Microbial genetics

  • 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
  • Letter |

    The CRISPR/Cas system known to aid bacterial defences by targeting invading DNA can also act to evade eukaryotic defences through a different class of small RNAs downregulating an endogenous immunogenic bacterial lipoprotein.

    • Timothy R. Sampson
    • , Sunil D. Saroj
    •  & David S. Weiss
  • Article |

    Daily oxidation–reduction cycles of peroxiredoxin proteins are shown to be conserved in all domains of life, including Bacteria, Archaea and Eukaryota.

    • Rachel S. Edgar
    • , Edward W. Green
    •  & Akhilesh B. Reddy
  • Article |

    The human gut microbiome from a large cohort of more than 500 indivduals living on three continents with three distinct cultures is analysed, emphasizing the effect of host age, diet and environment on the composition and functional repertoire of fecal microbiota.

    • Tanya Yatsunenko
    • , Federico E. Rey
    •  & Jeffrey I. Gordon
  • Letter |

    Pyrrolysine is the twenty-second naturally occurring amino acid, and it is required for the formation of methane from methylamines. Pyrrolysine is the last remaining natural amino acid with a poorly characterized biosynthetic pathway. Here it is shown that the radical SAM protein PylB converts lysine to 3-methylornithine, which then undergoes a PylC-catalysed condensation with another lysine to generate a product that is oxidized by PylD to generate pyrrolysine.

    • Marsha A. Gaston
    • , Liwen Zhang
    •  & Joseph A. Krzycki
  • Letter |

    During replication, topological stress builds ahead of the polymerase. Current models propose that linear eukaryotic chromosomes are divided into topological domains, and that stress is relieved by the activity of a topoisomerase. Here, it is found that replication stress seems to be present throughout the chromosome, rather than in domains, and that the relief of stress in longer chromosomes is facilitated by the activity of the cohesin/condensin-like Smc5/6 complex as well as by topoisomerase. They propose that the Smc5/6 complex prevent formation of topological tension ahead of the replication fork by promoting fork rotation, leading to the formation of sister chromatin intertwinings behind.

    • Andreas Kegel
    • , Hanna Betts-Lindroos
    •  & Camilla Sjögren
  • Letter |

    As the rates of replication and transcription are different, the machineries that carry out these processes are bound to clash on DNA. In contrast to results from head-on collisions, co-directional encounters have been shown to have mild effects in vitro, requiring no additional replication restart factors. It is now shown that in bacterial cells, both types of events require the activities of restart proteins to resume replication when a transcription complex is encountered.

    • Houra Merrikh
    • , Cristina Machón
    •  & Panos Soultanas
  • Letter |

    Contact-dependent growth inhibition (CDI) through a two-component system was first described in Escherichia coli as a mechanism to inhibit growth of bacterial cells that do not possess this system. Now the widespread occurrence of CDI in bacteria and the molecular basis for some of these interactions have been elucidated. The data suggest that CDI is a common mechanism by which microbes compete with each other in the environment.

    • Stephanie K. Aoki
    • , Elie J. Diner
    •  & David A. Low
  • Letter |

    Bacterial chromosomes often carry integrated genetic elements (such as plasmids and prophages) that contribute to the evolutionary fitness of the host bacterium. In Vibrio cholerae, a prophage encodes cholera toxin. Here, the events that led to the acquisition of phage DNA have been reconstructed, revealing the cooperative interactions between multiple filamentous phages that contributed to the emergence of virulent V. cholerae strains.

    • Faizule Hassan
    • , M. Kamruzzaman
    •  & Shah M. Faruque
  • Letter |

    The oxidation of formate and water to bicarbonate and H2 is relatively common in microorganisms under anaerobic conditions. But can this reaction sustain growth in an isolated species? Here it is shown that several individual Thermococcus species can use formate oxidation for growth. Moreover, the biochemical basis of this ability is delineated.

    • Yun Jae Kim
    • , Hyun Sook Lee
    •  & Sung Gyun Kang
  • Letter |

    Clostridium difficile, an important nosocomial pathogen, produces two toxins. Studies with purified toxins have indicated that only toxin A is important for pathogenesis, but recently it has been suggested that toxin B causes the majority of the disease symptoms in the context of a bacterial infection. These authors demonstrate that both toxins are important for disease and will need to be considered for diagnosis and treatment.

    • Sarah A. Kuehne
    • , Stephen T. Cartman
    •  & Nigel P. Minton
  • Letter |

    The Escherichia coli isocitrate dehydrogenase kinase/phosphatase (AceK) is a bifunctional enzyme that can phosphorylate or dephosphorylate isocitrate dehydrogenase (ICDH) to either inactivate or activate it in response to environmental changes. Now the structures of AceK and the AceK–ICDH complex have been solved, revealing the conformational changes that occur when AceK changes from a kinase to a phosphatase and vice versa.

    • Jimin Zheng
    •  & Zongchao Jia
  • Article
    | Open Access

    Deep metagenomic sequencing and characterization of the human gut microbiome from healthy and obese individuals, as well as those suffering from inflammatory bowel disease, provide the first insights into this gene set and how much of it is shared among individuals. The minimal gut metagenome as well as the minimal gut bacterial genome is also described.

    • Junjie Qin
    • , Ruiqiang Li
    •  & Jun Wang
  • Article |

    The integrase protein of retroviruses such as HIV-1 catalyses insertion of the viral genome into that of the host. Here, the long-awaited structure of the full-length integrase complex is predicted, revealing not only details of the biochemistry of the integration reaction, but also the means by which current inhibitors affect this process.

    • Stephen Hare
    • , Saumya Shree Gupta
    •  & Peter Cherepanov