Volume 3 Issue 3, March 2018

Volume 3 Issue 3

Functional fluctuations in faecal flora

Longitudinal metagenomic and metatranscriptomic analyses of human faecal microbiomes reveal similar strain-level variation within and between individuals and allow dynamic functional variation to be tracked.

See Mehta et al. and Abu-Ali et al.

Image: Jason Lloyd-Price. Cover Design: Samantha Whitham.

Editorial

  • Editorial |

    Fittingly for a bacterium whose slow growth rate has frustrated researchers for decades, progress towards ending the TB epidemic has built only at a snail’s pace. 2018 should see a much needed stimulus, with increased political awareness of the scale of the problems faced, and the adoption of a coordinated global response.

Comment & Opinion

  • Comment |

    Antimicrobial resistance is one of the great challenges for twenty-first century healthcare. While new therapeutics are undoubtedly required, there are major challenges in rapidly identifying resistant infections and tailoring therapy accordingly; and in how we deploy antimicrobials with suppression of resistance in mind.

    • Gavin Barlow

News & Views

  • News & Views |

    CRISPR immunity begins with the acquisition of sequences from invading nucleic acids through spacer integration into a CRISPR locus. Off-target integration of spacers into other parts of the genome is now implicated as a spontaneous source of new CRISPR loci.

    • Alireza Edraki
    •  & Erik J. Sontheimer
  • News & Views |

    An alternative nitrogenase enzyme that only utilizes iron as its cofactor is shown to reduce carbon dioxide while actively fixing dinitrogen, so that it simultaneously produces ammonium, hydrogen and methane.

    • Oliver Einsle
  • News & Views |

    Geographic mapping of pathogen emergence risk, as recently done for viral haemorrhagic fever in Africa, provides an important tool for targeting interventions. More comprehensive preparedness and prediction systems that increase surveillance and forecast infectious disease outbreak growth and spread in real time are also needed.

    • Jeffrey Shaman
  • News & Views |

    Effective treatment and eradication of tuberculosis requires highly sensitive and specific, easy-to-use detection methods. New advances in molecular tools and technology are driving improved tuberculosis diagnostics, including ways to rapidly identify highly drug-resistant infections.

    • Eric J. Rubin

Reviews

  • Review Article |

    A review of the diversity of disulfide-bond-catalysing systems across prokaryotes.

    • Cristina Landeta
    • , Dana Boyd
    •  & Jon Beckwith

Research

  • Letter |

    Here the authors show that a bacterial iron-only nitrogenase can generate CH4 in a single step, which can consequently be used for growth by a CH4-utilizing Methylomonas strain.

    • Yanning Zheng
    • , Derek F. Harris
    • , Zheng Yu
    • , Yanfen Fu
    • , Saroj Poudel
    • , Rhesa N. Ledbetter
    • , Kathryn R. Fixen
    • , Zhi-Yong Yang
    • , Eric S. Boyd
    • , Mary E. Lidstrom
    • , Lance C. Seefeldt
    •  & Caroline S. Harwood
  • Letter |

    Two known anti-Japanese encephalitis virus antibodies are shown to bind quaternary epitopes spanning three envelope proteins, block viral attachment and prevent fusion. One low dose in mice is protective, underscoring their therapeutic potential.

    • Xiaodi Qiu
    • , Yingfeng Lei
    • , Pan Yang
    • , Qiang Gao
    • , Nan Wang
    • , Lei Cao
    • , Shuai Yuan
    • , Xiaofang Huang
    • , Yongqiang Deng
    • , Wenyu Ma
    • , Tianbing Ding
    • , Fanglin Zhang
    • , Xingan Wu
    • , Junjie Hu
    • , Shan-Lu Liu
    • , Chengfeng Qin
    • , Xiangxi Wang
    • , Zhikai Xu
    •  & Zihe Rao
  • Letter |

    To infect humans, Trypanosoma brucei rhodesiense relies on its SRA protein to subvert host trypanolytic factors, TLF1 and TLF2. This study reveals the structure of SRA and explores how it interacts with TLFs, elucidating how the parasite avoids host immunity.

    • Sebastian Zoll
    • , Harriet Lane-Serff
    • , Shahid Mehmood
    • , Jonathan Schneider
    • , Carol V. Robinson
    • , Mark Carrington
    •  & Matthew K. Higgins
  • Letter |

    The role of AXL receptor tyrosine kinase during Zika virus infection has been the subject of debate. Here, it is shown to inhibit type I interferon responses elicited by astrocyte infection in a STAT-dependent manner, enabling virus replication.

