Microbial genetics articles within Nature

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  • Article
    | Open Access

    Reconstruction of four Treponema pallidum genomes associated with human remains from around 2,000 years ago suggests that T. pallidum existed in the Americas and diverged to its modern subspecies before the fifteenth century European contact with the Americas.

    • Kerttu Majander
    • , Marta Pla-Díaz
    •  & Verena J. Schuenemann

  • Article
    | Open Access

    In response to bacterial CRISPR–Cas immunity, phages and plasmids have evolved small non-coding RNA anti-CRISPRs, known as Racrs, that sequester Cas proteins in abberrant complexes and thereby inhibit immunity.

    • Sarah Camara-Wilpert
    • , David Mayo-Muñoz
    •  & Rafael Pinilla-Redondo

  • Article
    | Open Access

    An engineered minimal cell evolves to escape the negative consequences of genome streamlining.

    • R. Z. Moger-Reischer
    • , J. I. Glass
    •  & J. T. Lennon

  • Article
    | Open Access

    A study examining bacterial gene expression in human-derived samples identifies a gene encoding a small RNA and describes how it orchestrates the transition between chronic and acute infection in Pseudomonas aeruginosa.

    • Pengbo Cao
    • , Derek Fleming
    •  & Marvin Whiteley

  • Article
    | Open Access

    A phylogeny-guided genome-resolved metagenomic analysis of DNA viruses in the ocean reveals atypical plankton-infecting relatives of herpesviruses that form a putative new phylum dubbed Mirusviricota.

    • Morgan Gaïa
    • , Lingjie Meng
    •  & Tom O. Delmont

  • Article |

    A case–control study investigating the causes of recent cases of acute hepatitis of unknown aetiology in 32 children identifies an association between adeno-associated virus infection and host genetics in disease susceptibility.

    • Antonia Ho
    • , Richard Orton
    •  & Emma C. Thomson

  • Article |

    A study details the creation of an Escherichia coli genetically recoded organism that is resistant to viral infection, and describes a further modification that keeps the organism and its genetic information biocontained.

    • Akos Nyerges
    • , Svenja Vinke
    •  & George M. Church

  • Article
    | Open Access

    Data from more than 9,700 human stool and oral metagenomes has been used to decipher the strain transmission patterns of the human microbiome from mother to infant, within households and within populations.

    • Mireia Valles-Colomer
    • , Aitor Blanco-Míguez
    •  & Nicola Segata

  • Article
    | Open Access

    Members of the DUF368-containing and DedA transmembrane protein families have conditional roles in undecaprenyl phosphate translocation in Gram-negative and Gram-positive bacteria and may have a widely conserved function in the biogenesis of microbial cell surface glycopolymers.

    • Brandon Sit
    • , Veerasak Srisuknimit
    •  & Matthew K. Waldor

  • Article
    | Open Access

    Experiments in yeast show that introns have a role in inducing phenotypic heterogeneity and that intron-mediated regulation of ribosomal proteins confers a fitness advantage by enabling yeast populations to diversify under nutrient-scarce conditions.

    • Martin Lukačišin
    • , Adriana Espinosa-Cantú
    •  & Tobias Bollenbach

  • Article |

    The mechanism of Thoeris—a bacterial anti-phage defence system—is described in detail, revealing that bacterial TIR-domain proteins recognize infection and produce signalling molecules to execute cell death, akin to the roles of these proteins in plants.

    • Gal Ofir
    • , Ehud Herbst
    •  & Rotem Sorek

  • Review Article |

    This Review outlines the gene and protein expression strategies used by viruses to expand the efficiency of their coding and regulatory sequences, and the implications of these mechanisms for developing antiviral agents.

    • Jessica Sook Yuin Ho
    • , Zeyu Zhu
    •  & Ivan Marazzi

  • Article
    | Open Access

    ‘Candidatus Azoamicus ciliaticola’ transfers energy to its ciliate host in the form of ATP and enables this host to breathe nitrate, demonstrating that eukaryotes with remnant mitochondria can secondarily acquire energy-providing endosymbionts.

    • Jon S. Graf
    • , Sina Schorn
    •  & Jana Milucka

  • Article |

    Thermal proteome profiling combined with a reverse genetics approach provides insights into the abundance and thermal stability of the global proteome of Escherichia coli.

    • André Mateus
    • , Johannes Hevler
    •  & Mikhail M. Savitski

  • Article |

    The authors systematically characterize structural variation in the genomes of gut microbiota and show that they are associated with bacterial fitness and with host risk factors, and that examining genes coded in these regions facilitates investigation of mechanisms that may underlie these associations.

    • David Zeevi
    • , Tal Korem
    •  & Eran Segal

  • Letter |

    Isolates of the Vibrio cholerae O1 serotype Ogawa from Yemen are from a single sublineage of the seventh pandemic El Tor (7PET) lineage and are susceptible to several commonly used antibiotics as well as to polymyxins.

