Small intestinal lymph node identity is defined by medullary stromal cells in humans

Lymph nodes (LNs) along the murine gastrointestinal tract are immunologically distinct. Here, we investigated what defines gut LN identity at large in humans and mice and drives their regional differences. Using transcriptional profiling and imaging, we found that stromal cells in the LN medulla and sinus are susceptible to location along the intestine, with high conservation between human and mouse. Specifically, the medulla of small intestine-draining LNs was enriched for fibroblastic reticular cell subpopulations implicated in extracellular matrix remodeling and stromal cell replenishment, lymphatic endothelial cells, and macrophages compared to LNs draining colon and other sites like lung. In mice, this unique medullary cellular network was established around weaning age by Vitamin A, while the gut microbiota regulated the effect’s amplitude. Our study posits the LN medulla as a location for tissue-specific immune responses and uncovers privileged access to lipid-soluble vitamins as a pivotal driving force for small intestinal LN properties.