News & Comment

  • Editorial |

    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.

  • News & Views |

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

    • Haoping Liu
  • News & Views |

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

    • Margaret Alexander
    •  & Peter J. Turnbaugh
  • Comment |

    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.

    • Michael D. L. Johnson
    • , David A. Baltrus
    •  & Jennifer Gardy
  • News & Views |

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

    • Alice Prince
  • News & Views |

    The dogma that conversion of the RNA genome of HIV into DNA occurs in the cytoplasm before nuclear entry is challenged using nuclear pore blockade experiments.

    • Nathalie Jane Arhel
  • News & Views |

    A virus has been found inserted into the genome of the most abundant bacteria in the oceans. Even though the virus can kill its host, the genes carried by the prophage may help these bacteria flourish around the world.

    • David L. Kirchman
  • News & Views |

    A dual-mechanism compound with antibacterial activity that targets both folate metabolism and membrane integrity, with a favourable resistance profile in vitro, is identified by screening a small molecule library.

    • Ursula Theuretzbacher
  • News & Views |

    Marine bacteria that produce an enormous panoply of glycan-degrading enzymes are identified as having a role in releasing fixed carbon present in glycan-rich cell walls of brown algae.

    • Fiona Cuskin
    •  & Elisabeth C. Lowe
  • News & Views |

    Iron-scavenging molecules called siderophores that are produced by the native microbial residents of plant roots fend off plant pathogens such as Ralstonia solanacearum.

    • Shaul Pollak
    •  & Otto X. Cordero
  • News & Views |

    Cooperative behaviour enables populations of yeast cells to survive high temperatures.

    • Kevin R. Lauterjung
    • , Neydis Moreno Morales
    •  & Megan N. McClean
  • News & Views |

    Some cytosolic bacteria deform the plasma membrane to spread from cell to cell. Secretion of 25-hydroxy-cholesterol by macrophages has emerged as a protective response that depletes the cholesterol pool used by these bacteria to disseminate through epithelia.

    • Norma W. Andrews
  • News & Views |

    Monkeypox, a zoonotic disease that is marked in humans by a smallpox-like rash, may present as a rash-less respiratory disease in wild chimpanzees.

    • Jens H. Kuhn
  • 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
  • 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
  • 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
  • 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
  • News & Views |

    Resistance to antibiotics is a hot topic in microbiology, but there is much less coverage on resistance to vaccines. The associated risk to disease control has potentially devastating implications, but advances are being made towards smarter vaccine design that reduces the risk of antibiotic-resistant disease.

    • Stephen Bentley
  • News & Views |

    Bacteriophage therapeutics has emerged as one of the few potential beacons that represent possible solutions to the growing global crisis of antimicrobial resistance. Bringing science to the bedside (and vice versa) will maximize the potential of this compelling opportunity.

    • Robert T. Schooley
    •  & Steffanie Strathdee
  • Comment |

    Mutation. The word naturally conjures fears of unexpected and freakish changes. Ill-informed discussions of mutations thrive during virus outbreaks, including the ongoing spread of SARS-CoV-2. In reality, mutations are a natural part of the virus life cycle and rarely impact outbreaks dramatically.

    • Nathan D. Grubaugh
    • , Mary E. Petrone
    •  & Edward C. Holmes
  • Comment |

    The atmosphere has undergone extensive physico-chemical change due to anthropogenic emissions. The impact on the ecology of the atmospheric microbiome has so far not been considered. Here, we define the scope of change to the atmosphere and identify potential microbial responses.

    • Stephen D. J. Archer
    •  & Stephen B. Pointing
  • News & Views |

    Mosquitoes have been known for over a century to transmit viruses such as yellow fever. However, laboratory studies to identify the species capable of natural transmission still fail to explain some outbreaks, such as Zika. Now, this paradox is partially explained by a simple methodological shortcoming.

    • Scott C. Weaver
  • News & Views |

    Antibiotic overuse has led to a rise of multidrug-resistant pathogens and increased morbidity. A new study shows that the microbiome can prime two different host response pathways in the intestine and lungs that protect against an antibiotic-resistant pathogen.

    • Angel G. Solis
    •  & Maayan Levy
  • Editorial |

    As the international community responds to an outbreak of coronavirus-induced pneumonia in Wuhan, China, early and open data sharing — which are vital for its control — depend on the trust that the data will not be used without proper attribution to those who generated it.

  • Editorial |

    Nature Microbiology will offer authors the option of publishing a peer-review file that includes anonymous peer-review reports, author responses and our decision letters. We will also request that articles include more source data and are more transparent in reporting data availability.

  • Comment |

    As microbiome science expands, academic centres scramble to fill many needs, from service provider to industry liaison. A newly created network aims to share strategies and accelerate knowledge transfer, and invites others to join the efforts.

