Kyle Kimler

Publication

Integrated Human Gut Cell Atlas

Published: 2026-08-14T14:42:40.697Z

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.

Datasets (5)

Human Gut Cell Atlas (HGCA) v1 - Epithelial Lineage269,780 cells
Human Gut Cell Atlas (HGCA) v1 - Lymphoid Lineage572,267 cells
Human Gut Cell Atlas (HGCA) v1 - Stromal Lineage52,159 cells
Human Gut Cell Atlas (HGCA) v1 - Myeloid Lineage50,296 cells
Human Gut Cell Atlas (HGCA) v1 - All Cells944,502 cells

Publication

Concerted changes in the pediatric single-cell intestinal ecosystem before and after anti-TNF blockade

Published: 2024-09-24T15:40:26.739Z

Crohn’s disease is an inflammatory bowel disease (IBD) commonly treated through anti-TNF blockade. However, most patients still relapse and inevitably progress. Comprehensive single-cell RNA-sequencing (scRNA-seq) atlases have largely sampled patients with established treatment-refractory IBD, limiting our understanding of which cell types, subsets, and states at diagnosis anticipate disease severity and response to treatment. Here, through combining clinical, flow cytometry, histology, and scRNA-seq methods, we profile diagnostic human biopsies from the terminal ileum of treatment-naïve pediatric patients with Crohn’s disease (pediCD; n=14), matched repeat biopsies (pediCD-treated; n=8) and from non-inflamed pediatric controls with functional gastrointestinal disorders (FGID; n=13). To resolve and annotate epithelial, stromal, and immune cell states among the 201,883 baseline single-cell transcriptomes, we develop a principled and unbiased tiered clustering approach, ARBOL. Through flow cytometry and scRNA-seq, we observe that treatment-naïve pediCD and FGID have similar broad cell type composition. However, through high-resolution scRNA-seq analysis and microscopy, we identify significant differences in cell subsets and states that arise during pediCD relative to FGID. By closely linking our scRNA-seq analysis with clinical meta-data, we resolve a vector of T cell, innate lymphocyte, myeloid, and epithelial cell states in treatment-naïve pediCD (pediCD-TIME) samples which can distinguish patients along the trajectory of disease severity and anti-TNF response. By using ARBOL with integration, we position repeat on-treatment biopsies from our patients between treatment-naïve pediCD and on-treatment adult CD. We identify that anti-TNF treatment pushes the pediatric cellular ecosystem towards an adult, more treatment-refractory state. Our study jointly leverages a treatment-naïve cohort, high-resolution principled scRNA-seq data analysis, and clinical outcomes to understand which baseline cell states may predict Crohn’s disease trajectory.

Datasets (1)

Concerted changes in the pediatric single-cell intestinal ecosystem before and after anti-TNF blockade197,281 cells

Kyle Kimler

Publications

Integrated Human Gut Cell Atlas

Datasets (5)

Concerted changes in the pediatric single-cell intestinal ecosystem before and after anti-TNF blockade

Datasets (1)