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Mechanobiology

A Roadmap for the Human Gut Cell Atlas

AUTHORS

Zilbauer MMatthias , James KRKylie R , Kaur MMandeep , Pott SSebastian , Li ZZhixin , Burger AAlbert , Thiagarajah JRJay R , Burclaff JJoseph , Jahnsen FLFrode L , Perrone FFrancesca , Ross ADAlexander D , Matteoli GGianluca , Stakenborg NNathalie , Sujino TTomohisa , Moor AAndreas , Bartolome-Casado RRaquel , Bækkevold ESEspen S , Zhou RRan , Xie BBingqing , Lau KSKen S , Din SShahida , Magness STScott T , Yao QQiuming , Beyaz SSemir , Arends MMark , Denadai-Souza AAlexandre , Coburn LALori A , Gaublomme JTJellert T , Baldock RRichard , Papatheodorou IIrene , Ordovas-Montanes JJose , Boeckxstaens GGuy , Hupalowska AAnna , Teichmann SASarah A , Regev AAviv , Xavier RJRamnik J , Simmons AAlison , Snyder MPMichael P , Wilson KTKeith T , , . Nature reviews. Gastroenterology & hepatology. 2023 05 31; ().

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.