Plate IV.2 · Publications
The Human Gut Cell Atlas v1.0: A Unified, Community-Built Reference of Cellular Diversity Across the Gut
Preprint in bioRxiv, 12 October 2026.
Abstract
Single-cell RNA-sequencing (scRNA-seq) studies have transformed our understanding of cellular diversity in the human intestine, but differences in anatomical sampling, experimental processing and cell-type nomenclature limit comparison across datasets. Here, we present the Human Gut Cell Atlas (HGCA) V1, a community-curated reference of 944,390 healthy and disease-adjacent intestinal cells from 502 samples, 265 donors and 24 landmark studies, linked to detailed anatomical, clinical, and technical metadata. As this metadata is of critical importance to human biology, we developed MetaManager, an open source data management framework for standardized metadata collection and tracking. A five-level consensus taxonomy resolves 94 homeostatic cell identities and enables transferrable, high-resolution annotation of new gut datasets. By assembling cell identity, sampling metadata, and independent spatial validation, intestinal segment and radial tissue depth were revealed to systematically shape cellular composition and transcriptional state, enabling inference of the presence of sampling-dependent tissue niches, including lymphoid follicles. Reference mapping accurately and rapidly recovered cohort-level Crohn’s disease and treatment signatures without de novo annotation, while mapping human intestinal organoids quantified cell-type-specific identity, regional specification, maturation, and transcriptional fidelity to native tissue. The HGCA V1 provides a standardized cellular, anatomical coordinate, and metadata system for reproducible, high-quality analysis of intestinal biology across healthy tissue, disease-associated remodelling, and experimental models, providing a continuously evolving community reference for cumulative discovery in human intestinal biology.
Cite
@misc{kimler2026human,
title = {{The Human Gut Cell Atlas v1.0: A Unified, Community-Built Reference of Cellular Diversity Across the Gut}},
author = {Kimler, Kyle and Lance, Christopher and Bohar, Balazs and Ahmed, Abdalla and Zhou, Ran and Bartolome-Casado, Raquel and Gudino, Victoria and Ramirez Flores, Ricardo O. and Junghus, Fredrik V. and Morbe, Urs M. and Domanska, Diana and Mueller, Michaela F. and Moy, Madelyn R. and Sanzo-Machuca, Angela and Olbei, Marton and Cakir, Batuhan and Weinert, Benjamin and Frey, Benjamin M. and Glinka, Michael and Alegbe, Tobi and Pham, Duy and de Sousa Casal, Joshua and Predeus, Alexander V. and Denadai-Souza, Alexandre and Perrone, Francesca and Lee, Hyun Chang and Maddipatla, Sushma Chowdary and Rogers, David and Futey, Mary K. and Chatzigeorgiou, Arsenios and Zucchi, Ida and Belfiore, Jasmine and Robson, Lucia and Antanaviciute, Agne and Rainbow, Daniel B. and Karakasheva, Tatiana A. and Baldock, Richard and Houghton, Derek and Shitov, Vladimir A. and Zhu, Chenchen and Lee, Chloe Hyun-Jung and Novoa-del-Toro, Elva Maria and Kimler, Sara and Hupalowska, Anna and Boeckxstaens, Guy E. and Butcher, Eugene C. and Coburn, Lori A. and Din, Shahida and Gaublomme, Jellert T. and Kasthuri, Narayanan and Knoppers, Bartha M. and McGovern, Dermot P. B. and Moffitt, Jeffrey R. and Moor, Andreas E. and Qiu, Peng and Wilson, Keith T. and the Helmsley Gut Cell Atlas Crohn’s Disease Consortium and Cham, Candace M. and Chang, Eugene B. and Ergen, Can and Farber, Donna L. and Ghouraba, Mennatallah and Koval, Jason and Lengner, Christopher J. and Mark, Michal and Rubin, David T. and Sims, Peter A. and Wells, Steven B. and Xie, Bingqing and Yosef, Nir and Zhou, Yusen and Fawkner-Corbett, David and Fenton, Thomas M. and Magness, Scott T. and Itzkovitz, Shalev and Krzak, Monika and McIntyre, Rebecca E and Luoma, Adrienne and Wickham, Gregory J. and Burclaff, Joseph and Suo, Shengbao and Konnikova, Liza and Breau, Keith Alexander and Gu, Weihong and Baekkevold, Espen S and the Human Cell Atlas Gut Bionetwork and Taylor, D Leland and Jones, Joanne L. and Hickey, John W. and Anderson, Carl A and Raine, Tim and Saez-Rodriguez, Julio and Pott, Sebastian and Papatheodorou, Irene and Adams, David J and Simmons, Alison and Burger, Albert and Korcsmaros, Tamas and Arends, Mark J and Basu, Anindita and Hamilton, Kathryn E. and Agace, William W. and Osumi-Sutherland, David and James, Kylie R. and Oliver, Amanda J. and Elmentaite, Rasa and Snyder, Michael P. and Teichmann, Sarah A. and Randell, John and Salas, Azucena and Theis, Fabian J. and Luecken, Malte D. and Kotlarz, Daniel and Zilbauer, Matthias and Ordovas-Montanes, Jose},
howpublished = {bioRxiv},
publisher = {openRxiv},
year = {2026},
month = oct,
doi = {10.64898/2026.10.09.753994},
url = {https://doi.org/10.64898/2026.10.09.753994},
note = {Preprint}
}