Single-Cell and Spatial Multi-Omics in Small-Intestinal Homeostasis and Ischemia/Reperfusion Injury: Current Advances, Applications, and Future Perspectives.

The intestinal tract acts as a dynamic barrier between the external and internal environments, and intestinal homeostasis fundamentally influences human health. This homeostasis depends on complex interactions among the epithelium, immune cells, and microbiota. Intestinal ischemia/reperfusion (II/R) disrupts these interactions and can cause local barrier failure and distant organ injury. However, the transition of the intestinal microenvironment from homeostasis to injury and repair remains incompletely characterized. This narrative review summarizes single-cell RNA sequencing, single-cell multi-omics, spatial transcriptomics, and spatial multi-omics, including their underlying methods. We compare intestinal reference atlases with direct II/R studies and examine how these approaches complement bulk sequencing and histology. Human intestinal atlases reveal spatially organized epithelial states, whereas experimental II/R studies identify altered Paneth-cell states, endothelial regenerative signals, and epithelial stress responses. These findings differ in their model systems, sampling times, and degree of functional validation. Dissociation bias, batch effects, limited biological replication, spatial resolution, and uncertain integration across modalities constrain interpretation. Most disease-specific evidence remains preclinical, and inferred cell interactions should not be equated with demonstrated therapeutic mechanisms. Translation will require standardized human sampling, spatial and protein-level validation, causal perturbation, and prospective assessment of clinically accessible markers. Single-cell and spatial omics can therefore refine mechanistic hypotheses and guide validation in II/R, but currently do not constitute established clinical diagnostic or treatment pathways.