News & Views

  • News & Views |

    Eukaryotes evolved from a symbiosis involving Alphaproteobacteria and archaea phylogenetically nested within the Asgard clade. Two recent studies explore the metabolic capabilities of Asgard lineages, supporting refined symbiotic metabolic interactions that might have operated at the dawn of eukaryogenesis.

    • Purificación López-García
    •  & David Moreira
  • News & Views |

    Biofilms are communities of bacteria that accumulate on surfaces such as replacement joints or intravenous catheters. By silencing a key communication system, Staphylococcus aureus builds tightly packed biofilms that can withstand attack by host immune cells.

    • Andrew M. Edwards
  • News & Views |

    Microscopy and genomic analyses reveal an intriguing symbiosis between eukaryotic protists and Deltaproteobacteria in anoxic marine sediments that involves division of labour and interspecies hydrogen transfer, and enables collective magnetotactic motility by the consortium.

    • Virginia Edgcomb
  • News & Views |

    The rapidly dividing bacterium Vibrio natriegens holds promise for transforming traditional molecular biology and biotechnology processes. New work demonstrates that CRISPR interference technology is a robust tool for rapid, genome-wide screens in V. natriegens, facilitating future bioengineering efforts.

    • Jonathan D. D’Gama
    •  & Matthew K. Waldor
  • News & Views |

    The secondary metabolite cepacin A is the essential compound made by Burkholderia ambifaria needed for biocontrol of plant pathogens. In this organism, genes responsible for virulence and for cepacin A biosynthesis reside on different replicons, allowing for the engineering of avirulent mutants that retain their biocontrol properties.

    • Tom Coenye
  • News & Views |

    A recent study finds that viruses cooperate altruistically to overcome innate host immunity and that this can be explained in the same way we explain altruism between animals.

    • Asher Leeks
    •  & Stuart West
  • News & Views |

    A class of drugs approved to treat schizophrenia can cause rapid loss of the pilus, an essential virulence factor necessary for the disease-causing properties in the strict human pathogen Neisseria meningitidis.

    • H Steven Seifert
  • News & Views |

    Differences in microbial genomes can result in vastly different phenotypes and functions. Consequently, it is critical to understand the genome variations that differentiate microbial strains. Here, we discuss recent exciting advances that enable structural variant measurement, their associated phenotypes and the horizon for future discovery.

    • Matthew G. Durrant
    •  & Ami S. Bhatt
  • News & Views |

    Computational analysis of fungal genomes revealed that some early-branching fungi use selenocysteine, the selenium-containing amino acid, that was thought to be missing from proteins in this lineage.

    • Sergi Castellano
  • News & Views |

    Inflammatory molecules evolved partly to protect hosts from viruses, but increasing evidence suggests that they cause disease pathology and chronic conditions, and play a role in aging. By mitigating these effects, bats are able to both tolerate viral infections and live well beyond expectations.

    • David T. S. Hayman
  • News & Views |

    A large-scale comparative genomic survey of Cryptosporidium species and subtypes reveals a cryptic anthroponotic Cryptosporidium parvum branch and a large, recent superclade of species and subtypes that undergo genetic exchange, potentially facilitating host associations.

    • Jessica C. Kissinger
  • News & Views |

    Animal studies have strongly implicated the gut microbiome as a key regulator of brain and behaviour. Recent work using two large population cohorts and bioinformatics tools has strengthened the link between microbial disturbances and depression (or quality of life in general).

    • John F. Cryan
    •  & Timothy G. Dinan
  • News & Views |

    Eradicating the viral reservoir remains a formidable barrier to curing human immunodeficiency virus (HIV). The first challenge is to characterize the cells and tissues where HIV hides. In this issue of Nature Microbiology, urethral macrophages are shown to retain infectious HIV particles, prompting us to rethink strategies to eliminate the reservoir.

    • Vasco Rodrigues
    •  & Philippe Benaroch
  • News & Views |

    Megaphages, the largest phage genomes sequenced to date, are abundant in faecal microbiomes from humans, baboons and pigs, leading us to question whether there is an upper limit to the size of viruses relative to their hosts.

