Integrated Human Gut Cell Atlas

The Human Gut Cell Atlas (HGCA) brings together the collective expertise of gut biologists, clinicians, and data generators to create a community-driven, healthy reference for the human gut. It integrates 27 datasets representing several sample collection and library preparation methods from donors across age groups, with samples dissected or biopsied from the duodenum to the rectum.

The gut is a complex organ, stratified along its longitudinal and radial axes and responsible for everything from nutrient absorption and excretion to immune regulation. The HGCA integrates 959,289 cells of 503 samples from 266 donors and provides community-informed annotations for a preliminary 105 cell types, including location-specific transcriptional states and rare intestinal populations.

The atlas will continue to be versioned to reflect expanding cell type, technological, and population diversity, supporting a high-quality, community-maintained resource for the field. We invite gut and single-cell researchers to put their critical thinking caps on and help shape the HGCA's annotations by voting, reasoning, and contributing directly here on CAP.