A Roadmap for the Human Gut Cell Atlas

Zilbauer, Matthias, James, Kylie R, Kaur, Mandeep, Pott, Sebastian, Li, Zhixin, Burger, Albert, Thiagarajah, Jay R, Burclaff, Joseph, Jahnsen, Frode L, Perrone, Francesca, Ross, Alexander D, Matteoli, Gianluca, Stakenborg, Nathalie, Sujino, Tomohisa, Moor, Andreas, Bartolome-Casado, Raquel, Bækkevold, Espen S, Zhou, Ran, Xie, Bingqing, Lau, Ken S, Din, Shahida, Magness, Scott T, Yao, Qiuming, Beyaz, Semir, Arends, Mark, Denadai-Souza, Alexandre, Coburn, Lori A, Gaublomme, Jellert T, Baldock, Richard, Papatheodorou, Irene, Ordovas-Montanes, Jose, Boeckxstaens, Guy, Hupalowska, Anna, Teichmann, Sarah A, Regev, Aviv, Xavier, Ramnik J, Simmons, Alison, Snyder, Michael P, Wilson, Keith T, Gut Cell Atlas Consortium, Human Cell Atlas Gut Biological Network Consortium (September 2023) A Roadmap for the Human Gut Cell Atlas. Nature Reviews Gastroenterology & Hepatology, 20 (9). pp. 597-614. ISSN 1759-5045

URL: https://www.ncbi.nlm.nih.gov/pubmed/37258747
DOI: 10.1038/s41575-023-00784-1


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.

Item Type: Paper
Subjects: Investigative techniques and equipment
organism description > animal
Investigative techniques and equipment > cell culture > cancer organoids
Investigative techniques and equipment > cell culture
organism description > animal > mammal > primates > hominids
organism description > animal > mammal > primates > hominids > human
organism description > animal > mammal
organism description > animal > mammal > primates
CSHL Authors:
Communities: CSHL labs > Beyaz lab
CSHL Cancer Center Program
CSHL Cancer Center Program > Cancer Genetics and Genomics Program
SWORD Depositor: CSHL Elements
Depositing User: CSHL Elements
Date: September 2023
Date Deposited: 22 Sep 2023 15:27
Last Modified: 29 Apr 2024 18:50
PMCID: PMC10527367
Related URLs:
URI: https://repository.cshl.edu/id/eprint/40977

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