    • François-Xavier Weill
    • , Daryl Domman
    •  & Marie-Laure Quilici

  • Letter |

    Finely tuned control of strain engraftment and abundance in the mouse gut microbiota was achieved using the marine polysaccharide porphyran, which could exclusively be used by an introduced subset of wild-type or genetically modified Bacteroides strains.

    • Elizabeth Stanley Shepherd
    • , William C. DeLoache
    •  & Justin L. Sonnenburg

  • Article |

    Statistical analyses of a metagenomics-sequenced human cohort identify a relatively minor role for genetics in determining microbiome composition and show that several human phenotypes are as strongly associated with the gut microbiome as with host genetics.

    • Daphna Rothschild
    • , Omer Weissbrod
    •  & Eran Segal

  • Article |

    Two hypervirulent ribotypes of the enteric pathogen Clostridium difficile, RT027 and RT078, have independently acquired unique mechanisms to metabolize low concentrations of the disaccharide trehalose, suggesting a correlation between the emergence of these ribotypes and the widespread adoption of trehalose in the human diet.

    • J. Collins
    • , C. Robinson
    •  & R. A. Britton

  • Letter |

    Both F17-like and type 1 pili promote intestinal colonization in mouse colonic crypts, and the high-affinity mannoside M4284 reduces intestinal colonization of uropathogenic Escherichia coli while simultaneously treating urinary tract infections without disrupting the composition of the gut microbiota.

    • Caitlin N. Spaulding
    • , Roger D. Klein
    •  & Scott J. Hultgren

  • Article |

    Whole-genome sequencing of 264 clones sampled from 12 Escherichia coli populations evolved over 50,000 generations under identical culture conditions is used to characterize the patterns and dynamics of genome evolution over time.

    • Olivier Tenaillon
    • , Jeffrey E. Barrick
    •  & Richard E. Lenski

  • Article |

    Increased potential for branched-chain amino acid and lipopolysaccharide biosynthesis in the gut microbiome of insulin-resistant individuals suggests that changes in the serum metabolome induced by dysbiosis, and driven by only a handful of species, contribute to the development of diabetes.

    • Helle Krogh Pedersen
    • , Valborg Gudmundsdottir
    •  & Oluf Pedersen

  • Letter |

    When transcription and replication machineries collide on DNA, they can cause mutations to occur in the area near the collision; these mutations are now shown to include two types—duplications/deletions within the transcription unit and base substitutions in the cis-regulatory element of gene expression.

    • T. Sabari Sankar
    • , Brigitta D. Wastuwidyaningtyas
    •  & Jue D. Wang

  • Letter |

    Maximum-depth sequencing (MDS), a new method of detecting extremely rare variants within a bacterial population, is used to show that mutation rates in Escherichia coli vary across the genome by at least an order of magnitude, and also to uncover mechanisms of antibiotic-induced mutagenesis.

    • Justin Jee
    • , Aviram Rasouly
    •  & Evgeny Nudler

  • Letter |

    A nanopore DNA sequencer is used for real-time genomic surveillance of the Ebola virus epidemic in the field in Guinea; the authors demonstrate that it is possible to pack a genomic surveillance laboratory in a suitcase and transport it to the field for on-site virus sequencing, generating results within 24 hours of sample collection.

    • Joshua Quick
    • , Nicholas J. Loman
    •  & Miles W. Carroll

  • Article |

    Eukaryotes acquired their prokaryotic genes in two episodes of evolutionary influx corresponding to the origin of mitochondria and plastids, respectively, followed by extensive differential gene loss, uncovering a massive imprint of endosymbiosis in the nuclear genomes of complex cells.

    • Chuan Ku
    • , Shijulal Nelson-Sathi
    •  & William F. Martin

  • Letter |

    Documented cases of horizontal gene transfer from bacteria to eukaryotes are rare, but now, not only is a new class of transferred genes identified, the function of one representative is also demonstrated in its new setting, where it controls bacterial growth.

    • Seemay Chou
    • , Matthew D. Daugherty
    •  & Joseph D. Mougous

  • Article |

    Previous work has shown that human skin is home to a rich and varied microbiota; here a metagenomic approach for samples from physiologically diverse body sites illuminates that the skin microbiota, including bacterial, fungal and viral members, is shaped by the local biogeography and yet marked by strong individuality.

    • Julia Oh
    • , Allyson L. Byrd
    •  & Julia A. Segre

  • Article
    | Open Access

    Uncultivated archaeal and bacterial cells of major uncharted branches of the tree of life are targeted and sequenced using single-cell genomics; this enables resolution of many intra- and inter-phylum-level relationships, uncovers unexpected metabolic features that challenge established boundaries between the three domains of life, and leads to the proposal of two new superphyla.

    • Christian Rinke
    • , Patrick Schwientek
    •  & Tanja Woyke

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