Volume 569 Issue 7758, 30 May 2019

Inside story

The Integrative Human Microbiome Project (iHMP or HMP2) concludes a ten-year initiative from the US National Institutes of Health aimed at exploring the interactions between humans and the diverse range of microorganisms living in their bodies. In this issue, teams from the iHMP Research Network Consortium present results and analyses from the project. In one paper, Curtis Huttenhower and his colleagues examine the dynamic changes in host–microbe interactions that occur in inflammatory bowel disease. In a second paper, Michael Snyder and his co-workers report on host–microbe dynamics in prediabetes, a condition that can lead to type 2 diabetes. A Perspective article provides an overview of the project and highlights how the results are providing insights into disease onset and progression that could pave the way for better diagnostics and treatments. The cover image is an artist’s concept of the diversity of human–microbe interactions.

Credit: AXS Studio

This Week

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Careers

Futures

Research

    News & Views

  • News & Views |

    The Human Microbiome Project put the health-associated microbes found in humans on centre stage. The project’s second phase shows how microbial disturbance in disease is linked to host processes.

    • Verónica Lloréns-Rico
    •  & Jeroen Raes
  • News & Views |

    It is extremely difficult to observe the radiation that is thought to be emitted by black holes. The properties of this radiation have now been analysed using an analogue black hole comprising a system of ultracold atoms.

    • Silke Weinfurtner
  • News & Views |

    How Nature reported Apollo 10 in 1969, and the permanent establishment of the US National Research Council in 1919.

  • News & Views |

    The protein-import systems of organelles can become clogged by proteins. A protein from one organelle, the endoplasmic reticulum, is found to also unclog such blockages in mitochondrial organelles.

    • Sylvie Callegari
    •  & Peter Rehling
  • News & Views |

    Prostate cancer contains nerve cells that are linked to disease progression, but their source was unknown. A mouse study reveals that cells from the brain invade prostate tumours and give rise to this nerve-cell population.

    • Simon T. Schafer
    •  & Fred H. Gage
  • News & Views |

    Object manipulation using an innovative glove allows large databases of detailed pressure maps to be obtained. Such data could lead to advances in robotic sensing and in our understanding of the role of touch in manipulation.

    • Giulia Pasquale
  • Perspectives

  • Perspective | | Open Access

    Over ten years, the Human Microbiome Project has provided resources for studying the microbiome and its relationship to disease; this Perspective summarizes the key achievements and findings of the project and its relationship to the broader field.

    • Lita M. Proctor
    • , Heather H. Creasy
    • , Jennifer M. Fettweis
    • , Jason Lloyd-Price
    • , Anup Mahurkar
    • , Wenyu Zhou
    • , Gregory A. Buck
    • , Michael P. Snyder
    • , Jerome F. Strauss III
    • , George M. Weinstock
    • , Owen White
    •  & Curtis Huttenhower
  • Articles

  • Article | | Open Access

    The Inflammatory Bowel Disease Multi’omics Database includes longitudinal data encompassing a multitude of analyses of stool, blood and biopsies of more than 100 individuals, and provides a comprehensive description of host and microbial activities in inflammatory bowel diseases.

    • Jason Lloyd-Price
    • , Cesar Arze
    • , Ashwin N. Ananthakrishnan
    • , Melanie Schirmer
    • , Julian Avila-Pacheco
    • , Tiffany W. Poon
    • , Elizabeth Andrews
    • , Nadim J. Ajami
    • , Kevin S. Bonham
    • , Colin J. Brislawn
    • , David Casero
    • , Holly Courtney
    • , Antonio Gonzalez
    • , Thomas G. Graeber
    • , A. Brantley Hall
    • , Kathleen Lake
    • , Carol J. Landers
    • , Himel Mallick
    • , Damian R. Plichta
    • , Mahadev Prasad
    • , Gholamali Rahnavard
    • , Jenny Sauk
    • , Dmitry Shungin
    • , Yoshiki Vázquez-Baeza
    • , Richard A. White III
    • , Jason Bishai
    • , Kevin Bullock
    • , Amy Deik
    • , Courtney Dennis
    • , Jess L. Kaplan
    • , Hamed Khalili
    • , Lauren J. McIver
    • , Christopher J. Moran
    • , Long Nguyen
    • , Kerry A. Pierce
    • , Randall Schwager
    • , Alexandra Sirota-Madi
    • , Betsy W. Stevens
    • , William Tan
    • , Johanna J. ten Hoeve
    • , George Weingart
    • , Robin G. Wilson
    • , Vijay Yajnik
    • , Jonathan Braun
    • , Lee A. Denson
    • , Janet K. Jansson
    • , Rob Knight
    • , Subra Kugathasan
    • , Dermot P. B. McGovern
    • , Joseph F. Petrosino
    • , Thaddeus S. Stappenbeck
    • , Harland S. Winter
    • , Clary B. Clish
    • , Eric A. Franzosa
    • , Hera Vlamakis
    • , Ramnik J. Xavier
    •  & Curtis Huttenhower
  • Article | | Open Access

