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Using Human Intestinal Organoids to Understand the Small Intestine Epithelium at the Single Cell Transcriptional Level

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Leveraging Single-Cell and Spatial Transcriptomics in Gut Nutrition and Mucosal Immunology.

Jiaxing Yang¹, Nan Gao²

¹Department of Biological Sciences, Rutgers University, Newark, NJ, United States.

The Journal of Nutrition

|June 11, 2026

Summary

This summary is machine-generated.

Single-cell transcriptomics is revolutionizing intestinal nutrition biology by revealing epithelial-immune cell communication. Emerging spatial transcriptomics and in vivo models offer new ways to study nutrient-modulated cell interactions.

Keywords:

cell–cell communication infection inflammatory bowel disease single-cell RNA sequencing spatial transcriptomics

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Area of Science:

Intestinal nutrition biology
Mucosal immunology
Cellular communication

Background:

Recent studies highlight single-cell transcriptomics' impact on understanding nutrient metabolism.
Investigating nutrient metabolism requires understanding cellular interactions within the intestinal mucosa.

Purpose of the Study:

To describe how single-cell transcriptomics advances intestinal nutrition biology.
To discuss emerging technologies like spatial transcriptomics and in vivo labeling models.
To explore nutrient-modulated cell-cell communication in the gut.

Main Methods:

Single-cell transcriptomics analysis of intestinal cells.
Review of recent studies in intestinal nutrition biology.
Discussion of spatial transcriptomics and in vivo labeling models.

Main Results:

Uncovered potential communication pathways between intestinal epithelial and immune cells.
Generated novel hypotheses on nutrient metabolism influenced by mucosal immunology.
Identified opportunities for spatial transcriptomics and in vivo models to advance research.

Conclusions:

Single-cell transcriptomics is a powerful tool for dissecting intestinal nutrition biology.
Emerging technologies will enhance the study of physical and spatial cell-cell interactions.
Understanding nutrient-modulated communication is key for future intestinal health interventions.