    • Robert A. Edwards
  • News & Views |

    Three recent metagenomic studies analyse methanogenesis-related genes in previously uncharacterized, sediment-inhabiting archaeal lineages. They elucidate the metabolic capacity encoded in the genomes of these lineages, yet how these organisms harness energy is still a mystery.

    • Joana C. Xavier
    •  & William F. Martin
  • News & Views |

    Rapid diagnostic tests capable of detecting any potential pathogen are needed to improve the efficacy of antimicrobial therapy and inform antimicrobial stewardship efforts. A new metagenomics-based test that detects microbial DNA in human blood can identify a diverse array of pathogens from any source in the body.

    • Justin O’Grady
  • 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
  • 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
  • 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
  • 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
  • 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
  • News & Views |

    Streptococcus pneumoniae strains colonizing the nasopharynx use quorum sensing and fratricide to outcompete incoming strains, thereby retaining ownership of the host. This occurs via activation of the competence regulon, induction of lytic proteins, and turning the invader into a source of DNA for genetic exchange.

    • James C. Paton
    •  & Claudia Trappetti
  • News & Views |

    Primate immunodeficiency virus accessory proteins Vpx/Vpr associate with and induce proteasomal degradation of the HUSH complex, thereby counteracting HUSH-mediated epigenetic transcriptional repression of proviral and cellular genes. These findings open new therapeutic avenues against HIV.

    • Carine Van Lint
  • News & Views |

    It is now clear that key autophagy proteins possess alternative functions, distinct from their conventional roles in autophagy. Adding to this emerging field, a new study shows how ATG16L1 acts to promote plasma membrane repair following damage by pore-forming bacteria.

    • Oliver Florey
  • News & Views |

    Bacteria employ a specialized weapon known as the type VI secretion system to defend themselves from competing organisms. A new study reveals the molecular architecture of the type VI secretion system and highlights conserved mechanistic similarities with contractile phage tails.

    • Alan R. Davidson
    •  & Karen L. Maxwell
  • News & Views |

    Gut microbiota are known to produce an intermediate metabolite in the production of trimethylamine N-oxide that promotes atherosclerosis. Now, another metabolite produced by the same bacteria has been identified that prevents atherosclerosis. The basis for these opposing microbial effects are dictated by diet.

    • Scott J. Bultman
  • News & Views |

    Protein translocation across bacterial membranes can take many routes through dedicated transport machines. A new study finds that Salmonella Typhi utilizes a distinct pathway to translocate typhoid toxin across the peptidoglycan layer and prime the bacterium for host intoxication.

    • Anastassios Economou
  • News & Views |

    A key step of the antiviral immune response is detection of the viral intruder. Infection with highly pathogenic strains of influenza virus is now shown to produce short aberrant viral RNAs that potently trigger activation of innate immunity.

    • William Riedl
    •  & Michaela U. Gack
  • News & Views |

    A powerful in vivo biotinylation approach identifies TagA as a binding partner of TssA, a central regulator of the assembly of the type VI secretion system (T6SS). TagA terminates assembly of the T6SS tail and tethers it to the membrane, acting as a crossbow latch that allows for efficient firing.

    • Olivera Francetic
  • News & Views |

    The discovery of CD153 as a novel driver of T-cell-mediated host defence against Mycobacterium tuberculosis infection advances our understanding of the requirements for protective immunity. Future investigation of CD153 as a potential correlate of tuberculosis immunity could open new avenues for vaccine design.

    • Sara B. Cohen
    •  & Kevin B. Urdahl
  • News & Views |

    Components of the sphingolipid biosynthetic pathway induce a favourable conformation in the proteinaceous murine norovirus receptor (CD300lf) that facilitates virus entry.