    Deep profiling of transcriptomes, metabolomes, cytokines, and proteomes, alongside changes in the microbiome, in samples from individuals with and without prediabetes reveal insights into inter-individual variability and associations between changes in the microbiome and other factors.

    • Wenyu Zhou
    • , M. Reza Sailani
    • , Kévin Contrepois
    • , Yanjiao Zhou
    • , Sara Ahadi
    • , Shana R. Leopold
    • , Martin J. Zhang
    • , Varsha Rao
    • , Monika Avina
    • , Tejaswini Mishra
    • , Jethro Johnson
    • , Brittany Lee-McMullen
    • , Songjie Chen
    • , Ahmed A. Metwally
    • , Thi Dong Binh Tran
    • , Hoan Nguyen
    • , Xin Zhou
    • , Brandon Albright
    • , Bo-Young Hong
    • , Lauren Petersen
    • , Eddy Bautista
    • , Blake Hanson
    • , Lei Chen
    • , Daniel Spakowicz
    • , Amir Bahmani
    • , Denis Salins
    • , Benjamin Leopold
    • , Melanie Ashland
    • , Orit Dagan-Rosenfeld
    • , Shannon Rego
    • , Patricia Limcaoco
    • , Elizabeth Colbert
    • , Candice Allister
    • , Dalia Perelman
    • , Colleen Craig
    • , Eric Wei
    • , Hassan Chaib
    • , Daniel Hornburg
    • , Jessilyn Dunn
    • , Liang Liang
    • , Sophia Miryam Schüssler-Fiorenza Rose
    • , Kim Kukurba
    • , Brian Piening
    • , Hannes Rost
    • , David Tse
    • , Tracey McLaughlin
    • , Erica Sodergren
    • , George M. Weinstock
    •  & Michael Snyder
  • Article |

    In a mouse model of prostate cancer, neural progenitors from the central nervous system that express doublecortin infiltrate tumours and metastases, and can generate new adrenergic neurons in tumours.

    • Philippe Mauffrey
    • , Nicolas Tchitchek
    • , Vilma Barroca
    • , Alexis-Pierre Bemelmans
    • , Virginie Firlej
    • , Yves Allory
    • , Paul-Henri Roméo
    •  & Claire Magnon
  • Article |

    In Saccharomyces cerevisiae, Ubx2 promotes clearing trapped precursor proteins from the channel of the translocase of the outer membrane, in a translocation-associated degradation pathway that maintains the protein import capacity of mitochondria.

    • Christoph U. Mårtensson
    • , Chantal Priesnitz
    • , Jiyao Song
    • , Lars Ellenrieder
    • , Kim Nguyen Doan
    • , Felix Boos
    • , Alessia Floerchinger
    • , Nicole Zufall
    • , Silke Oeljeklaus
    • , Bettina Warscheid
    •  & Thomas Becker
  • Letters

  • Letter |

    The merger of two white dwarfs created a massive, hot, luminous, rotating and magnetized star with a lifetime of several thousand years, which will collapse into a type Ic supernova.

    • Vasilii V. Gvaramadze
    • , Götz Gräfener
    • , Norbert Langer
    • , Olga V. Maryeva
    • , Alexei Y. Kniazev
    • , Alexander S. Moskvitin
    •  & Olga I. Spiridonova
  • Letter |

    An array of superconducting qubits in an open one-dimensional waveguide is precisely controlled to create an artificial quantum cavity–atom system that reaches the strong-coupling regime without substantial decoherence.

    • Mohammad Mirhosseini
    • , Eunjong Kim
    • , Xueyue Zhang
    • , Alp Sipahigil
    • , Paul B. Dieterle
    • , Andrew J. Keller
    • , Ana Asenjo-Garcia
    • , Darrick E. Chang
    •  & Oskar Painter
  • Letter |

    Tactile patterns obtained from a scalable sensor-embedded glove and deep convolutional neural networks help to explain how the human hand can identify and grasp individual objects and estimate their weights.

