihiko Yoshimura
    • , Kenya Honda
    • , Toshiro Sato
    •  & Takanori Kanai
  • Article |

    A type I secretion effector, TesG, suppresses host immune response to promote chronic Pseudomonas aeruginosa infection.

    • Kelei Zhao
    • , Wujiao Li
    • , Jing Li
    • , Teng Ma
    • , Kailun Wang
    • , Yang Yuan
    • , Jing Shirley Li
    • , Rou Xie
    • , Ting Huang
    • , Yige Zhang
    • , Yingshun Zhou
    • , Nongyu Huang
    • , Wenling Wu
    • , Zhen Wang
    • , Jun Zhang
    • , Bisong Yue
    • , Zongguang Zhou
    • , Jiong Li
    • , Yu-Quan Wei
    • , Xiuyue Zhang
    •  & Xikun Zhou
  • Letter |

    The development of mobile CRISPR interference (CRISPRi), a modular dCas9-based system that facilitates blocking of gene expression and is easily transferred via conjugation, enables genetic investigations in non-model bacteria.

    • Jason M. Peters
    • , Byoung-Mo Koo
    • , Ramiro Patino
    • , Gary E. Heussler
    • , Cameron C. Hearne
    • , Jiuxin Qu
    • , Yuki F. Inclan
    • , John S. Hawkins
    • , Candy H. S. Lu
    • , Melanie R. Silvis
    • , M. Michael Harden
    • , Hendrik Osadnik
    • , Joseph E. Peters
    • , Joanne N. Engel
    • , Rachel J. Dutton
    • , Alan D. Grossman
    • , Carol A. Gross
    •  & Oren S. Rosenberg
  • Letter |

    Měnglà virus (MLAV) is a phylogenetically distinct bat filovirus, whose genome shares 32–54% nucleotide sequence identity with known filoviruses. MLAV glycoprotein-typed pseudo-types can transduce cell lines derived from humans, monkeys, dogs, hamsters and bats.

    • Xing-Lou Yang
    • , Chee Wah Tan
    • , Danielle E. Anderson
    • , Ren-Di Jiang
    • , Bei Li
    • , Wei Zhang
    • , Yan Zhu
    • , Xiao Fang Lim
    • , Peng Zhou
    • , Xiang-Ling Liu
    • , Wuxiang Guan
    • , Libiao Zhang
    • , Shi-Yue Li
    • , Yun-Zhi Zhang
    • , Lin-Fa Wang
    •  & Zheng-Li Shi
  • Letter |

    The non-structural protein NSs of the severe fever with thrombocytopenia syndrome virus interacts with ABIN2 and promotes formation and signalling of the TPL2–ABIN2–p105 kinase complex to induce expression of the immune-suppressive cytokine IL-10 and enhance viral pathogenesis.

    • Younho Choi
    • , Su-Jin Park
    • , Yinyan Sun
    • , Ji-Seung Yoo
    • , Raghavendra Sumanth Pudupakam
    • , Suan-Sin Foo
    • , Woo-Jin Shin
    • , Sally B. Chen
    • , Philip N. Tsichlis
    • , Won-Ja Lee
    • , Jong-Soo Lee
    • , Wenhui Li
    • , Benjamin Brennan
    • , Young-Ki Choi
    •  & Jae U. Jung
  • Article |

    Antimicrobial peptide resistance genes are found to be widespread in the gut microbiome but are exchanged at lower rates compared to antibiotic resistance genes, with functional compatibility between bacteria being important for gene exchange.

    • Bálint Kintses
    • , Orsolya Méhi
    • , Eszter Ari
    • , Mónika Számel
    • , Ádám Györkei
    • , Pramod K. Jangir
    • , István Nagy
    • , Ferenc Pál
    • , Gergely Fekete
    • , Roland Tengölics
    • , Ákos Nyerges
    • , István Likó
    • , Anita Bálint
    • , Tamás Molnár
    • , Balázs Bálint
    • , Bálint Márk Vásárhelyi
    • , Misshelle Bustamante
    • , Balázs Papp
    •  & Csaba Pál
  • Article |

    Integration of longitudinal gut metagenomic datasets from children in Finland, Estonia and Russian Karelia reveals high strain-level diversity, which consequently impacts the functional capabilities of the early life microbiome.

    • Tommi Vatanen
    • , Damian R. Plichta
    • , Juhi Somani
    • , Philipp C. Münch
    • , Timothy D. Arthur
    • , Andrew Brantley Hall
    • , Sabine Rudolf
    • , Edward J. Oakeley
    • , Xiaobo Ke
    • , Rachel A. Young
    • , Henry J. Haiser
    • , Raivo Kolde
    • , Moran Yassour
    • , Kristiina Luopajärvi
    • , Heli Siljander
    • , Suvi M. Virtanen
    • , Jorma Ilonen
    • , Raivo Uibo
    • , Vallo Tillmann
    • , Sergei Mokurov
    • , Natalya Dorshakova
    • , Jeffrey A. Porter
    • , Alice C. McHardy
    • , Harri Lähdesmäki
    • , Hera Vlamakis
    • , Curtis Huttenhower
    • , Mikael Knip
    •  & Ramnik J. Xavier
  • Editorial |

    Despite major advances in dissecting how pathogens cause disease and the development of treatments to combat infection, infectious diseases remain a major cause of death today. This month’s issue includes a special ‘Focus on Infectious Disease’, which highlights efforts to develop new ways to prevent, detect and treat infections.

  • News & Views |

    Hydrolysis of phosphatidylcholine to choline was found to be catalysed by phospholipase D enzymes from diverse members of the gut microbiota, revealing a mechanism by which commensals obtain choline for subsequent production of disease-associated trimethylamine.

    • Aaron T. Wright
  • Review Article |

    This Review Article describes how recent advances in viral genome sequencing and phylogenetics have enabled key issues associated with outbreak epidemiology to be more accurately addressed, and highlights the requirements and challenges for generating, sharing and using such data when tackling a viral outbreak.

    • Nathan D. Grubaugh
    • , Jason T. Ladner
    • , Philippe Lemey
    • , Oliver G. Pybus
    • , Andrew Rambaut
    • , Edward C. Holmes
    •  & Kristian G. Andersen
  • News & Views |

    APOBEC3 restriction, known to inhibit retroviruses by interfering with genome replication and hypermutating viral DNA, targets the γ-herpesvirus Epstein–Barr virus and is antagonized by the viral BORF2 protein.

    • Michael H. Malim
    •  & Darja Pollpeter
  • News & Views |

    The early identification of repetitive genomic loci in Haloferax species was instrumental in igniting interest in CRISPR–Cas systems. Now, work in this genus has revealed an important role of CRISPR–Cas in reducing an unusual form of inter-species archaeal mating that occurs by cell fusion.

    • Peter C. Fineran