Intestinal fibroblast heterogeneity – unifying RNA-seq studies and introducing consensus-driven nomenclature

In the colon, the single-layered epithelium forms crypts that extend into the mucosa and are surrounded by a fibroblast network essential for extracellular matrix (ECM) production, remodeling and epithelial support. Fibroblasts are heterogeneous, but inconsistent nomenclature and lack of markers have hindered their classification. Using single-cell RNA sequencing (scRNA-seq), we identified six distinct fibroblast subpopulations in mouse colonic mucosa, each with unique molecular profiles and specialized functions. Some fibroblasts focus on ECM production and remodeling, whereas others show high contractility. Certain subsets of the fibroblasts secrete cytokines promoting epithelial differentiation or stem cell niche maintenance. Spatial mapping revealed their organization within the mucosa, and trajectory analysis suggested distinct differentiation pathways. Cell cycle scoring confirmed that fibroblasts remain largely non-proliferative under homeostasis. By integrating our dataset with published ones, we identify conserved fibroblast populations and propose a standardized nomenclature for intestinal fibroblasts. This framework enhances communication and understanding of fibroblast diversity and their roles in gut homeostasis and disease.