    • Subramanian Sundaram
    • , Petr Kellnhofer
    • , Yunzhu Li
    • , Jun-Yan Zhu
    • , Antonio Torralba
    •  & Wojciech Matusik
  • Letter |

    An approach in which quaternary centres are leveraged to improve synthetic planning can lead to shorter and optimized syntheses, demonstrated here on a series of polycyclic terpenes.

    • Pengfei Hu
    • , Hyung Min Chi
    • , Kenneth C. DeBacker
    • , Xu Gong
    • , Jonathan H. Keim
    • , Ian Tingyung Hsu
    •  & Scott A. Snyder
  • Letter |

    The authors identify a role for genome architecture reorganization in anterior dorsal cerebellar vermis granule neurons in learning a conditioned startle paradigm in mice.

    • Tomoko Yamada
    • , Yue Yang
    • , Pamela Valnegri
    • , Ivan Juric
    • , Armen Abnousi
    • , Kelly H. Markwalter
    • , Arden N. Guthrie
    • , Abigail Godec
    • , Anna Oldenborg
    • , Ming Hu
    • , Timothy E. Holy
    •  & Azad Bonni
  • Letter |

    Hypoxia in the shoot meristem of Arabidopsis links the regulation of metabolic activity to development by inhibiting proteolysis of a substrate of the N-degron pathway, which controls class-III homeodomain-leucine zipper transcription factors.

    • Daan A. Weits
    • , Alicja B. Kunkowska
    • , Nicholas C. W. Kamps
    • , Katharina M. S. Portz
    • , Niko K. Packbier
    • , Zoe Nemec Venza
    • , Christophe Gaillochet
    • , Jan U. Lohmann
    • , Ole Pedersen
    • , Joost T. van Dongen
    •  & Francesco Licausi
  • Letter |

    A molecular model of STING-mediated signalling is proposed, as structural analysis identifies a crucial motif for the binding of TBK1 to STING, and a separate model involved in IRF-3 binding.

    • Baoyu Zhao
    • , Fenglei Du
    • , Pengbiao Xu
    • , Chang Shu
    • , Banumathi Sankaran
    • , Samantha L. Bell
    • , Mengmeng Liu
    • , Yuanjiu Lei
    • , Xinsheng Gao
    • , Xiaofeng Fu
    • , Fanxiu Zhu
    • , Yang Liu
    • , Arthur Laganowsky
    • , Xueyun Zheng
    • , Jun-Yuan Ji
    • , A. Phillip West
    • , Robert O. Watson
    •  & Pingwei Li
  • Letter |

    The authors find that stromal methyltransferase nicotinamide N-methyltransferase (NNMT) regulates the transition of normal fibroblasts to cancer-associated fibroblasts through histone methylation and promotes ovarian cancer growth and metastasis.

    • Mark A. Eckert
    • , Fabian Coscia
    • , Agnieszka Chryplewicz
    • , Jae Won Chang
    • , Kyle M. Hernandez
    • , Shawn Pan
    • , Samantha M. Tienda
    • , Dominik A. Nahotko
    • , Gang Li
    • , Ivana Blaženović
    • , Ricardo R. Lastra
    • , Marion Curtis
    • , S. Diane Yamada
    • , Ruth Perets
    • , Stephanie M. McGregor
    • , Jorge Andrade
    • , Oliver Fiehn
    • , Raymond E. Moellering
    • , Matthias Mann
    •  & Ernst Lengyel
  • Letter |

    Spatial genome organization into lamina-associated domains is first established in the mouse zygote immediately after fertilization without inheritance from the maternal germline—with the paternal and maternal pronucleus exhibiting different organization, which subsequently converges prior to implantation of the embryo.

    • Máté Borsos
    • , Sara M. Perricone
    • , Tamás Schauer
    • , Julien Pontabry
    • , Kim L. de Luca
    • , Sandra S. de Vries
    • , Elias R. Ruiz-Morales
    • , Maria-Elena Torres-Padilla
    •  & Jop Kind

Amendments & Corrections

Collections

  • Spotlight |

    Non-Western Biotechnology

    Nature meets five scientists working in non-Western nations making the most out of the resources available to them.

  • Spotlight |

    AI in China

    Despite obstacles, such as an ongoing trade war with the United States, Chinese researchers are working to ensure they can collaborate internationally.

  • Special |

    Human Microbiome Project, part 2

    The second phase of the 10-year NIH-funded Human Microbiome Project (HMP2) has reached its fruition in the form of a collection of studies addressing the role of the microbiota in inflammatory bowel disease, the onset of type 2 diabetes and in pregnancy and preterm birth.

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