A Roadmap for the Human Gut Cell Atlas

Matthias Zilbauer*, Kylie R. James, Mandeep Kaur, Sebastian Pott, Zhixin Li, Albert Burger, Jay R. Thiagarajah, Joseph Burclaff, Frode L. Jahnsen, Francesca Perrone, Alexander D. Ross, Gianluca Matteoli, Nathalie Stakenborg, Tomohisa Sujino, Andreas Moor, Raquel Bartolome-Casado, Espen S. Bækkevold, Ran Zhou, Bingqing Xie, Ken S. LauShahida Din, Scott T. Magness, Qiuming Yao, Semir Beyaz, Mark Arends, Alexandre Denadai-Souza, Lori A. Coburn, Jellert T. Gaublomme, Richard Baldock, Irene Papatheodorou, Jose Ordovas-Montanes, Guy Boeckxstaens, Anna Hupalowska, Sarah A. Teichmann, Aviv Regev, Ramnik J. Xavier, Alison Simmons, Michael P. Snyder, Keith T. Wilson, Gut Cell Atlas Consortium, Human Cell Atlas Gut Biological Network Consortium

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

3 Citations (Scopus)


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.

Original languageEnglish
Pages (from-to)597-614
Number of pages18
JournalNature Reviews Gastroenterology and Hepatology
Issue number9
Early online date31 May 2023
Publication statusPublished - Sept 2023

ASJC Scopus subject areas

  • Hepatology
  • Gastroenterology


Dive into the research topics of 'A Roadmap for the Human Gut Cell Atlas'. Together they form a unique fingerprint.

Cite this