    • Jennifer B. H. Martiny
    • , Katrine L. Whiteson
    • , Brendan J. M. Bohannan
    • , Lawrence A. David
    • , Nicole A. Hynson
    • , Margaret McFall-Ngai
    • , John F. Rawls
    • , Thomas M. Schmidt
    • , Zaid Abdo
    • , Martin J. Blaser
    • , Seth Bordenstein
    • , Christian Bréchot
    • , Carolee T. Bull
    • , Pieter Dorrestein
    • , Jonathan A. Eisen
    • , Ferran Garcia-Pichel
    • , Jack Gilbert
    • , Kirsten S. Hofmockel
    • , Mary L. Holtz
    • , Rob Knight
    • , David B. Mark Welch
    • , Daniel McDonald
    • , Barbara Methé
    • , Nigel J. Mouncey
    • , Noel T. Mueller
    • , Catherine A. Pfister
    • , Lita Proctor
    •  & Joel L. Sachs
  • News & Views |

    Two recent studies reveal a virus anti-defence strategy whereby large, ‘jumbo’ phages protect themselves from both restriction endonucleases and DNA-targeting CRISPR–Cas systems, but not from RNA-targeting ones, by encapsulating the phage genome inside the cell in a ‘nucleus’-like shell that is impenetrable for CRISPR effectors.

    • Eugene V. Koonin
    •  & Mart Krupovic
  • News & Views |

    Metabolic adaptation plays a key role in determining the composition of microbial ecosystems. A new study shows that in the inflamed gut, pathogenic Enterobacteriaceae can reprogramme their metabolism towards diet-derived l-serine utilization to outcompete the resident microbiota and cause disease.

    • Woongjae Yoo
    •  & Mariana X. Byndloss
  • News & Views |

    Baloxavir marboxil (BXM) represents a promising advance in antiviral chemotherapies for influenza infections. Identification of transmissible BXM-resistant strains in Japan may hit pause on widespread adoption of this therapy and could lead to revision of surveillance practices for emerging viruses.

    • Karen A. Kormuth
    •  & Seema S. Lakdawala
  • News & Views |

    Adding a flap on the top of an insecticide-treated bednet helps to intercept blood-seeking mosquitoes and allows a wider range of insecticides to be used together. Net buyers must now make a challenging decision for each target area: which net product will be most cost-effective, given the resistance in local vectors?

    • Jo Lines
  • News & Views |

    The host protein cyclophilin A binds to the HIV-1 capsid and its role in infection has long been enigmatic. A new study shows that this interaction protects the virus from inhibition by TRIM5α in physiologically relevant primary human cells.

    • Christopher Aiken
  • Editorial |

    It’s an exciting time to be a microbiologist and we have the honour and privilege of having front-row tickets to see the field develop and progress. As we take stock of the past year, we will count down the days until 2020 by celebrating the field and the season with a microbiology advent calendar.

  • News & Views |

    A newly discovered energy-linked carbonic anhydrase, DabBA2, is a two-protein complex responsible for inorganic carbon accumulation in the sulfur bacterium Halothiobacillus neapolitanus. DABs are present in a wide range of proteobacterial clades, suggesting that they function in diverse metabolic pathways.

    • G. Dean Price
    • , Benedict M. Long
    •  & Britta Förster
  • News & Views |

    Influenza vaccine strain selection is informed by international efforts to track antigenic change, focusing on the viral hemagglutinin protein. Recent research advocates monitoring neuraminidase for immune escape mutations that could reduce vaccine efficacy.

    • Annette Fox
    •  & Louise Carolan
  • News & Views |

    Culture-independent methods capable of connecting bacteriophages (phages) to their target host bacteria will help define the roles of phages in host-associated microbiotas. A recent study used fluorescently dyed intestinal phages to identify novel phage–bacterial interactions from the human intestine.

    • Cydney N. Johnson
    •  & Breck A. Duerkop
  • News & Views |

    12,13-diHOME produced by the gut microbiome promotes an asthma-like immunophenotype in the lungs of a murine experimental model. Accordingly, the metabolite is elevated in neonates who developed asthma during childhood, potentially providing a biomarker for early risk prediction and a novel therapeutic target.

    • Christopher J. Stewart
  • News & Views |

    Some RNAs have to be made at maximal achievable rates, yet RNA polymerase encounters many obstacles that slow it down. A new study shows that a group of co-transcribing RNA polymerases communicate over long distances to work more efficiently than a solo enzyme.

    • Irina Artsimovitch
  • Editorial |

    With drug resistance on the rise, improvements in clinical antibiotic susceptibility testing and investment in widespread implementation are needed to usher in a new generation of diagnostics that can inform on diverse types of drug resistance and quickly predict drug susceptibility with high accuracy.

  • News & Views |

    Clinicians have long observed that infections diagnosed as susceptible to antibiotics can sometimes resist treatment. New studies show that such treatment failures can be explained by subpopulations of transiently resistant cells that are often missed by standard clinical diagnostics, offering new therapeutic avenues.

    • Viktória Lázár
    •  & Roy Kishony
  • News & Views |

    Lab-based studies, combined with metatranscriptomic and metabolomic field analyses, reveal important diel-linked roles for sulfonates in the major classes of phytoplankton that produce them, and in the environment in which they feed ubiquitous heterotrophic bacteria.

    • Beth T. Williams
    •  & Jonathan D. Todd
  • News & Views |

    The Mla phospholipid transporter is a multi-subunit ATP-binding cassette transport system widely understood to move phospholipids in a retrograde direction; that is, from the outer membrane to the inner membrane. However, recent studies reveal that Mla might move phospholipids in the opposite, anterograde direction.

    • Russell E. Bishop