    • Jian Chen
    • , Yi-feng Yang
    • , Yu Yang
    • , Peng Zou
    • , Jun Chen
    • , Yongquan He
    • , Sai-lan Shui
    • , Yan-ru Cui
    • , Ru Bai
    • , Ya-jun Liang
    • , Yunwen Hu
    • , Biao Jiang
    • , Lu Lu
    • , Xiaoyan Zhang
    • , Jia Liu
    •  & Jianqing Xu
  • Article |

    VarQuest—a method to search for new peptidic natural products (PNPs) based on existing mass spectra and chemical structure databases that incorporates potential modifications of known PNPs—identifies an order of magnitude more compounds than previous strategies.

    • Alexey Gurevich
    • , Alla Mikheenko
    • , Alexander Shlemov
    • , Anton Korobeynikov
    • , Hosein Mohimani
    •  & Pavel A. Pevzner
  • Article | | Open Access

    Analysis of a CO2-driven geyser over a complete eruption cycle showed temporal changes in microbial community composition and function, associated with eruption phase and aquifer water depth, and revealed a putative archaeal symbiosis.

    • Alexander J. Probst
    • , Bethany Ladd
    • , Jessica K. Jarett
    • , David E. Geller-McGrath
    • , Christian M. K. Sieber
    • , Joanne B. Emerson
    • , Karthik Anantharaman
    • , Brian C. Thomas
    • , Rex R. Malmstrom
    • , Michaela Stieglmeier
    • , Andreas Klingl
    • , Tanja Woyke
    • , M. Cathryn Ryan
    •  & Jillian F. Banfield
  • Article |

    Analysis of paired metagenomes and metatranscriptomes associated with patients with inflammatory bowel disease (IBD) and non-IBD controls over time provides some insights into microbial community variation and potential pathways influencing IBD symptoms.

    • Melanie Schirmer
    • , Eric A. Franzosa
    • , Jason Lloyd-Price
    • , Lauren J. McIver
    • , Randall Schwager
    • , Tiffany W. Poon
    • , Ashwin N. Ananthakrishnan
    • , Elizabeth Andrews
    • , Gildardo Barron
    • , Kathleen Lake
    • , Mahadev Prasad
    • , Jenny Sauk
    • , Betsy Stevens
    • , Robin G. Wilson
    • , Jonathan Braun
    • , Lee A. Denson
    • , Subra Kugathasan
    • , Dermot P. B. McGovern
    • , Hera Vlamakis
    • , Ramnik J. Xavier
    •  & Curtis Huttenhower
  • Article |

    Metagenomic and metatranscriptomic analyses of stool samples from 308 individuals over time indicate that longitudinal sampling is important for detecting dynamic functional features of the gut microbiome.

    • Raaj S. Mehta
    • , Galeb S. Abu-Ali
    • , David A. Drew
    • , Jason Lloyd-Price
    • , Ayshwarya Subramanian
    • , Paul Lochhead
    • , Amit D. Joshi
    • , Kerry L. Ivey
    • , Hamed Khalili
    • , Gordon T. Brown
    • , Casey DuLong
    • , Mingyang Song
    • , Long H. Nguyen
    • , Himel Mallick
    • , Eric B. Rimm
    • , Jacques Izard
    • , Curtis Huttenhower
    •  & Andrew T. Chan
  • Article |

    Analysis of human faecal metatranscriptomes and metagenomes reveals core and variable metatranscriptomes across time and individuals, and similar strain-level variation within and between subjects, providing further insights into human microbial ecology.

    • Galeb S. Abu-Ali
    • , Raaj S. Mehta
    • , Jason Lloyd-Price
    • , Himel Mallick
    • , Tobyn Branck
    • , Kerry L. Ivey
    • , David A. Drew
    • , Casey DuLong
    • , Eric Rimm
    • , Jacques Izard
    • , Andrew T. Chan
    •  & Curtis Huttenhower
  • Article |

    During CRISPR–Cas immunity, a long precursor transcript must be cleaved into short CRISPR-derived RNAs that can be used by the interference complex. Here, one of the CRISPR–Cas systems of Synechocystis sp. PCC 6803 is shown to rely on RNase E for this cleavage.

    • Juliane Behler
    • , Kundan Sharma
    • , Viktoria Reimann
    • , Annegret Wilde
    • , Henning Urlaub
    •  & Wolfgang R. Hess

Amendments & Corrections