Fig. 2. ScRNAseq advances in understanding mucosal immunity throughout life and during disease.

(1) Building from observations of lymphocyte maturation in the prenatal intestines, single-cell studies have promoted the concept that T and B cell activation up to second-trimester development is in support of intestinal development rather than in response to microbial seeding^21,74–76. (2) Key players in gut-associated lymphoid tissue (GALT) formation previously identified in developing mouse gut have been identified in scRNAseq studies of human fetal gut, with additional cell heterogeneity identified^21,24. (3) TNF-α-producing CD4+ T cells resolved at single-cell level are enriched in the preterm intestines, likely contributing to epithelial damage observed in necrotising enterocolitis (NEC)⁷⁷. (4) Intestinal stromal heterogeneity has been determined, and expanded subtypes in inflammatory bowel disease linked with pathology^16–18. (5) Inlaid box depicts the classical idea of discrete immune cell subsets versus a spectrum of phenotypes determined through scRNAseq analyses⁸⁸. LTi lymphoid tissue inducer, LTo lymphoid tissue organiser.