    • Benhur Lee
  • News & Views |

    How the immune system handles the relentless presence of commensal bacteria is an area of great interest. Here, researchers describe a role for autophagy in mediating tolerance to the microbiota, the absence of which can impart beneficial resistance to infection but also possible detriment in the form of autoimmunity.

    • Jennifer Martinez
  • News & Views |

    The H445Y mutation in the β-subunit of RNA polymerase in Mycobacterium tuberculosis causes resistance to the antibiotic rifampicin and changes mycobacterial lipid composition. Infection with rpoB H445Y results in metabolic shifts that allow the bacteria to bypass a key host inflammatory response.

    • Yu-Xiang Chen
    •  & Babak Javid
  • News & Views |

    An experimental evolution study shows that selection of a marine bacterium by warming favours adaptations that facilitate growth at low oxygen concentrations, linking evolutionary responses to these two key components of climate change in the ocean.

    • David A. Hutchins
  • News & Views |

    Plasmodium parasites possess a unique PEXEL sorting pathway to deliver secretory proteins into the host cells in which they reside. A new study shows the existence of independent sorting/entry complexes to detect and deliver PEXEL proteins into the parasite endoplasmic reticulum.

    • Martin R. Pool
    •  & Ilaria Russo
  • News & Views |

    Genome-wide association studies and genetic analyses have identified a clinically prevalent alteration in the Mycobacterium tuberculosis genome that rewires bacterial propionate metabolism, conditionally reduces antibiotic killing without affecting minimum inhibitory concentrations, and may drive emergence of drug resistance.

    • Thomas Dick
    •  & Véronique Dartois
  • News & Views |

    Studies in Drosophila reveal that the insect homologue of the stimulator of interferon genes (STING) exerts antiviral activity against Zika virus infection in the fly brain through the induction of autophagy, providing key insights into the possible evolutionary function of STING in antiviral defence.

    • Carolyn B. Coyne
  • News & Views |

    It has been assumed that bacteria adapt to nutrient limitation by adjusting the number of ribosomes, no matter what they are being starved for. Instead, two recent studies show that Escherichia coli uses different approaches depending on whether its growth is limited by the availability of carbon, nitrogen or phosphate.

    • Katarzyna Potrykus
    •  & Michael Cashel
  • News & Views |

    Bacteria use sophisticated translocation systems to manipulate or kill host cells and competing bacteria. A new study shows that bacteria also deliver anti-fungal effectors.

    • Sascha Brunke
    •  & Bernhard Hube
  • News & Views |

    Commensal bacteria living on the skin can enhance the virulence of a skin pathogen, changing the way we think about the role of healthy skin microbiota in disease susceptibility.

    • Michelle Spoto
    •  & Julia Oh
  • News & Views |

    What evolutionary strategies are used by parasites to flourish for long periods within their mammalian hosts? These are questions that have been addressed by Pinger et al. in a recent study that identifies variable O-glycosylation as a novel immune-evasion mechanism employed by African trypanosomes.

    • Mark Carrington
    •  & Matthew K. Higgins
  • News & Views |

    Widespread use of antibiotics in animals either as growth promoters or for metaphylaxis may drive the spread of clinically relevant drug resistance genes and pathogens. New work uncovers drug resistance gene patterns from livestock across European farms and finds a correlation with agricultural antibiotic use.

    • Timothy R. Walsh
  • News & Views |

    Rare species tend to degrade complex substrates while common species contribute most to biomass and respiration, moving us towards a solution for structure–function mapping in microbial communities.

    • Lei Ma
    •  & Otto X. Cordero
  • News & Views |

    Antibiotic resistance against β-lactams is of paramount therapeutic importance. Although such resistance is known to involve degradation by hydrolysis, the molecular details of what happens next remain unclear. A new study reveals how soil microbes perform β-lactam catabolism and how this process can support bacterial growth.

    • Christopher J. Schofield
  • News & Views |

    The discovery and characterization of a phylum-level archaeal lineage in iron-rich hot springs—the Marsarchaeota—expands the phylogenetic depth and physiological diversity of aerobic archaea.

    • Andreas Teske