A Roadmap for the Human Gut Cell Atlas

Authors

• Matthias Zilbauer, University of CambridgeFollow
• Kylie R. James, Garvan Institute of Medical Research
• Mandeep Kaur, University of the Witwatersrand, Johannesburg
• Sebastian Pott, Department of Medicine, The University of Chicago
• Zhixin Li, Dana-Farber Cancer Institute
• Albert Burger, Heriot-Watt University
• Jay R. Thiagarajah, Harvard Medical School
• Joseph Burclaff, The University of North Carolina at Chapel Hill
• Frode L. Jahnsen, Oslo Universitetssykehus
• Francesca Perrone, University of Cambridge
• Alexander D. Ross, University of Cambridge
• Gianluca Matteoli, Departement Chronische Ziekten, Metabolisme en Veroudering
• Nathalie Stakenborg, Departement Chronische Ziekten, Metabolisme en Veroudering
• Tomohisa Sujino, Keio University School of Medicine
• Andreas Moor, ETH Zürich
• Raquel Bartolome-Casado, Oslo Universitetssykehus
• Espen S. Bækkevold, Oslo Universitetssykehus
• Ran Zhou, Department of Medicine, The University of Chicago
• Bingqing Xie, Department of Medicine, The University of Chicago
• Ken S. Lau, Vanderbilt University School of Medicine
• Shahida Din, Western General Hospital
• Scott T. Magness, The University of North Carolina at Chapel Hill
• Qiuming Yao, University of Nebraska-LincolnFollow
• Semir Beyaz, Cold Spring Harbor Laboratory
• Mark Arends, The University of Edinburgh
• Alexandre Denadai-Souza, Departement Chronische Ziekten, Metabolisme en Veroudering
• Lori A. Coburn, Vanderbilt University Medical Center
• Jellert T. Gaublomme, Columbia University
• Richard Baldock, The University of Edinburgh
• Irene Papatheodorou, EMBL’s European Bioinformatics Institute
• Jose Ordovas-Montanes, Harvard Medical School
• Guy Boeckxstaens, Departement Chronische Ziekten, Metabolisme en Veroudering
• Anna Hupalowska, Genentech, Inc
• Sarah A. Teichmann, Wellcome Sanger Institute

Document Type

Article

Date of this Version

9-1-2023

Citation

Nature Reviews Gastroenterology & Hepatology, Volume 20 (September 2023), pp 597–614

doi:10.1038/s41575-023-00784-1

Comments

U.S. government work

Abstract

The number of studies investigating the human gastrointestinal tract using various single-cell profiling methods has increased substantially in the past few years. Although this increase provides a unique opportunity for the generation of the first comprehensive Human Gut Cell Atlas (HGCA), there remains a range of major challenges ahead. Above all, the ultimate success will largely depend on a structured and coordinated approach that aligns global efforts undertaken by a large number of research groups. In this Roadmap, we discuss a comprehensive forward-thinking direction for the generation of the HGCA on behalf of the Gut Biological Network of the Human Cell Atlas. Based on the consensus opinion of experts from across the globe, we outline the main requirements for the first complete HGCA by summarizing existing data sets and highlighting anatomical regions and/or tissues with limited coverage. We provide recommendations for future studies and discuss key methodologies and the importance of integrating the healthy gut atlas with related diseases and gut organoids. Importantly, we critically overview the computational tools available and provide recommendations to overcome key challenges.