The Human Gut Cell Atlas v1.0: A Unified, Community-BuiltReference of Cellular Diversity Across the Gut
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.
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BibTeX
@misc{kimler2026human,
title = {{The Human Gut Cell Atlas v1.0: A Unified, Community-BuiltReference of Cellular Diversity Across the Gut}},
author = {Kyle Kimler and Christopher Lance and Balazs Bohar and Abdalla Ahmed and Ran Zhou and Raquel Bartolome-Casado and Victoria Gudino and Ricardo O. Ramirez Flores and Fredrik V. Junghus and Urs M. Morbe and Diana Domanska and Michaela F. Mueller and Madelyn R. Moy and Angela Sanzo-Machuca and Marton Olbei and Batuhan Cakir and Benjamin Weinert and Benjamin M. Frey and Michael Glinka and Tobi Alegbe and Duy Pham and Joshua de Sousa Casal and Alexander V. Predeus and Alexandre Denadai-Souza and Francesca Perrone and Hyun Chang Lee and Sushma Chowdary Maddipatla and David Rogers and Mary K. Futey and Arsenios Chatzigeorgiou and Ida Zucchi and Jasmine Belfiore and Lucia Robson and Agne Antanaviciute and Daniel B. Rainbow and Tatiana A. Karakasheva and Richard Baldock and Derek Houghton and Vladimir A. Shitov and Chenchen Zhu and Chloe Hyun-Jung Lee and Elva Maria Novoa-del-Toro and Sara Kimler and Anna Hupalowska and Guy E. Boeckxstaens and Eugene C. Butcher and Lori A. Coburn and Shahida Din and Jellert T. Gaublomme and Narayanan Kasthuri and Bartha M. Knoppers and Dermot P. B. McGovern and Jeffrey R. Moffitt and Andreas E. Moor and Peng Qiu and Keith T. Wilson and the Helmsley Gut Cell Atlas Crohn’s Disease Consortium and Candace M. Cham and Eugene B. Chang and Can Ergen},
howpublished = {bioRxiv},
year = {2026},
month = oct,
doi = {10.64898/2026.10.09.753994},
url = {https://www.biorxiv.org/content/10.64898/2026.10.09.753994v1},
note = {CC BY-NC-ND},
}
RIS
TY - UNPB
TI - The Human Gut Cell Atlas v1.0: A Unified, Community-BuiltReference of Cellular Diversity Across the Gut
AU - Kyle Kimler
AU - Christopher Lance
AU - Balazs Bohar
AU - Abdalla Ahmed
AU - Ran Zhou
AU - Raquel Bartolome-Casado
AU - Victoria Gudino
AU - Ricardo O. Ramirez Flores
AU - Fredrik V. Junghus
AU - Urs M. Morbe
AU - Diana Domanska
AU - Michaela F. Mueller
AU - Madelyn R. Moy
AU - Angela Sanzo-Machuca
AU - Marton Olbei
AU - Batuhan Cakir
AU - Benjamin Weinert
AU - Benjamin M. Frey
AU - Michael Glinka
AU - Tobi Alegbe
AU - Duy Pham
AU - Joshua de Sousa Casal
AU - Alexander V. Predeus
AU - Alexandre Denadai-Souza
AU - Francesca Perrone
AU - Hyun Chang Lee
AU - Sushma Chowdary Maddipatla
AU - David Rogers
AU - Mary K. Futey
AU - Arsenios Chatzigeorgiou
AU - Ida Zucchi
AU - Jasmine Belfiore
AU - Lucia Robson
AU - Agne Antanaviciute
AU - Daniel B. Rainbow
AU - Tatiana A. Karakasheva
AU - Richard Baldock
AU - Derek Houghton
AU - Vladimir A. Shitov
AU - Chenchen Zhu
AU - Chloe Hyun-Jung Lee
AU - Elva Maria Novoa-del-Toro
AU - Sara Kimler
AU - Anna Hupalowska
AU - Guy E. Boeckxstaens
AU - Eugene C. Butcher
AU - Lori A. Coburn
AU - Shahida Din
AU - Jellert T. Gaublomme
AU - Narayanan Kasthuri
AU - Bartha M. Knoppers
AU - Dermot P. B. McGovern
AU - Jeffrey R. Moffitt
AU - Andreas E. Moor
AU - Peng Qiu
AU - Keith T. Wilson
AU - the Helmsley Gut Cell Atlas Crohn’s Disease Consortium
AU - Candace M. Cham
AU - Eugene B. Chang
AU - Can Ergen
PY - 2026
DA - 2026/10/09
PB - bioRxiv
DO - 10.64898/2026.10.09.753994
UR - https://www.biorxiv.org/content/10.64898/2026.10.09.753994v1
AB - 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.
SN - 2692-8205
ER -